Development of an Aeroelastic Modeling Capability for Transient Nozzle Side Load Analysis

NASA Technical Reports Server (NTRS)

Wang, Ten-See; Zhao, Xiang; Zhang, Sijun; Chen, Yen-Sen

2013-01-01

Lateral nozzle forces are known to cause severe structural damage to any new rocket engine in development. Currently there is no fully coupled computational tool to analyze this fluid/structure interaction process. The objective of this study was to develop a fully coupled aeroelastic modeling capability to describe the fluid/structure interaction process during the transient nozzle operations. The aeroelastic model composes of three components: the computational fluid dynamics component based on an unstructured-grid, pressure-based computational fluid dynamics formulation, the computational structural dynamics component developed in the framework of modal analysis, and the fluid-structural interface component. The developed aeroelastic model was applied to the transient nozzle startup process of the Space Shuttle Main Engine at sea level. The computed nozzle side loads and the axial nozzle wall pressure profiles from the aeroelastic nozzle are compared with those of the published rigid nozzle results, and the impact of the fluid/structure interaction on nozzle side loads is interrogated and presented.

Analysis of genetic effects of nuclear-cytoplasmic interaction on quantitative traits: genetic model for diploid plants.

PubMed

Han, Lide; Yang, Jian; Zhu, Jun

2007-06-01

A genetic model was proposed for simultaneously analyzing genetic effects of nuclear, cytoplasm, and nuclear-cytoplasmic interaction (NCI) as well as their genotype by environment (GE) interaction for quantitative traits of diploid plants. In the model, the NCI effects were further partitioned into additive and dominance nuclear-cytoplasmic interaction components. Mixed linear model approaches were used for statistical analysis. On the basis of diallel cross designs, Monte Carlo simulations showed that the genetic model was robust for estimating variance components under several situations without specific effects. Random genetic effects were predicted by an adjusted unbiased prediction (AUP) method. Data on four quantitative traits (boll number, lint percentage, fiber length, and micronaire) in Upland cotton (Gossypium hirsutum L.) were analyzed as a worked example to show the effectiveness of the model.

Two component Feebly Interacting Massive Particle (FIMP) dark matter

NASA Astrophysics Data System (ADS)

Pandey, Madhurima; Majumdar, Debasish; Prasad Modak, Kamakshya

2018-06-01

We explore the idea of an alternative candidate for particle dark matter namely Feebly Interacting Massive Particle (FIMP) in the framework of a two component singlet scalar model. Singlet scalar dark matter has already been demonstrated to be a viable candidate for WIMP (Weakly Interacting Massive Particle) dark matter in literature. In the FIMP scenario, dark matter particles are slowly produced via "thermal freeze-in" mechanism in the early Universe and are never abundant enough to reach thermal equilibrium or to undergo pair annihilation inside the Universe's plasma due to their extremely small couplings. We demonstrate that for smaller couplings too, required for freeze-in process, a two component scalar dark matter model considered here could well be a viable candidate for FIMP . In this scenario, the Standard Model of particle physics is extended by two gauge singlet real scalars whose stability is protected by an unbroken Z2× Z'2 symmetry and they are assumed to acquire no VEV after Spontaneous Symmetry Breaking. We explore the viable mass regions in the present two scalar DM model that is in accordance with the FIMP scenario. We also explore the upper limits of masses of the two components from the consideration of their self interactions.

Pharmacokinetic Modeling of JP-8 Jet Fuel Components: II. A Conceptual Framework

DTIC Science & Technology

2003-12-01

example, a single type of (simple) binary interaction between 300 components would require the specification of some 105 interaction coefficients . One...individual substances, via binary mechanisms, is enough to predict the interactions present in the mixture. Secondly, complex mixtures can often be...approximated as pseudo- binary systems, consisting of the compound of interest plus a single interacting complex vehicle with well-defined, composite

Analysis of whisker-toughened CMC structural components using an interactive reliability model

NASA Technical Reports Server (NTRS)

Duffy, Stephen F.; Palko, Joseph L.

1992-01-01

Realizing wider utilization of ceramic matrix composites (CMC) requires the development of advanced structural analysis technologies. This article focuses on the use of interactive reliability models to predict component probability of failure. The deterministic William-Warnke failure criterion serves as theoretical basis for the reliability model presented here. The model has been implemented into a test-bed software program. This computer program has been coupled to a general-purpose finite element program. A simple structural problem is presented to illustrate the reliability model and the computer algorithm.

Bayesian spatiotemporal crash frequency models with mixture components for space-time interactions.

PubMed

Cheng, Wen; Gill, Gurdiljot Singh; Zhang, Yongping; Cao, Zhong

2018-03-01

The traffic safety research has developed spatiotemporal models to explore the variations in the spatial pattern of crash risk over time. Many studies observed notable benefits associated with the inclusion of spatial and temporal correlation and their interactions. However, the safety literature lacks sufficient research for the comparison of different temporal treatments and their interaction with spatial component. This study developed four spatiotemporal models with varying complexity due to the different temporal treatments such as (I) linear time trend; (II) quadratic time trend; (III) Autoregressive-1 (AR-1); and (IV) time adjacency. Moreover, the study introduced a flexible two-component mixture for the space-time interaction which allows greater flexibility compared to the traditional linear space-time interaction. The mixture component allows the accommodation of global space-time interaction as well as the departures from the overall spatial and temporal risk patterns. This study performed a comprehensive assessment of mixture models based on the diverse criteria pertaining to goodness-of-fit, cross-validation and evaluation based on in-sample data for predictive accuracy of crash estimates. The assessment of model performance in terms of goodness-of-fit clearly established the superiority of the time-adjacency specification which was evidently more complex due to the addition of information borrowed from neighboring years, but this addition of parameters allowed significant advantage at posterior deviance which subsequently benefited overall fit to crash data. The Base models were also developed to study the comparison between the proposed mixture and traditional space-time components for each temporal model. The mixture models consistently outperformed the corresponding Base models due to the advantages of much lower deviance. For cross-validation comparison of predictive accuracy, linear time trend model was adjudged the best as it recorded the highest value of log pseudo marginal likelihood (LPML). Four other evaluation criteria were considered for typical validation using the same data for model development. Under each criterion, observed crash counts were compared with three types of data containing Bayesian estimated, normal predicted, and model replicated ones. The linear model again performed the best in most scenarios except one case of using model replicated data and two cases involving prediction without including random effects. These phenomena indicated the mediocre performance of linear trend when random effects were excluded for evaluation. This might be due to the flexible mixture space-time interaction which can efficiently absorb the residual variability escaping from the predictable part of the model. The comparison of Base and mixture models in terms of prediction accuracy further bolstered the superiority of the mixture models as the mixture ones generated more precise estimated crash counts across all four models, suggesting that the advantages associated with mixture component at model fit were transferable to prediction accuracy. Finally, the residual analysis demonstrated the consistently superior performance of random effect models which validates the importance of incorporating the correlation structures to account for unobserved heterogeneity. Copyright © 2017 Elsevier Ltd. All rights reserved.

All-particle energy spectrum of KASCADE-Grande based on shower size and different hadronic interaction models

NASA Astrophysics Data System (ADS)

Kang, D.; Apel, W. D.; Arteaga-Velazquez, J. C.; Bekk, K.; Bertaina, M.; Blümer, J.; Bozdog, H.; Brancus, I. M.; Cantoni, E.; Chiavassa, A.; Cossavella, F.; Daumiller, K.; de Souza, V.; Di Pierro, F.; Doll, P.; Engel, R.; Engler, J.; Finger, M.; Fuchs, B.; Fuhrmann, D.; Gils, H. J.; Glasstetter, R.; Grupen, C.; Haungs, A.; Heck, D.; Hörandel, J. R.; Huber, D.; Huege, T.; Kampert, K.-H.; Klages, H. O.; Link, K.; Łuczak, P.; Ludwig, M.; Mathes, H. J.; Mayer, H. J.; Melissas, M.; Milke, J.; Morello, C.; Oehlschläger, J.; Ostapchenko, S.; Palmieri, N.; Petcu, M.; Pierog, T.; Rebel, H.; Roth, M.; Schieler, H.; Schoo, S.; Schroder, F.; Sima, O.; Toma, G.; Trinchero, G. C.; Ulrich, H.; Weindl, A.; Wochele, J.; Wommer, M.; Zabierowski, J.

2013-02-01

KASCADE-Grande is a large detector array for observations of the energy spectrum as well as the chemical composition of cosmic ray air showers up to primary energies of 1 EeV. The multi-detector arrangement allows to measure the electromagnetic and muonic components for individual air showers. In this analysis, the reconstruction of the all-particle energy spectrum is based on the size spectra of the charged particle component. The energy is calibrated by using Monte Carlo simulations performed with CORSIKA and high-energy interaction models QGSJet, EPOS and SIBYLL. In all cases FLUKA has been used as low-energy interaction model. In this contribution the resulting spectra by means of different hadronic interaction models will be compared and discussed.

Electrostatic, elastic and hydration-dependent interactions in dermis influencing volume exclusion and macromolecular transport.

PubMed

Øien, Alf H; Wiig, Helge

2016-07-07

Interstitial exclusion refers to the limitation of space available for plasma proteins and other macromolecules based on collagen and negatively charged glycosaminoglycans (GAGs) in the interstitial space. It is of particular importance to interstitial fluid and plasma volume regulation. Here we present a novel mechanical and mathematical model of the dynamic interactions of structural elements within the interstitium of the dermis at the microscopic level that may explain volume exclusion of charged and neutral macroparticles. At this level, the interstitium is considered to consist of elements called extracellular matrix (ECM) cells, again containing two main interacting structural components on a fluid background including anions and cations setting up osmotic forces: one smaller GAG component, having an intrinsic expansive electric force, and one bigger collagen component, having an intrinsic elastic force. Because of size differences, the GAG component interacts with a fraction of the collagen component only at normal hydration. This fraction, however, increases with rising hydration as a consequence of the modeled form of the interaction force between the GAGs and collagen. Collagen is locally displaced at variable degrees as hydration changes. Two models of GAGs are considered, having largely different geometries which demands different, but related, forms of GAG-collagen interaction forces. The effects of variable fixed charges on GAGs and of GAG density in tissue are evaluated taking into account observed volume exclusion properties of charged macromolecules as a function of tissue hydration. The presented models may improve our biophysical understanding of acting forces influencing tissue fluid dynamics. Such knowledge is significant when evaluating the transport of electrically charged and neutral macromolecules into and through the interstitium, and therefore to drug uptake and the therapeutic effects of macromolecular agents. Copyright © 2016 Elsevier Ltd. All rights reserved.

ξTauri: a unique laboratory to study the dynamic interaction in a compact hierarchical quadruple system

NASA Astrophysics Data System (ADS)

Nemravová, J. A.; Harmanec, P.; Brož, M.; Vokrouhlický, D.; Mourard, D.; Hummel, C. A.; Cameron, C.; Matthews, J. M.; Bolton, C. T.; Božić, H.; Chini, R.; Dembsky, T.; Engle, S.; Farrington, C.; Grunhut, J. H.; Guenther, D. B.; Guinan, E. F.; Korčáková, D.; Koubský, P.; Kříček, R.; Kuschnig, R.; Mayer, P.; McCook, G. P.; Moffat, A. F. J.; Nardetto, N.; Prša, A.; Ribeiro, J.; Rowe, J.; Rucinski, S.; Škoda, P.; Šlechta, M.; Tallon-Bosc, I.; Votruba, V.; Weiss, W. W.; Wolf, M.; Zasche, P.; Zavala, R. T.

2016-10-01

Context. Compact hierarchical systems are important because the effects caused by the dynamical interaction among its members occur ona human timescale. These interactions play a role in the formation of close binaries through Kozai cycles with tides. One such system is ξ Tauri: it has three hierarchical orbits: 7.14 d (eclipsing components Aa, Ab), 145 d (components Aa+Ab, B), and 51 yr (components Aa+Ab+B, C). Aims: We aim to obtain physical properties of the system and to study the dynamical interaction between its components. Methods: Our analysis is based on a large series of spectroscopic photometric (including space-borne) observations and long-baseline optical and infrared spectro-interferometric observations. We used two approaches to infer the system properties: a set of observation-specific models, where all components have elliptical trajectories, and an N-body model, which computes the trajectory of each component by integrating Newton's equations of motion. Results: The triple subsystem exhibits clear signs of dynamical interaction. The most pronounced are the advance of the apsidal line and eclipse-timing variations. We determined the geometry of all three orbits using both observation-specific and N-body models. The latter correctly accounted for observed effects of the dynamical interaction, predicted cyclic variations of orbital inclinations, and determined the sense of motion of all orbits. Using perturbation theory, we demonstrate that prominent secular and periodic dynamical effects are explainable with a quadrupole interaction. We constrained the basic properties of all components, especially of members of the inner triple subsystem and detected rapid low-amplitude light variations that we attribute to co-rotating surface structures of component B. We also estimated the radius of component B. Properties of component C remain uncertain because of its low relative luminosity. We provide an independent estimate of the distance to the system. Conclusions: The accuracy and consistency of our results make ξ Tau an excellent test bed for models of formation and evolution of hierarchical systems. Full Tables D.1-D.7 are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/594/A55Based on data from the MOST satellite, a former Canadian Space Agency mission, jointly operated by Microsatellite Systems Canada Inc. (MSCI; formerly Dynacon Inc.), the University of Toronto Institute for Aerospace Studies and the University of British Columbia, with the assistance of the University of Vienna.

Learning Gene Expression Through Modelling and Argumentation. A Case Study Exploring the Connections Between the Worlds of Knowledge

NASA Astrophysics Data System (ADS)

Puig, Blanca; Ageitos, Noa; Jiménez-Aleixandre, María Pilar

2017-12-01

There is emerging interest on the interactions between modelling and argumentation in specific contexts, such as genetics learning. It has been suggested that modelling might help students understand and argue on genetics. We propose modelling gene expression as a way to learn molecular genetics and diseases with a genetic component. The study is framed in Tiberghien's (2000) two worlds of knowledge, the world of "theories & models" and the world of "objects & events", adding a third component, the world of representations. We seek to examine how modelling and argumentation interact and connect the three worlds of knowledge while modelling gene expression. It is a case study of 10th graders learning about diseases with a genetic component. The research questions are as follows: (1) What argumentative and modelling operations do students enact in the process of modelling gene expression? Specifically, which operations allow connecting the three worlds of knowledge? (2) What are the interactions between modelling and argumentation in modelling gene expression? To what extent do these interactions help students connect the three worlds of knowledge and modelling gene expression? The argumentative operation of using evidence helps students to relate the three worlds of knowledge, enacted in all the connections. It seems to be a relationship among the number of interactions between modelling and argumentation, the connections between world of knowledge and students' capacity to develop a more sophisticated representation. Despite this is a case study, this approach of analysis reveals potentialities for a deeper understanding of learning genetics though scientific practices.

The role of perceived interactivity in virtual communities: building trust and increasing stickiness

NASA Astrophysics Data System (ADS)

Wang, Hongwei; Meng, Yuan; Wang, Wei

2013-03-01

Although previous research has explored factors affecting trust building in websites, little research has been analysed from the perceived interactivity perspective in virtual communities (VCs). A research model for verifying interactivity antecedents to trust and its impact on member stickiness behaviour is presented. Two social interactivity components and two system interactivity components are, respectively, theorised as process-based antecedents and institution-based antecedents to trust in the model. Data were collected from 310 members of VCs to test the model. The results show that connectedness and reciprocity are important antecedents to trust in members, while responsiveness and active control are important antecedents to trust in systems. The results also indicate that trust has significant influence on the members' duration and retention, which are two dimensions of member stickiness measured in this research. These findings have theoretical implications for online interaction-related literature and critical business implications for practitioners of VCs.

Log-Linear Models for Gene Association

PubMed Central

Hu, Jianhua; Joshi, Adarsh; Johnson, Valen E.

2009-01-01

We describe a class of log-linear models for the detection of interactions in high-dimensional genomic data. This class of models leads to a Bayesian model selection algorithm that can be applied to data that have been reduced to contingency tables using ranks of observations within subjects, and discretization of these ranks within gene/network components. Many normalization issues associated with the analysis of genomic data are thereby avoided. A prior density based on Ewens’ sampling distribution is used to restrict the number of interacting components assigned high posterior probability, and the calculation of posterior model probabilities is expedited by approximations based on the likelihood ratio statistic. Simulation studies are used to evaluate the efficiency of the resulting algorithm for known interaction structures. Finally, the algorithm is validated in a microarray study for which it was possible to obtain biological confirmation of detected interactions. PMID:19655032

Design and Implementation of Scientific Software Components to Enable Multiscale Modeling: The Effective Fragment Potential (QM/EFP) Method

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

Gaenko, Alexander; Windus, Theresa L.; Sosonkina, Masha

2012-10-19

The design and development of scientific software components to provide an interface to the effective fragment potential (EFP) methods are reported. Multiscale modeling of physical and chemical phenomena demands the merging of software packages developed by research groups in significantly different fields. Componentization offers an efficient way to realize new high performance scientific methods by combining the best models available in different software packages without a need for package readaptation after the initial componentization is complete. The EFP method is an efficient electronic structure theory based model potential that is suitable for predictive modeling of intermolecular interactions in large molecularmore » systems, such as liquids, proteins, atmospheric aerosols, and nanoparticles, with an accuracy that is comparable to that of correlated ab initio methods. The developed components make the EFP functionality accessible for any scientific component-aware software package. The performance of the component is demonstrated on a protein interaction model, and its accuracy is compared with results obtained with coupled cluster methods.« less

Dike/Drift Interactions

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

E. Gaffiney

2004-11-23

This report presents and documents the model components and analyses that represent potential processes associated with propagation of a magma-filled crack (dike) migrating upward toward the surface, intersection of the dike with repository drifts, flow of magma in the drifts, and post-magma emplacement effects on repository performance. The processes that describe upward migration of a dike and magma flow down the drift are referred to as the dike intrusion submodel. The post-magma emplacement processes are referred to as the post-intrusion submodel. Collectively, these submodels are referred to as a conceptual model for dike/drift interaction. The model components and analyses ofmore » the dike/drift interaction conceptual model provide the technical basis for assessing the potential impacts of an igneous intrusion on repository performance, including those features, events, and processes (FEPs) related to dike/drift interaction (Section 6.1).« less

Interactions of Metacognition with Motivation and Affect in Self-Regulated Learning: The MASRL Model

ERIC Educational Resources Information Center

Efklides, Anastasia

2011-01-01

Metacognition, motivation, and affect are components of self-regulated learning (SRL) that interact. The "metacognitive and affective model of self-regulated learning" (the MASRL model) distinguishes two levels of functioning in SRL, namely, the Person level and the Task x Person level. At the Person level interactions between trait-like…

Understanding Language Learning: Review of the Application of the Interaction Model in Foreign Language Contexts

ERIC Educational Resources Information Center

Dixon, L. Quentin; Wu, Shuang

2014-01-01

Purpose: This paper examined the application of the input-interaction-output model in English-as-Foreign-Language (EFL) learning environments with four specific questions: (1) How do the three components function in the model? (2) Does interaction in the foreign language classroom seem to be effective for foreign language acquisition? (3) What…

Diffusion in silicate melts: III. Empirical models for multicomponent diffusion

NASA Astrophysics Data System (ADS)

Yan, Liang; Richter, Frank M.; Chamberlin, Laurinda

1997-12-01

Empirical models for multicomponent diffusion in an isotropic fluid were derived by splitting the component's dispersion velocity into two parts: (a) an intrinsic velocity which is proportional to each component's electrochemical potential gradient and independent of reference frame and (b) a net interaction velocity which is both model and reference frame dependent. Simple molecules (e.g., M pO q) were chosen as endmember components. The interaction velocity is assumed to be either the same for each component (leading to a common relaxation velocity U) or proportional to a common interaction force ( F). U or F is constrained by requiring no local buildup in either volume or charge. The most general form of the model-derived diffusion matrix [ D] can be written as a product of a model-dependent kinetic matrix [ L] and a model independent thermodynamic matrix [ G], [ D] = [ L] · [ G]. The elements of [ G] are functions of derivatives of chemical potential with respect to concentration. The elements of [ L] are functions of concentration and partial molar volume of the endmember components, Cio and Vio, and self diffusivity Di, and charge number zi of individual diffusing species. When component n is taken as the dependent variable they can be written in a common form L ij = D jδ ij + C io[V noD n - V joD j)A i + (p nz nD n - p jz jD j)B i] where the functional forms of the scaling factors Ai and Bi depend on the model considered. The off-diagonal element Lij ( i ≠ j) is directly proportional to the concentration of component i, and thus negligible when i is a dilute component. The salient feature of kinetic interaction or relaxation is to slow down larger (volume or charge) and faster diffusing components and to speed up smaller (volume or charge) and slower moving species, in order to prevent local volume or charge buildup. Empirical models for multicomponent diffusion were tested in the ternary system CaOAl 2O 3SiO 2 at 1500°C and 1 GPa over a large range of melt compositions. Model-derived diffusion matrices calculated using measured self diffusivities (Ca, Al, Si, and O), partial molar volumes, and activities were compared with experimentally derived diffusion matrices at two melt compositions. Chemical diffusion profiles computed using the model-derived diffusion matrices, accounting for the compositional dependency of self diffusivities and activity coefficients, were also compared with the experimentally measured ones. Good agreement was found between the ionic common-force model derived diffusion profiles and the experimentally measured ones. Secondary misfits could result from either inadequacies of the model or inaccuracies in activity-composition relationship. The results show that both kinetic interactions and thermodynamic nonideality contribute significantly to the observed diffusive coupling in the molten CaOAl 2O 3SiO 2.

Experimental and mathematical model of the interactions in the mixed culture of links in the "producer-consumer" cycle

NASA Astrophysics Data System (ADS)

Pisman, T. I.; Galayda, Ya. V.

The paper presents experimental and mathematical model of interactions between invertebrates the ciliates Paramecium caudatum and the rotifers Brachionus plicatilis and algae Chlorella vulgaris and Scenedesmus quadricauda in the producer -- consumer aquatic biotic cycle with spatially separated components The model describes the dynamics of the mixed culture of ciliates and rotifers in the consumer component feeding on the mixed algal culture of the producer component It has been found that metabolites of the algae Scenedesmus produce an adverse effect on the reproduction of the ciliates P caudatum Taking into account this effect the results of investigation of the mathematical model were in qualitative agreement with the experimental results In the producer -- consumer biotic cycle it was shown that coexistence is impossible in the mixed algal culture of the producer component and in the mixed culture of invertebrates of the consumer component The ciliates P caudatum are driven out by the rotifers Brachionus plicatilis

Experimental and mathematical model of the interactions in the mixed culture of links in the “producer-consumer” cycle

NASA Astrophysics Data System (ADS)

Pisman, T. I.

2009-07-01

The paper presents a experimental and mathematical model of interactions between invertebrates (the ciliates Paramecium caudatum and the rotifers Brachionus plicatilis) in the "producer-consumer" aquatic biotic cycle with spatially separated components. The model describes the dynamics of the mixed culture of ciliates and rotifers in the "consumer" component, feeding on the mixed algal culture of the "producer" component. It has been found that metabolites of the algae Scenedesmus produce an adverse effect on the reproduction of the ciliates P. caudatum. Taking into account this effect, the results of investigation of the mathematical model were in qualitative agreement with the experimental results. In the "producer-consumer" biotic cycle it was shown that coexistence is impossible in the mixed culture of invertebrates of the "consumer" component. The ciliates P. caudatum are driven out by the rotifers B. plicatilis.

Superfluid drag in the two-component Bose-Hubbard model

NASA Astrophysics Data System (ADS)

Sellin, Karl; Babaev, Egor

2018-03-01

In multicomponent superfluids and superconductors, co- and counterflows of components have, in general, different properties. A. F. Andreev and E. P. Bashkin [Sov. Phys. JETP 42, 164 (1975)] discussed, in the context of He3/He4 superfluid mixtures, that interparticle interactions produce a dissipationless drag. The drag can be understood as a superflow of one component induced by phase gradients of the other component. Importantly, the drag can be both positive (entrainment) and negative (counterflow). The effect is known to have crucial importance for many properties of diverse physical systems ranging from the dynamics of neutron stars and rotational responses of Bose mixtures of ultracold atoms to magnetic responses of multicomponent superconductors. Although substantial literature exists that includes the drag interaction phenomenologically, only a few regimes are covered by quantitative studies of the microscopic origin of the drag and its dependence on microscopic parameters. Here we study the microscopic origin and strength of the drag interaction in a quantum system of two-component bosons on a lattice with short-range interaction. By performing quantum Monte Carlo simulations of a two-component Bose-Hubbard model we obtain dependencies of the drag strength on the boson-boson interactions and properties of the optical lattice. Of particular interest are the strongly correlated regimes where the ratio of coflow and counterflow superfluid stiffnesses can diverge, corresponding to the case of saturated drag.

Development of a railway wagon-track interaction model: Case studies on excited tracks

NASA Astrophysics Data System (ADS)

Xu, Lei; Chen, Xianmai; Li, Xuwei; He, Xianglin

2018-02-01

In this paper, a theoretical framework for modeling the railway wagon-ballast track interactions is presented, in which the dynamic equations of motion of wagon-track systems are constructed by effectively coupling the linear and nonlinear dynamic characteristics of system components. For the linear components, the energy-variational principle is directly used to derive their dynamic matrices, while for the nonlinear components, the dynamic equilibrium method is implemented to deduce the load vectors, based on which a novel railway wagon-ballast track interaction model is developed, and being validated by comparing with the experimental data measured from a heavy haul railway and another advanced model. With this study, extensive contributions in figuring out the critical speed of instability, limits and localizations of track irregularities over derailment accidents are presented by effectively integrating the dynamic simulation model, the track irregularity probabilistic model and time-frequency analysis method. The proposed approaches can provide crucial information to guarantee the running safety and stability of the wagon-track system when considering track geometries and various running speeds.

The GPRIME approach to finite element modeling

NASA Technical Reports Server (NTRS)

Wallace, D. R.; Mckee, J. H.; Hurwitz, M. M.

1983-01-01

GPRIME, an interactive modeling system, runs on the CDC 6000 computers and the DEC VAX 11/780 minicomputer. This system includes three components: (1) GPRIME, a user friendly geometric language and a processor to translate that language into geometric entities, (2) GGEN, an interactive data generator for 2-D models; and (3) SOLIDGEN, a 3-D solid modeling program. Each component has a computer user interface of an extensive command set. All of these programs make use of a comprehensive B-spline mathematics subroutine library, which can be used for a wide variety of interpolation problems and other geometric calculations. Many other user aids, such as automatic saving of the geometric and finite element data bases and hidden line removal, are available. This interactive finite element modeling capability can produce a complete finite element model, producing an output file of grid and element data.

Test of interaction models up to 40 PeV by studying hadronic cores of EAS

NASA Astrophysics Data System (ADS)

KASCADE Collaboration; Apel, W. D.; Badea, A. F.; Bekk, K.; Blümer, J.; Bozdog, H.; Brancus, I. M.; Daumiller, K.; Doll, P.; Engel, R.; Engler, J.; Gils, H. J.; Glasstetter, R.; Haungs, A.; Heck, D.; Hörandel, J. R.; Kampert, K.-H.; Klages, H. O.; Mathes, H. J.; Mayer, H. J.; Milke, J.; Oehlschläger, J.; Ostapchenko, S.; Petcu, M.; Pierog, T.; Rebel, H.; Risse, A.; Risse, M.; Roth, M.; Schatz, G.; Schieler, H.; Ulrich, H.; van Buren, J.; Weindl, A.; Wochele, J.; Zabierowski, J.

2007-12-01

The interpretation of extensive air shower measurements often requires a comparison with shower simulations in the atmosphere. These calculations rely on hadronic interaction models which have to extrapolate into kinematical and energy regions not explored by present-day collider experiments. The KASCADE experiment with its large hadron calorimeter and the detector array for the electromagnetic and muonic components provides experimental data to check such interaction models. For the simulations the program CORSIKA is used, which has several hadronic event generators embedded. For high-energy interactions (E_{\\rm{lab}}\\gtrsim100 \\ {\\rm{GeV}}) the models DPMJET, \\{\\sc NEX{\\sc US}} , QGSJET and SIBYLL have been used. Low-energy interactions have been treated by GHEISHA and FLUKA. Different hadronic observables are investigated as well as their correlations with the electromagnetic and muonic shower components up to primary energies of about 40 PeV. Although the predictions of the more recent models are to a large extent compatible with the measured data within the range given by proton and iron primary particles, there are still significant differences between the individual models.

Towards end-to-end models for investigating the effects of climate and fishing in marine ecosystems

NASA Astrophysics Data System (ADS)

Travers, M.; Shin, Y.-J.; Jennings, S.; Cury, P.

2007-12-01

End-to-end models that represent ecosystem components from primary producers to top predators, linked through trophic interactions and affected by the abiotic environment, are expected to provide valuable tools for assessing the effects of climate change and fishing on ecosystem dynamics. Here, we review the main process-based approaches used for marine ecosystem modelling, focusing on the extent of the food web modelled, the forcing factors considered, the trophic processes represented, as well as the potential use and further development of the models. We consider models of a subset of the food web, models which represent the first attempts to couple low and high trophic levels, integrated models of the whole ecosystem, and size spectrum models. Comparisons within and among these groups of models highlight the preferential use of functional groups at low trophic levels and species at higher trophic levels and the different ways in which the models account for abiotic processes. The model comparisons also highlight the importance of choosing an appropriate spatial dimension for representing organism dynamics. Many of the reviewed models could be extended by adding components and by ensuring that the full life cycles of species components are represented, but end-to-end models should provide full coverage of ecosystem components, the integration of physical and biological processes at different scales and two-way interactions between ecosystem components. We suggest that this is best achieved by coupling models, but there are very few existing cases where the coupling supports true two-way interaction. The advantages of coupling models are that the extent of discretization and representation can be targeted to the part of the food web being considered, making their development time- and cost-effective. Processes such as predation can be coupled to allow the propagation of forcing factors effects up and down the food web. However, there needs to be a stronger focus on enabling two-way interaction, carefully selecting the key functional groups and species, reconciling different time and space scales and the methods of converting between energy, nutrients and mass.

Influence of World and Gravity Model Selection on Surface Interacting Vehicle Simulations

NASA Technical Reports Server (NTRS)

Madden, Michael M.

2007-01-01

A vehicle simulation is surface-interacting if the state of the vehicle (position, velocity, and acceleration) relative to the surface is important. Surface-interacting simulations perform ascent, entry, descent, landing, surface travel, or atmospheric flight. Modeling of gravity is an influential environmental factor for surface-interacting simulations. Gravity is the free-fall acceleration observed from a world-fixed frame that rotates with the world. Thus, gravity is the sum of gravitation and the centrifugal acceleration due to the world s rotation. In surface-interacting simulations, the fidelity of gravity at heights above the surface is more significant than gravity fidelity at locations in inertial space. A surface-interacting simulation cannot treat the gravity model separately from the world model, which simulates the motion and shape of the world. The world model's simulation of the world's rotation, or lack thereof, produces the centrifugal acceleration component of gravity. The world model s reproduction of the world's shape will produce different positions relative to the world center for a given height above the surface. These differences produce variations in the gravitation component of gravity. This paper examines the actual performance of world and gravity/gravitation pairs in a simulation using the Earth.

Vortices in a rotating two-component Bose–Einstein condensate with tunable interactions and harmonic potential

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

Zhang, Xiao-Fei, E-mail: xfzhang@ntsc.ac.cn; Du, Zhi-Jing; Tan, Ren-Bing

We consider a pair of coupled nonlinear Schrödinger equations modeling a rotating two-component Bose–Einstein condensate with tunable interactions and harmonic potential, with emphasis on the structure of vortex states by varying the strength of inter-component interaction, rotational frequency, and the aspect ratio of the harmonic potential. Our results show that the inter-component interaction greatly enhances the effect of rotation. For the case of isotropic harmonic potential and small inter-component interaction, the initial vortex structure remains unchanged. As the ratio of inter- to intra-component interactions increases, each component undergoes a transition from a vortex lattice (vortex line) in an isotropic (anisotropic)more » harmonic potential to an alternatively arranged stripe pattern, and eventually to the interwoven “serpentine” vortex sheets. Moreover, in the case of anisotropic harmonic potential the system can develop to a rotating droplet structure. -- Highlights: •Different vortex structures are obtained within the full parameter space. •Effects of system parameters on the ground state structure are discussed. •Phase transition between different vortex structures is also examined. •Present one possible way to obtain the rotating droplet structure. •Provide many possibilities to manipulate vortex in two-component BEC.« less

The Analysis of Three-Way Contingency Tables by Three-Mode Association Models.

ERIC Educational Resources Information Center

Anderson, Carolyn J.

1996-01-01

Generalizations of L. A. Goodman's RC(M) association model (1991 and earlier) are presented for three-way tables. These three-mode association models use L. R. Tucker's three-mode components model (1964, 1966) to represent the three-factor interaction or the combined effects of two- and three-factor interactions. (SLD)

On the sufficiency of pairwise interactions in maximum entropy models of networks

NASA Astrophysics Data System (ADS)

Nemenman, Ilya; Merchan, Lina

Biological information processing networks consist of many components, which are coupled by an even larger number of complex multivariate interactions. However, analyses of data sets from fields as diverse as neuroscience, molecular biology, and behavior have reported that observed statistics of states of some biological networks can be approximated well by maximum entropy models with only pairwise interactions among the components. Based on simulations of random Ising spin networks with p-spin (p > 2) interactions, here we argue that this reduction in complexity can be thought of as a natural property of some densely interacting networks in certain regimes, and not necessarily as a special property of living systems. This work was supported in part by James S. McDonnell Foundation Grant No. 220020321.

Continuum mesoscopic framework for multiple interacting species and processes on multiple site types and/or crystallographic planes.

PubMed

Chatterjee, Abhijit; Vlachos, Dionisios G

2007-07-21

While recently derived continuum mesoscopic equations successfully bridge the gap between microscopic and macroscopic physics, so far they have been derived only for simple lattice models. In this paper, general deterministic continuum mesoscopic equations are derived rigorously via nonequilibrium statistical mechanics to account for multiple interacting surface species and multiple processes on multiple site types and/or different crystallographic planes. Adsorption, desorption, reaction, and surface diffusion are modeled. It is demonstrated that contrary to conventional phenomenological continuum models, microscopic physics, such as the interaction potential, determines the final form of the mesoscopic equation. Models of single component diffusion and binary diffusion of interacting particles on single-type site lattice and of single component diffusion on complex microporous materials' lattices consisting of two types of sites are derived, as illustrations of the mesoscopic framework. Simplification of the diffusion mesoscopic model illustrates the relation to phenomenological models, such as the Fickian and Maxwell-Stefan transport models. It is demonstrated that the mesoscopic equations are in good agreement with lattice kinetic Monte Carlo simulations for several prototype examples studied.

The Influence of AN Interacting Vacuum Energy on the Gravitational Collapse of a Star Fluid

NASA Astrophysics Data System (ADS)

Campos, M.

2014-02-01

To explain the accelerated expansion of the universe, models with interacting dark components has been considered in the literature. Generally, the dark energy component is physically interpreted as the vacuum energy. However, at the other side of the same coin, the influence of the vacuum energy in the gravitational collapse is a topic of scientific interest. Based in a simple assumption on the collapsed rate of the matter fluid density that is altered by the inclusion of a vacuum energy component that interacts with the matter fluid, we study the final fate of the collapse process.

Hierarchical, parallel computing strategies using component object model for process modelling responses of forest plantations to interacting multiple stresses

Treesearch

J. G. Isebrands; G. E. Host; K. Lenz; G. Wu; H. W. Stech

2000-01-01

Process models are powerful research tools for assessing the effects of multiple environmental stresses on forest plantations. These models are driven by interacting environmental variables and often include genetic factors necessary for assessing forest plantation growth over a range of different site, climate, and silvicultural conditions. However, process models are...

Twisted-Light-Ion Interaction: The Role of Longitudinal Fields

NASA Astrophysics Data System (ADS)

Quinteiro, G. F.; Schmidt-Kaler, Ferdinand; Schmiegelow, Christian T.

2017-12-01

The propagation of light beams is well described using the paraxial approximation, where field components along the propagation direction are usually neglected. For strongly inhomogeneous or shaped light fields, however, this approximation may fail, leading to intriguing variations of the light-matter interaction. This is the case of twisted light having opposite orbital and spin angular momenta. We compare experimental data for the excitation of a quadrupole transition in a single trapped 40Ca+ ion from Schmiegelow et al. [Nat. Commun. 7, 12998 (2016), 10.1038/ncomms12998] with a complete model where longitudinal components of the electric field are taken into account. Our model matches the experimental data and excludes by 11 standard deviations the approximation of a complete transverse field. This demonstrates the relevance of all field components for the interaction of twisted light with matter.

Self-assembly kinetics of microscale components: A parametric evaluation

NASA Astrophysics Data System (ADS)

Carballo, Jose M.

The goal of the present work is to develop, and evaluate a parametric model of a basic microscale Self-Assembly (SA) interaction that provides scaling predictions of process rates as a function of key process variables. At the microscale, assembly by "grasp and release" is generally challenging. Recent research efforts have proposed adapting nanoscale self-assembly (SA) processes to the microscale. SA offers the potential for reduced equipment cost and increased throughput by harnessing attractive forces (most commonly, capillary) to spontaneously assemble components. However, there are challenges for implementing microscale SA as a commercial process. The existing lack of design tools prevents simple process optimization. Previous efforts have characterized a specific aspect of the SA process. However, the existing microscale SA models do not characterize the inter-component interactions. All existing models have simplified the outcome of SA interactions as an experimentally-derived value specific to a particular configuration, instead of evaluating it outcome as a function of component level parameters (such as speed, geometry, bonding energy and direction). The present study parameterizes the outcome of interactions, and evaluates the effect of key parameters. The present work closes the gap between existing microscale SA models to add a key piece towards a complete design tool for general microscale SA process modeling. First, this work proposes a simple model for defining the probability of assembly of basic SA interactions. A basic SA interaction is defined as the event where a single part arrives on an assembly site. The model describes the probability of assembly as a function of kinetic energy, binding energy, orientation and incidence angle for the component and the assembly site. Secondly, an experimental SA system was designed, and implemented to create individual SA interactions while controlling process parameters independently. SA experiments measured the outcome of SA interactions, while studying the independent effects of each parameter. As a first step towards a complete scaling model, experiments were performed to evaluate the effects of part geometry and part travel direction under low kinetic energy conditions. Experimental results show minimal dependence of assembly yield on the incidence angle of the parts, and significant effects induced by changes in part geometry. The results from this work indicate that SA could be modeled as an energy-based process due to the small path dependence effects. Assembly probability is linearly related to the orientation probability. The proportionality constant is based on the area fraction of the sites with an amplification factor. This amplification factor accounts for the ability of capillary forces to align parts with only very small areas of contact when they have a low kinetic energy. Results provide unprecedented insight about SA interactions. The present study is a key step towards completing a basic model of a general SA process. Moreover, the outcome from this work can complement existing SA process models, in order to create a complete design tool for microscale SA systems. In addition to SA experiments, Monte Carlo simulations of experimental part-site interactions were conducted. This study confirmed that a major contributor to experimental variation is the stochastic nature of experimental SA interactions and the limited sample size of the experiments. Furthermore, the simulations serve as a tool for defining an optimum sampling strategy to minimize the uncertainty in future SA experiments.

Transport of Solar Wind Fluctuations: A Two-Component Model

NASA Technical Reports Server (NTRS)

Oughton, S.; Matthaeus, W. H.; Smith, C. W.; Breech, B.; Isenberg, P. A.

2011-01-01

We present a new model for the transport of solar wind fluctuations which treats them as two interacting incompressible components: quasi-two-dimensional turbulence and a wave-like piece. Quantities solved for include the energy, cross helicity, and characteristic transverse length scale of each component, plus the proton temperature. The development of the model is outlined and numerical solutions are compared with spacecraft observations. Compared to previous single-component models, this new model incorporates a more physically realistic treatment of fluctuations induced by pickup ions and yields improved agreement with observed values of the correlation length, while maintaining good observational accord with the energy, cross helicity, and temperature.

Learning Tasks, Peer Interaction, and Cognition Process: An Online Collaborative Design Model

ERIC Educational Resources Information Center

Du, Jianxia; Durrington, Vance A.

2013-01-01

This paper illustrates a model for Online Group Collaborative Learning. The authors based the foundation of the Online Collaborative Design Model upon Piaget's concepts of assimilation and accommodation, and Vygotsky's theory of social interaction. The four components of online collaborative learning include: individual processes, the task(s)…

Importance of Matching Physical Friction, Hardness, and Texture in Creating Realistic Haptic Virtual Surfaces.

PubMed

Culbertson, Heather; Kuchenbecker, Katherine J

2017-01-01

Interacting with physical objects through a tool elicits tactile and kinesthetic sensations that comprise your haptic impression of the object. These cues, however, are largely missing from interactions with virtual objects, yielding an unrealistic user experience. This article evaluates the realism of virtual surfaces rendered using haptic models constructed from data recorded during interactions with real surfaces. The models include three components: surface friction, tapping transients, and texture vibrations. We render the virtual surfaces on a SensAble Phantom Omni haptic interface augmented with a Tactile Labs Haptuator for vibration output. We conducted a human-subject study to assess the realism of these virtual surfaces and the importance of the three model components. Following a perceptual discrepancy paradigm, subjects compared each of 15 real surfaces to a full rendering of the same surface plus versions missing each model component. The realism improvement achieved by including friction, tapping, or texture in the rendering was found to directly relate to the intensity of the surface's property in that domain (slipperiness, hardness, or roughness). A subsequent analysis of forces and vibrations measured during interactions with virtual surfaces indicated that the Omni's inherent mechanical properties corrupted the user's haptic experience, decreasing realism of the virtual surface.

Use of fatal real-life crashes to analyze a safe road transport system model, including the road user, the vehicle, and the road.

PubMed

Stigson, Helena; Krafft, Maria; Tingvall, Claes

2008-10-01

To evaluate if the Swedish Road Administration (SRA) model for a safe road transport system, which includes the interaction between the road user, the vehicle, and the road, could be used to classify fatal car crashes according to some safety indicators. Also, to present a development of the model to better identify system weakness. Real-life crashes with a fatal outcome were classified according to the vehicle's safety rating by Euro NCAP (European Road Assessment Programme) and fitment of ESC (Electronic Stability Control). For each crash, the road was also classified according to EuroRAP (European Road Assessment Programme) criteria, and human behavior in terms of speeding, seat belt use, and driving under the influence of alcohol. Each crash was compared with the model criteria, to identify components that might have contributed to fatal outcome. All fatal crashes where a car occupant was killed that occurred in Sweden during 2004 were included: in all, 215 crashes with 248 fatalities. The data were collected from the in-depth fatal crash data of the Swedish Road Administration (SRA). It was possible to classify 93% of the fatal car crashes according to the SRA model. A number of shortcomings in the criteria were identified since the model did not address rear-end or animal collisions or collisions with stationary/parked vehicles or trailers (18 out of 248 cases). Using the further developed model, it was possible to identify that most of the crashes occurred when two or all three components interacted (in 85 of the total 230 cases). Noncompliance with safety criteria for the road user, the vehicle, and the road led to fatal outcome in 43, 27, and 75 cases, respectively. The SRA model was found to be useful for classifying fatal crashes but needs to be further developed to identify how the components interact and thereby identify weaknesses in the road traffic system. This developed model might be a tool to systematically identify which of the components are linked to fatal outcome. In the presented study, fatal outcomes were mostly related to an interaction between the three components: the road, the vehicle, and the road user. Of the three components, the road was the one that was most often linked to a fatal outcome.

Energy Efficient Engine Low Pressure Subsystem Flow Analysis

NASA Technical Reports Server (NTRS)

Hall, Edward J.; Lynn, Sean R.; Heidegger, Nathan J.; Delaney, Robert A.

1998-01-01

The objective of this project is to provide the capability to analyze the aerodynamic performance of the complete low pressure subsystem (LPS) of the Energy Efficient Engine (EEE). The analyses were performed using three-dimensional Navier-Stokes numerical models employing advanced clustered processor computing platforms. The analysis evaluates the impact of steady aerodynamic interaction effects between the components of the LPS at design and off-design operating conditions. Mechanical coupling is provided by adjusting the rotational speed of common shaft-mounted components until a power balance is achieved. The Navier-Stokes modeling of the complete low pressure subsystem provides critical knowledge of component aero/mechanical interactions that previously were unknown to the designer until after hardware testing.

Energy Efficient Engine Low Pressure Subsystem Aerodynamic Analysis

NASA Technical Reports Server (NTRS)

Hall, Edward J.; Delaney, Robert A.; Lynn, Sean R.; Veres, Joseph P.

1998-01-01

The objective of this study was to demonstrate the capability to analyze the aerodynamic performance of the complete low pressure subsystem (LPS) of the Energy Efficient Engine (EEE). Detailed analyses were performed using three- dimensional Navier-Stokes numerical models employing advanced clustered processor computing platforms. The analysis evaluates the impact of steady aerodynamic interaction effects between the components of the LPS at design and off- design operating conditions. Mechanical coupling is provided by adjusting the rotational speed of common shaft-mounted components until a power balance is achieved. The Navier-Stokes modeling of the complete low pressure subsystem provides critical knowledge of component acro/mechanical interactions that previously were unknown to the designer until after hardware testing.

Self-organized network of fractal-shaped components coupled through statistical interaction.

PubMed

Ugajin, R

2001-09-01

A dissipative dynamics is introduced to generate self-organized networks of interacting objects, which we call coupled-fractal networks. The growth model is constructed based on a growth hypothesis in which the growth rate of each object is a product of the probability of receiving source materials from faraway and the probability of receiving adhesives from other grown objects, where each object grows to be a random fractal if isolated, but connects with others if glued. The network is governed by the statistical interaction between fractal-shaped components, which can only be identified in a statistical manner over ensembles. This interaction is investigated using the degree of correlation between fractal-shaped components, enabling us to determine whether it is attractive or repulsive.

Validation of the Fully-Coupled Air-Sea-Wave COAMPS System

NASA Astrophysics Data System (ADS)

Smith, T.; Campbell, T. J.; Chen, S.; Gabersek, S.; Tsu, J.; Allard, R. A.

2017-12-01

A fully-coupled, air-sea-wave numerical model, COAMPS®, has been developed by the Naval Research Laboratory to further enhance understanding of oceanic, atmospheric, and wave interactions. The fully-coupled air-sea-wave system consists of an atmospheric component with full physics parameterizations, an ocean model, NCOM (Navy Coastal Ocean Model), and two wave components, SWAN (Simulating Waves Nearshore) and WaveWatch III. Air-sea interactions between the atmosphere and ocean components are accomplished through bulk flux formulations of wind stress and sensible and latent heat fluxes. Wave interactions with the ocean include the Stokes' drift, surface radiation stresses, and enhancement of the bottom drag coefficient in shallow water due to the wave orbital velocities at the bottom. In addition, NCOM surface currents are provided to SWAN and WaveWatch III to simulate wave-current interaction. The fully-coupled COAMPS system was executed for several regions at both regional and coastal scales for the entire year of 2015, including the U.S. East Coast, Western Pacific, and Hawaii. Validation of COAMPS® includes observational data comparisons and evaluating operational performance on the High Performance Computing (HPC) system for each of these regions.

A Performance Enhanced Interactive Learning Workshop Model as a Supplement for Organic Chemistry Instruction

ERIC Educational Resources Information Center

Phillips, Karen E. S.; Grose-Fifer, Jilliam

2011-01-01

In this study, the authors describe a Performance Enhanced Interactive Learning (PEIL) workshop model as a supplement for organic chemistry instruction. This workshop model differs from many others in that it includes public presentations by students and other whole-class-discussion components that have not been thoroughly investigated in the…

The role of the cell wall in fungal pathogenesis

PubMed Central

Arana, David M.; Prieto, Daniel; Román, Elvira; Nombela, César; Alonso‐Monge, Rebeca; Pla, Jesús

2009-01-01

Summary Fungal infections are a serious health problem. In recent years, basic research is focusing on the identification of fungal virulence factors as promising targets for the development of novel antifungals. The wall, as the most external cellular component, plays a crucial role in the interaction with host cells mediating processes such as adhesion or phagocytosis that are essential during infection. Specific components of the cell wall (called PAMPs) interact with specific receptors in the immune cell (called PRRs), triggering responses whose molecular mechanisms are being elucidated. We review here the main structural carbohydrate components of the fungal wall (glucan, mannan and chitin), how their biogenesis takes place in fungi and the specific receptors that they interact with. Different model fungal pathogens are chosen to illustrate the functional consequences of this interaction. Finally, the identification of the key components will have important consequences in the future and will allow better approaches to treat fungal infections. PMID:21261926

Internal friction and mode relaxation in a simple chain model.

PubMed

Fugmann, S; Sokolov, I M

2009-12-21

We consider the equilibrium relaxation properties of the end-to-end distance and of the principal components in a one-dimensional polymer chain model with nonlinear interaction between the beads. While for the single-well potentials these properties are similar to the ones of a Rouse chain, for the double-well interaction potentials, modeling internal friction, they differ vastly from the ones of the harmonic chain at intermediate times and intermediate temperatures. This minimal description within a one-dimensional model mimics the relaxation properties found in much more complex polymer systems. Thus, the relaxation time of the end-to-end distance may grow by orders of magnitude at intermediate temperatures. The principal components (whose directions are shown to coincide with the normal modes of the harmonic chain, whatever interaction potential is assumed) not only display larger relaxation times but also subdiffusive scaling.

Inference on the Strength of Balancing Selection for Epistatically Interacting Loci

PubMed Central

Buzbas, Erkan Ozge; Joyce, Paul; Rosenberg, Noah A.

2011-01-01

Existing inference methods for estimating the strength of balancing selection in multi-locus genotypes rely on the assumption that there are no epistatic interactions between loci. Complex systems in which balancing selection is prevalent, such as sets of human immune system genes, are known to contain components that interact epistatically. Therefore, current methods may not produce reliable inference on the strength of selection at these loci. In this paper, we address this problem by presenting statistical methods that can account for epistatic interactions in making inference about balancing selection. A theoretical result due to Fearnhead (2006) is used to build a multi-locus Wright-Fisher model of balancing selection, allowing for epistatic interactions among loci. Antagonistic and synergistic types of interactions are examined. The joint posterior distribution of the selection and mutation parameters is sampled by Markov chain Monte Carlo methods, and the plausibility of models is assessed via Bayes factors. As a component of the inference process, an algorithm to generate multi-locus allele frequencies under balancing selection models with epistasis is also presented. Recent evidence on interactions among a set of human immune system genes is introduced as a motivating biological system for the epistatic model, and data on these genes are used to demonstrate the methods. PMID:21277883

Modelling robot construction systems

NASA Technical Reports Server (NTRS)

Grasso, Chris

1990-01-01

TROTER's are small, inexpensive robots that can work together to accomplish sophisticated construction tasks. To understand the issues involved in designing and operating a team of TROTER's, the robots and their components are being modeled. A TROTER system that features standardized component behavior is introduced. An object-oriented model implemented in the Smalltalk programming language is described and the advantages of the object-oriented approach for simulating robot and component interactions are discussed. The presentation includes preliminary results and a discussion of outstanding issues.

Interactions in the Dark Sector of Cosmology

NASA Astrophysics Data System (ADS)

Bean, Rachel

The success of modern cosmology hinges on two dramatic augmentations beyond the minimalist assumption of baryonic matter interacting gravitationally through general relativity. The first assumption is that there must exist either new gravitational dynamics or a new component of the cosmic energy budget - dark matter - that allows structure to form and accounts for weak lensing and galactic rotation curves. The second assumption is that a further dynamical modification or energy component - dark energy - exists, driving late-time cosmic acceleration. The need for these is now firmly established through a host of observations, which have raised crucial questions, and present a deep challenge to fundamental physics. The central theme of this proposal is the detailed understanding of the nature of the dark sector through the inevitable interactions between its individual components and with the visible universe. Such interactions can be crucial to a given model's viability, affecting its capability to reproduce the cosmic expansion history; the detailed predictions or structure formation; the gravitational dynamics on astrophysical and solar system scales; the stability of the microphysical model, and its ultimate consistency. While many models are consistent with cosmology on the coarsest scales, as is often the case, the devil may lie in the details. In this proposal we plan a comprehensive analysis of these details, focusing on the interactions within the dark sector and between it and visible matter, and on how these interactions affect the observational and theoretical consistency of models. Since it is unlikely that there will be a silver bullet allowing us to isolate the cause of cosmic acceleration, it is critical to develop a coherent view of the landscape of proposed models, extract clear predictions, and determine what combination of experiments and observations might allow us to test these predictions.

Specification, testing, and interpretation of gene-by-measured-environment interaction models in the presence of gene-environment correlation

PubMed Central

Rathouz, Paul J.; Van Hulle, Carol A.; Lee Rodgers, Joseph; Waldman, Irwin D.; Lahey, Benjamin B.

2009-01-01

Purcell (2002) proposed a bivariate biometric model for testing and quantifying the interaction between latent genetic influences and measured environments in the presence of gene-environment correlation. Purcell’s model extends the Cholesky model to include gene-environment interaction. We examine a number of closely-related alternative models that do not involve gene-environment interaction but which may fit the data as well Purcell’s model. Because failure to consider these alternatives could lead to spurious detection of gene-environment interaction, we propose alternative models for testing gene-environment interaction in the presence of gene-environment correlation, including one based on the correlated factors model. In addition, we note mathematical errors in the calculation of effect size via variance components in Purcell’s model. We propose a statistical method for deriving and interpreting variance decompositions that are true to the fitted model. PMID:18293078

Multiple Component Event-Related Potential (mcERP) Estimation

NASA Technical Reports Server (NTRS)

Knuth, K. H.; Clanton, S. T.; Shah, A. S.; Truccolo, W. A.; Ding, M.; Bressler, S. L.; Trejo, L. J.; Schroeder, C. E.; Clancy, Daniel (Technical Monitor)

2002-01-01

We show how model-based estimation of the neural sources responsible for transient neuroelectric signals can be improved by the analysis of single trial data. Previously, we showed that a multiple component event-related potential (mcERP) algorithm can extract the responses of individual sources from recordings of a mixture of multiple, possibly interacting, neural ensembles. McERP also estimated single-trial amplitudes and onset latencies, thus allowing more accurate estimation of ongoing neural activity during an experimental trial. The mcERP algorithm is related to informax independent component analysis (ICA); however, the underlying signal model is more physiologically realistic in that a component is modeled as a stereotypic waveshape varying both in amplitude and onset latency from trial to trial. The result is a model that reflects quantities of interest to the neuroscientist. Here we demonstrate that the mcERP algorithm provides more accurate results than more traditional methods such as factor analysis and the more recent ICA. Whereas factor analysis assumes the sources are orthogonal and ICA assumes the sources are statistically independent, the mcERP algorithm makes no such assumptions thus allowing investigators to examine interactions among components by estimating the properties of single-trial responses.

Fluid dynamic mechanisms and interactions within separated flows and their effects on missile aerodynamics

NASA Astrophysics Data System (ADS)

Addy, A. L.; Chow, W. L.; Korst, H. H.; White, R. A.

1983-05-01

Significant data and detailed results of a joint research effort investigating the fluid dynamic mechanisms and interactions within separated flows are presented. The results were obtained through analytical, experimental, and computational investigations of base flow related configurations. The research objectives focus on understanding the component mechanisms and interactions which establish and maintain separated flow regions. Flow models and theoretical analyses were developed to describe the base flowfield. The research approach has been to conduct extensive small-scale experiments on base flow configurations and to analyze these flows by component models and finite-difference techniques. The modeling of base flows of missiles (both powered and unpowered) for transonic and supersonic freestreams has been successful by component models. Research on plume effects and plume modeling indicated the need to match initial plume slope and plume surface curvature for valid wind tunnel simulation of an actual rocket plume. The assembly and development of a state-of-the-art laser Doppler velocimeter (LDV) system for experiments with two-dimensional small-scale models has been completed and detailed velocity and turbulence measurements are underway. The LDV experiments include the entire range of base flowfield mechanisms - shear layer development, recompression/reattachment, shock-induced separation, and plume-induced separation.

Correlations and enlarged superconducting phase of t -J⊥ chains of ultracold molecules on optical lattices

NASA Astrophysics Data System (ADS)

Manmana, Salvatore R.; Möller, Marcel; Gezzi, Riccardo; Hazzard, Kaden R. A.

2017-10-01

We compute physical properties across the phase diagram of the t -J⊥ chain with long-range dipolar interactions, which describe ultracold polar molecules on optical lattices. Our results obtained by the density-matrix renormalization group indicate that superconductivity is enhanced when the Ising component Jz of the spin-spin interaction and the charge component V are tuned to zero and even further by the long-range dipolar interactions. At low densities, a substantially larger spin gap is obtained. We provide evidence that long-range interactions lead to algebraically decaying correlation functions despite the presence of a gap. Although this has recently been observed in other long-range interacting spin and fermion models, the correlations in our case have the peculiar property of having a small and continuously varying exponent. We construct simple analytic models and arguments to understand the most salient features.

Modeling Cross-Situational Word–Referent Learning: Prior Questions

PubMed Central

Yu, Chen; Smith, Linda B.

2013-01-01

Both adults and young children possess powerful statistical computation capabilities—they can infer the referent of a word from highly ambiguous contexts involving many words and many referents by aggregating cross-situational statistical information across contexts. This ability has been explained by models of hypothesis testing and by models of associative learning. This article describes a series of simulation studies and analyses designed to understand the different learning mechanisms posited by the 2 classes of models and their relation to each other. Variants of a hypothesis-testing model and a simple or dumb associative mechanism were examined under different specifications of information selection, computation, and decision. Critically, these 3 components of the models interact in complex ways. The models illustrate a fundamental tradeoff between amount of data input and powerful computations: With the selection of more information, dumb associative models can mimic the powerful learning that is accomplished by hypothesis-testing models with fewer data. However, because of the interactions among the component parts of the models, the associative model can mimic various hypothesis-testing models, producing the same learning patterns but through different internal components. The simulations argue for the importance of a compositional approach to human statistical learning: the experimental decomposition of the processes that contribute to statistical learning in human learners and models with the internal components that can be evaluated independently and together. PMID:22229490

Conceptual model of iCAL4LA: Proposing the components using comparative analysis

NASA Astrophysics Data System (ADS)

Ahmad, Siti Zulaiha; Mutalib, Ariffin Abdul

2016-08-01

This paper discusses an on-going study that initiates an initial process in determining the common components for a conceptual model of interactive computer-assisted learning that is specifically designed for low achieving children. This group of children needs a specific learning support that can be used as an alternative learning material in their learning environment. In order to develop the conceptual model, this study extracts the common components from 15 strongly justified computer assisted learning studies. A comparative analysis has been conducted to determine the most appropriate components by using a set of specific indication classification to prioritize the applicability. The results of the extraction process reveal 17 common components for consideration. Later, based on scientific justifications, 16 of them were selected as the proposed components for the model.

Associations of Extrinsic and Intrinsic Components of Work Stress with Health: A Systematic Review of Evidence on the Effort-Reward Imbalance Model.

PubMed

Siegrist, Johannes; Li, Jian

2016-04-19

Mainstream psychological stress theory claims that it is important to include information on people's ways of coping with work stress when assessing the impact of stressful psychosocial work environments on health. Yet, some widely used respective theoretical models focus exclusively on extrinsic factors. The model of effort-reward imbalance (ERI) differs from them as it explicitly combines information on extrinsic and intrinsic factors in studying workers' health. As a growing number of studies used the ERI model in recent past, we conducted a systematic review of available evidence, with a special focus on the distinct contribution of its intrinsic component, the coping pattern "over-commitment", towards explaining health. Moreover, we explore whether the interaction of intrinsic and extrinsic components exceeds the size of effects on health attributable to single components. Results based on 51 reports document an independent explanatory role of "over-commitment" in explaining workers' health in a majority of studies. However, support in favour of the interaction hypothesis is limited and requires further exploration. In conclusion, the findings of this review support the usefulness of a work stress model that combines extrinsic and intrinsic components in terms of scientific explanation and of designing more comprehensive worksite stress prevention programs.

Associations of Extrinsic and Intrinsic Components of Work Stress with Health: A Systematic Review of Evidence on the Effort-Reward Imbalance Model

PubMed Central

Siegrist, Johannes; Li, Jian

2016-01-01

Mainstream psychological stress theory claims that it is important to include information on people’s ways of coping with work stress when assessing the impact of stressful psychosocial work environments on health. Yet, some widely used respective theoretical models focus exclusively on extrinsic factors. The model of effort-reward imbalance (ERI) differs from them as it explicitly combines information on extrinsic and intrinsic factors in studying workers’ health. As a growing number of studies used the ERI model in recent past, we conducted a systematic review of available evidence, with a special focus on the distinct contribution of its intrinsic component, the coping pattern “over-commitment”, towards explaining health. Moreover, we explore whether the interaction of intrinsic and extrinsic components exceeds the size of effects on health attributable to single components. Results based on 51 reports document an independent explanatory role of “over-commitment” in explaining workers’ health in a majority of studies. However, support in favour of the interaction hypothesis is limited and requires further exploration. In conclusion, the findings of this review support the usefulness of a work stress model that combines extrinsic and intrinsic components in terms of scientific explanation and of designing more comprehensive worksite stress prevention programs. PMID:27104548

A unification of mediation and interaction: a four-way decomposition

PubMed Central

VanderWeele, Tyler J.

2014-01-01

It is shown that the overall effect of an exposure on an outcome, in the presence of a mediator with which the exposure may interact, can be decomposed into four components: (i) the effect of the exposure in the absence of the mediator, (ii) the interactive effect when the mediator is left to what it would be in the absence of exposure, (iii) a mediated interaction, and (iv) a pure mediated effect. These four components, respectively, correspond to the portion of the effect that is due to neither mediation nor interaction, to just interaction (but not mediation), to both mediation and interaction, and to just mediation (but not interaction). This four-way decomposition unites methods that attribute effects to interactions and methods that assess mediation. Certain combinations of these four components correspond to measures for mediation, while other combinations correspond to measures of interaction previously proposed in the literature. Prior decompositions in the literature are in essence special cases of this four-way decomposition. The four-way decomposition can be carried out using standard statistical models, and software is provided to estimate each of the four components. The four-way decomposition provides maximum insight into how much of an effect is mediated, how much is due to interaction, how much is due to both mediation and interaction together, and how much is due to neither. PMID:25000145

Electromagnetic Interaction between the Component Coils of Multi-Plex Magnets

DOE PAGES

Nguyen, Quyen V. M.; Torrez, Lynette; Nguyen, Doan Ngoc

2017-12-04

Ultra-high field pulsed magnets are usually designed as a group of nested, concentric coils driven by separated power sources to reduce the required driving voltages and to distribute the mechanical load and to reduce the driving voltages. Since the magnet operates in a fast transient mode, there will be strong and complicated electromagnetic couplings between the component coils. The high eddy currents generated in the reinforcement shells of the component coils during the pulses also strongly affect these couplings. Therefore, understanding the electromagnetic interaction between the component coils will allow safer, more optimized design and operation of our magnets. Asmore » a result, this paper will focus on our finite element modeling and experimental results for the electromagnetic interactions between the component coils of the 100-T nondestructive magnet and 80-T duplex magnet at our facility.« less

Electromagnetic Interaction between the Component Coils of Multi-Plex Magnets

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

Nguyen, Quyen V. M.; Torrez, Lynette; Nguyen, Doan Ngoc

Ultra-high field pulsed magnets are usually designed as a group of nested, concentric coils driven by separated power sources to reduce the required driving voltages and to distribute the mechanical load and to reduce the driving voltages. Since the magnet operates in a fast transient mode, there will be strong and complicated electromagnetic couplings between the component coils. The high eddy currents generated in the reinforcement shells of the component coils during the pulses also strongly affect these couplings. Therefore, understanding the electromagnetic interaction between the component coils will allow safer, more optimized design and operation of our magnets. Asmore » a result, this paper will focus on our finite element modeling and experimental results for the electromagnetic interactions between the component coils of the 100-T nondestructive magnet and 80-T duplex magnet at our facility.« less

Flexible configuration-interaction shell-model many-body solver

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

Johnson, Calvin W.; Ormand, W. Erich; McElvain, Kenneth S.

BIGSTICK Is a flexible configuration-Interaction open-source shell-model code for the many-fermion problem In a shell model (occupation representation) framework. BIGSTICK can generate energy spectra, static and transition one-body densities, and expectation values of scalar operators. Using the built-in Lanczos algorithm one can compute transition probabflity distributions and decompose wave functions into components defined by group theory.

High-dimensional inference with the generalized Hopfield model: principal component analysis and corrections.

PubMed

Cocco, S; Monasson, R; Sessak, V

2011-05-01

We consider the problem of inferring the interactions between a set of N binary variables from the knowledge of their frequencies and pairwise correlations. The inference framework is based on the Hopfield model, a special case of the Ising model where the interaction matrix is defined through a set of patterns in the variable space, and is of rank much smaller than N. We show that maximum likelihood inference is deeply related to principal component analysis when the amplitude of the pattern components ξ is negligible compared to √N. Using techniques from statistical mechanics, we calculate the corrections to the patterns to the first order in ξ/√N. We stress the need to generalize the Hopfield model and include both attractive and repulsive patterns in order to correctly infer networks with sparse and strong interactions. We present a simple geometrical criterion to decide how many attractive and repulsive patterns should be considered as a function of the sampling noise. We moreover discuss how many sampled configurations are required for a good inference, as a function of the system size N and of the amplitude ξ. The inference approach is illustrated on synthetic and biological data.

Running vacuum cosmological models: linear scalar perturbations

NASA Astrophysics Data System (ADS)

Perico, E. L. D.; Tamayo, D. A.

2017-08-01

In cosmology, phenomenologically motivated expressions for running vacuum are commonly parameterized as linear functions typically denoted by Λ(H2) or Λ(R). Such models assume an equation of state for the vacuum given by bar PΛ = - bar rhoΛ, relating its background pressure bar PΛ with its mean energy density bar rhoΛ ≡ Λ/8πG. This equation of state suggests that the vacuum dynamics is due to an interaction with the matter content of the universe. Most of the approaches studying the observational impact of these models only consider the interaction between the vacuum and the transient dominant matter component of the universe. We extend such models by assuming that the running vacuum is the sum of independent contributions, namely bar rhoΛ = Σibar rhoΛi. Each Λ i vacuum component is associated and interacting with one of the i matter components in both the background and perturbation levels. We derive the evolution equations for the linear scalar vacuum and matter perturbations in those two scenarios, and identify the running vacuum imprints on the cosmic microwave background anisotropies as well as on the matter power spectrum. In the Λ(H2) scenario the vacuum is coupled with every matter component, whereas the Λ(R) description only leads to a coupling between vacuum and non-relativistic matter, producing different effects on the matter power spectrum.

Applications of statistical physics to technology price evolution

NASA Astrophysics Data System (ADS)

McNerney, James

Understanding how changing technology affects the prices of goods is a problem with both rich phenomenology and important policy consequences. Using methods from statistical physics, I model technology-driven price evolution. First, I examine a model for the price evolution of individual technologies. The price of a good often follows a power law equation when plotted against its cumulative production. This observation turns out to have significant consequences for technology policy aimed at mitigating climate change, where technologies are needed that achieve low carbon emissions at low cost. However, no theory adequately explains why technology prices follow power laws. To understand this behavior, I simplify an existing model that treats technologies as machines composed of interacting components. I find that the power law exponent of the price trajectory is inversely related to the number of interactions per component. I extend the model to allow for more realistic component interactions and make a testable prediction. Next, I conduct a case-study on the cost evolution of coal-fired electricity. I derive the cost in terms of various physical and economic components. The results suggest that commodities and technologies fall into distinct classes of price models, with commodities following martingales, and technologies following exponentials in time or power laws in cumulative production. I then examine the network of money flows between industries. This work is a precursor to studying the simultaneous evolution of multiple technologies. Economies resemble large machines, with different industries acting as interacting components with specialized functions. To begin studying the structure of these machines, I examine 20 economies with an emphasis on finding common features to serve as targets for statistical physics models. I find they share the same money flow and industry size distributions. I apply methods from statistical physics to show that industries cluster the same way according to industry type. Finally, I use these industry money flows to model the price evolution of many goods simultaneously, where network effects become important. I derive a prediction for which goods tend to improve most rapidly. The fastest-improving goods are those with the highest mean path lengths in the money flow network.

The decoupling of the glass transitions in the two-component p-spin spherical model

NASA Astrophysics Data System (ADS)

Ikeda, Harukuni; Ikeda, Atsushi

2016-07-01

Binary mixtures of large and small particles with a disparate size ratio exhibit a rich phenomenology at their glass transition points. In order to gain insights on such systems, we introduce and study a two-component version of the p-spin spherical spin glass model. We employ the replica method to calculate the free energy and the phase diagram. We show that when the strengths of the interactions of each component are not widely separated, the model has only one glass phase characterized by the conventional one-step replica symmetry breaking. However when the strengths of the interactions are well separated, the model has three glass phases depending on the temperature and component ratio. One is the ‘single’ glass phase in which only the spins of one component are frozen while the spins of the other component remain mobile. This phase is characterized by the one-step replica symmetry breaking. The second is the ‘double’ glass phase obtained by cooling the single glass phase further, in which the spins of the remaining mobile component are also frozen. This phase is characterized by the two-step replica symmetry breaking. The third is also the ‘double’ glass phase, which, however, is formed by the simultaneous freezing of the spins of both components at the same temperatures and is characterized by the one-step replica symmetry breaking. We discuss the implications of these results for the glass transitions of binary mixtures.

Critical point of gas-liquid type phase transition and phase equilibrium functions in developed two-component plasma model.

PubMed

Butlitsky, M A; Zelener, B B; Zelener, B V

2014-07-14

A two-component plasma model, which we called a "shelf Coulomb" model has been developed in this work. A Monte Carlo study has been undertaken to calculate equations of state, pair distribution functions, internal energies, and other thermodynamics properties. A canonical NVT ensemble with periodic boundary conditions was used. The motivation behind the model is also discussed in this work. The "shelf Coulomb" model can be compared to classical two-component (electron-proton) model where charges with zero size interact via a classical Coulomb law. With important difference for interaction of opposite charges: electrons and protons interact via the Coulomb law for large distances between particles, while interaction potential is cut off on small distances. The cut off distance is defined by an arbitrary ɛ parameter, which depends on system temperature. All the thermodynamics properties of the model depend on dimensionless parameters ɛ and γ = βe(2)n(1/3) (where β = 1/kBT, n is the particle's density, kB is the Boltzmann constant, and T is the temperature) only. In addition, it has been shown that the virial theorem works in this model. All the calculations were carried over a wide range of dimensionless ɛ and γ parameters in order to find the phase transition region, critical point, spinodal, and binodal lines of a model system. The system is observed to undergo a first order gas-liquid type phase transition with the critical point being in the vicinity of ɛ(crit) ≈ 13(T(*)(crit) ≈ 0.076), γ(crit) ≈ 1.8(v(*)(crit) ≈ 0.17), P(*)(crit) ≈ 0.39, where specific volume v* = 1/γ(3) and reduced temperature T(*) = ɛ(-1).

Interactive Reliability Model for Whisker-toughened Ceramics

NASA Technical Reports Server (NTRS)

Palko, Joseph L.

1993-01-01

Wider use of ceramic matrix composites (CMC) will require the development of advanced structural analysis technologies. The use of an interactive model to predict the time-independent reliability of a component subjected to multiaxial loads is discussed. The deterministic, three-parameter Willam-Warnke failure criterion serves as the theoretical basis for the reliability model. The strength parameters defining the model are assumed to be random variables, thereby transforming the deterministic failure criterion into a probabilistic criterion. The ability of the model to account for multiaxial stress states with the same unified theory is an improvement over existing models. The new model was coupled with a public-domain finite element program through an integrated design program. This allows a design engineer to predict the probability of failure of a component. A simple structural problem is analyzed using the new model, and the results are compared to existing models.

Evaluation of HardSys/HardDraw, An Expert System for Electromagnetic Interactions Modelling

DTIC Science & Technology

1993-05-01

interactions ir complex systems. This report gives a description of HardSys/HardDraw and reviews the main concepts used in its design. Various aspects of its ...HardDraw, an expert system for the modelling of electromagnetic interactions in complex systems. It consists of two main components: HardSys and HardDraw...HardSys is the advisor part of the expert system. It is knowledge-based, that is it contains a database of models and properties for various types of

Video modeling for children with dual diagnosis of deafness or hard of hearing and autism spectrum disorder to promote peer interaction.

PubMed

Thrasher, Amy

2014-11-01

This article describes an intervention program offered at the University of Colorado Boulder that supports peer interaction among young children with autism spectrum disorders and their typical peers using a multicomponent approach, including video modeling. Characteristics of autism that may interfere with the development of peer interaction in young children will be discussed. Components of the approach will be described and the evidence base for the application of these components examined in regards to children with autism and for the potential application to children with the dual diagnosis of autism and deafness or hard of hearing. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

A framework for modeling non-steady-state concentrations of semivolatile organic compounds indoors ― II. Interactions with particulate matter

EPA Science Inventory

This paper describes a method for dynamic modeling of the interactions of semivolatile organic compounds (SVOCs) with airborne and settled particulate matter in the indoor environment. This method is fully compatible with the other components within the framework. Despite the unc...

More Precise Estimation of Lower-Level Interaction Effects in Multilevel Models.

PubMed

Loeys, Tom; Josephy, Haeike; Dewitte, Marieke

2018-01-01

In hierarchical data, the effect of a lower-level predictor on a lower-level outcome may often be confounded by an (un)measured upper-level factor. When such confounding is left unaddressed, the effect of the lower-level predictor is estimated with bias. Separating this effect into a within- and between-component removes such bias in a linear random intercept model under a specific set of assumptions for the confounder. When the effect of the lower-level predictor is additionally moderated by another lower-level predictor, an interaction between both lower-level predictors is included into the model. To address unmeasured upper-level confounding, this interaction term ought to be decomposed into a within- and between-component as well. This can be achieved by first multiplying both predictors and centering that product term next, or vice versa. We show that while both approaches, on average, yield the same estimates of the interaction effect in linear models, the former decomposition is much more precise and robust against misspecification of the effects of cross-level and upper-level terms, compared to the latter.

Taking Venus models to new dimensions.

NASA Astrophysics Data System (ADS)

Murawski, K.

1997-11-01

Space plasma physicists in Poland and Japan have gained new insights into the interaction between the solar wind and Venus. Computer simulations of this 3D global interaction between the solar wind and nonmagnetized bodies have enabled greater understanding of the large-scale processes involved in such phenomena. A model that offers improved understanding of the solar wind interaction with Venus (as well as other nonmagnetized bodies impacted by the solar wind) has been developed. In this model, the interaction of the solar wind with the ionosphere of Venus is studied by calculating numerical solutions of the 3D MHD equations for two-component, chemically reactive plasma. The author describes the innovative model.

Assessment of Spacecraft Systems Integration Using the Electric Propulsion Interactions Code (EPIC)

NASA Technical Reports Server (NTRS)

Mikellides, Ioannis G.; Kuharski, Robert A.; Mandell, Myron J.; Gardner, Barbara M.; Kauffman, William J. (Technical Monitor)

2002-01-01

SAIC is currently developing the Electric Propulsion Interactions Code 'EPIC', an interactive computer tool that allows the construction of a 3-D spacecraft model, and the assessment of interactions between its subsystems and the plume from an electric thruster. EPIC unites different computer tools to address the complexity associated with the interaction processes. This paper describes the overall architecture and capability of EPIC including the physics and algorithms that comprise its various components. Results from selected modeling efforts of different spacecraft-thruster systems are also presented.

A Dynamic Network Model to Explain the Development of Excellent Human Performance

PubMed Central

Den Hartigh, Ruud J. R.; Van Dijk, Marijn W. G.; Steenbeek, Henderien W.; Van Geert, Paul L. C.

2016-01-01

Across different domains, from sports to science, some individuals accomplish excellent levels of performance. For over 150 years, researchers have debated the roles of specific nature and nurture components to develop excellence. In this article, we argue that the key to excellence does not reside in specific underlying components, but rather in the ongoing interactions among the components. We propose that excellence emerges out of dynamic networks consisting of idiosyncratic mixtures of interacting components such as genetic endowment, motivation, practice, and coaching. Using computer simulations we demonstrate that the dynamic network model accurately predicts typical properties of excellence reported in the literature, such as the idiosyncratic developmental trajectories leading to excellence and the highly skewed distributions of productivity present in virtually any achievement domain. Based on this novel theoretical perspective on excellent human performance, this article concludes by suggesting policy implications and directions for future research. PMID:27148140

Modelling the structure of a ceRNA-theoretical, bipartite microRNA-mRNA interaction network regulating intestinal epithelial cellular pathways using R programming.

PubMed

Robinson, J M; Henderson, W A

2018-01-12

We report a method using functional-molecular databases and network modelling to identify hypothetical mRNA-miRNA interaction networks regulating intestinal epithelial barrier function. The model forms a data-analysis component of our cell culture experiments, which produce RNA expression data from Nanostring Technologies nCounter ® system. The epithelial tight-junction (TJ) and actin cytoskeleton interact as molecular components of the intestinal epithelial barrier. Upstream regulation of TJ-cytoskeleton interaction is effected by the Rac/Rock/Rho signaling pathway and other associated pathways which may be activated or suppressed by extracellular signaling from growth factors, hormones, and immune receptors. Pathway activations affect epithelial homeostasis, contributing to degradation of the epithelial barrier associated with osmotic dysregulation, inflammation, and tumor development. The complexity underlying miRNA-mRNA interaction networks represents a roadblock for prediction and validation of competing-endogenous RNA network function. We developed a network model to identify hypothetical co-regulatory motifs in a miRNA-mRNA interaction network related to epithelial function. A mRNA-miRNA interaction list was generated using KEGG and miRWalk2.0 databases. R-code was developed to quantify and visualize inherent network structures. We identified a sub-network with a high number of shared, targeting miRNAs, of genes associated with cellular proliferation and cancer, including c-MYC and Cyclin D.

Postcollision interaction in noble gas clusters: observation of differences in surface and bulk line shapes.

PubMed

Lindblad, A; Fink, R F; Bergersen, H; Lundwall, M; Rander, T; Feifel, R; Ohrwall, G; Tchaplyguine, M; Hergenhahn, U; Svensson, S; Björneholm, O

2005-12-01

The surface and bulk components of the x-ray photoelectron spectra of free noble gas clusters are shown to display differences in the influence of postcollision interaction between the photoelectron and the Auger electron on the spectral line shape; the bulk component is observed to be less affected than the surface and atomic parts of the spectra. A model for postcollision interaction in nonmetallic solids and clusters is also provided which takes the polarization screening into account. Core-level photoelectron spectra of Ar, Kr, and Xe have been recorded to verify the dependence of the postcollision interaction effect on the polarizability of the sample.

Development of a 13 kW Hall Thruster Propulsion System Performance Model for AEPS

NASA Technical Reports Server (NTRS)

Stanley, Steven; Allen, May; Goodfellow, Keith; Chew, Gilbert; Rapetti, Ryan; Tofil, Todd; Herman, Dan; Jackson, Jerry; Myers, Roger

2017-01-01

The Advanced Electric Propulsion System (AEPS) program will develop a flight 13kW Hall thruster propulsion system based on NASA's HERMeS thruster. The AEPS system includes the Hall Thruster, the Power Processing Unit (PPU) and the Xenon Flow Controller (XFC). These three primary components must operate together to ensure that the system generates the required combinations of thrust and specific impulse at the required system efficiencies for the desired system lifetime. At the highest level, the AEPS system will be integrated into the spacecraft and will receive power, propellant, and commands from the spacecraft. Power and propellant flow rates will be determined by the throttle set points commanded by the spacecraft. Within the system, the major control loop is between the mass flow rate and thruster current, with time-dependencies required to handle all expected transients, and additional, much slower interactions between the thruster and cathode temperatures, flow controller and PPU. The internal system interactions generally occur on shorter timescales than the spacecraft interactions, though certain failure modes may require rapid responses from the spacecraft. The AEPS system performance model is designed to account for all these interactions in a way that allows evaluation of the sensitivity of the system to expected changes over the planned mission as well as to assess the impacts of normal component and assembly variability during the production phase of the program. This effort describes the plan for the system performance model development, correlation to NASA test data, and how the model will be used to evaluate the critical internal and external interactions. The results will ensure the component requirements do not unnecessarily drive the system cost or overly constrain the development program. Finally, the model will be available to quickly troubleshoot any future unforeseen development challenges.

Group Trust, Communication Media, and Interactivity: Toward an Integrated Model of Online Collaborative Learning

ERIC Educational Resources Information Center

Du, Jianxia; Wang, Chuang; Zhou, Mingming; Xu, Jianzhong; Fan, Xitao; Lei, Saosan

2018-01-01

The present investigation examines the multidimensional relationships among several critical components in online collaborative learning, including group trust, communication media, and interactivity. Four hundred eleven university students from 103 groups in the United States responded survey items on online collaboration, interactivity,…

A Three-Level Analysis of Collaborative Learning in Dual-Interaction Spaces

ERIC Educational Resources Information Center

Lonchamp, Jacques

2009-01-01

CSCL systems which follow the dual-interaction spaces paradigm support the synchronous construction and discussion of shared artifacts by distributed or colocated small groups of learners. The most recent generic dual-interaction space environments, either model based or component based, can be deeply customized by teachers for supporting…

Immune interaction between components of acellular pertussis-diphtheria-tetanus (DTaP) vaccine and Haemophilus influenzae b (Hib) conjugate vaccine in a rat model.

PubMed

Mawas, Fatme; Dickinson, Robert; Douglas-Bardsley, Alexandra; Xing, Dorothy K L; Sesardic, Dorothea; Corbel, Michael J

2006-04-24

We have previously shown that, consistent with clinical trial results, the immune response to a Haemophilus influenzae b (Hib) conjugate vaccine in a rat model was compromised and modulated when given combined with a DTaP3 vaccine, as compared to both vaccines given separately. The present study extended our investigation to evaluate the immunogenicity of all DTaP3 components in combined versus separate administration of Hib with DTaP3 and investigated immune interactions between Hib and individual components of DTaP3. Rats were immunised with Hib and DTaP3 or with Hib and individual DTaP3 components. Cellular and humoral immune responses to Hib and DTaP3 components were evaluated. Our results indicate that the immunogenicity of DTaP3 components was similar or greater in combined versus separate administration of Hib and DTaP3. Moreover, combined administration of Hib and TT reduced immunogenicity of both Hib and TT. Hib immunogenicity was also significantly reduced when given combined with FHA and following adsorption to Al(OH)3.

Tracing and separating plasma components causing matrix effects in hydrophilic interaction chromatography-electrospray ionization mass spectrometry.

PubMed

Ekdahl, Anja; Johansson, Maria C; Ahnoff, Martin

2013-04-01

Matrix effects on electrospray ionization were investigated for plasma samples analysed by hydrophilic interaction chromatography (HILIC) in gradient elution mode, and HILIC columns of different chemistries were tested for separation of plasma components and model analytes. By combining mass spectral data with post-column infusion traces, the following components of protein-precipitated plasma were identified and found to have significant effect on ionization: urea, creatinine, phosphocholine, lysophosphocholine, sphingomyelin, sodium ion, chloride ion, choline and proline betaine. The observed effect on ionization was both matrix-component and analyte dependent. The separation of identified plasma components and model analytes on eight columns was compared, using pair-wise linear correlation analysis and principal component analysis (PCA). Large changes in selectivity could be obtained by change of column, while smaller changes were seen when the mobile phase buffer was changed from ammonium formate pH 3.0 to ammonium acetate pH 4.5. While results from PCA and linear correlation analysis were largely in accord, linear correlation analysis was judged to be more straight-forward in terms of conduction and interpretation.

Polyelectrolyte Structure and Interactions in Model Cystic Fibrosis Sputum

NASA Astrophysics Data System (ADS)

Slimmer, Scott; Angelini, Thomas; Liang, Hongjun; Butler, John; Wong, Gerard C. L.

2002-03-01

Cystic fibrosis sputum is a complex fluid consisting of a number of components, including mucin (a glycoprotein), lysozyme (a cationic polypeptide), water, salt, as well as a high concentration of a number of anionic biological polyelectrolytes such as DNA and F-actin. The interactions governing these components are poorly understood, but may have important clinical consequences. For example, the formation of these biological polyelectrolytes into ordered gel phases may contribute significantly to the observed high viscosity of CF sputum. In this work, a number of model systems were created to simulate CF sputum in vitro, in order to elucidate the contributions of the different components. Preliminary results will be presented. This work was supported by NSF DMR-0071761, DOE DEFG02-91ER45439, the Beckman Young Investigator Program, and the Cystic Fibrosis Foundation.

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

Sahore, Ritu; Peebles, Cameron; Abraham, Daniel P.

Li 1.03(Ni 0.5Mn 0.3Co 0.2) 0.97O 2 (NMC)-based coin cells containing the electrolyte additives vinylene carbonate (VC) and tris(trimethylsilyl)phosphite (TMSPi) in the range of 0-2 wt% were cycled between 3.0 and 4.4 V. The changes in capacity at rates of C/10 and C/1 and resistance at 60% state of charge were found to follow linear-with-time kinetic rate laws. Further, the C/10 capacity and resistance data were amenable to modeling by a statistics of mixtures approach. Applying physical meaning to the terms in the empirical models indicated that the interactions between the electrolyte and additives were not simple. For example, theremore » were strong, synergistic interactions between VC and TMSPi affecting C/10 capacity loss, as expected, but there were other, more subtle interactions between the electrolyte components. In conclusion, the interactions between these components controlled the C/10 capacity decline and resistance increase.« less

A componential model of human interaction with graphs: 1. Linear regression modeling

NASA Technical Reports Server (NTRS)

Gillan, Douglas J.; Lewis, Robert

1994-01-01

Task analyses served as the basis for developing the Mixed Arithmetic-Perceptual (MA-P) model, which proposes (1) that people interacting with common graphs to answer common questions apply a set of component processes-searching for indicators, encoding the value of indicators, performing arithmetic operations on the values, making spatial comparisons among indicators, and repsonding; and (2) that the type of graph and user's task determine the combination and order of the components applied (i.e., the processing steps). Two experiments investigated the prediction that response time will be linearly related to the number of processing steps according to the MA-P model. Subjects used line graphs, scatter plots, and stacked bar graphs to answer comparison questions and questions requiring arithmetic calculations. A one-parameter version of the model (with equal weights for all components) and a two-parameter version (with different weights for arithmetic and nonarithmetic processes) accounted for 76%-85% of individual subjects' variance in response time and 61%-68% of the variance taken across all subjects. The discussion addresses possible modifications in the MA-P model, alternative models, and design implications from the MA-P model.

Further Investigations of Gravity Modeling on Surface-Interacting Vehicle Simulations

NASA Technical Reports Server (NTRS)

Madden, Michael M.

2009-01-01

A vehicle simulation is "surface-interacting" if the state of the vehicle (position, velocity, and acceleration) relative to the surface is important. Surface-interacting simulations perform ascent, entry, descent, landing, surface travel, or atmospheric flight. The dynamics of surface-interacting simulations are influenced by the modeling of gravity. Gravity is the sum of gravitation and the centrifugal acceleration due to the world s rotation. Both components are functions of position relative to the world s center and that position for a given set of geodetic coordinates (latitude, longitude, and altitude) depends on the world model (world shape and dynamics). Thus, gravity fidelity depends on the fidelities of the gravitation model and the world model and on the interaction of the gravitation and world model. A surface-interacting simulation cannot treat the gravitation separately from the world model. This paper examines the actual performance of different pairs of world and gravitation models (or direct gravity models) on the travel of a subsonic civil transport in level flight under various starting conditions.

Gravity Modeling Effects on Surface-Interacting Vehicles in Supersonic Flight

NASA Technical Reports Server (NTRS)

Madden, Michael M.

2010-01-01

A vehicle simulation is "surface-interacting" if the state of the vehicle (position, velocity, and acceleration) relative to the surface is important. Surface-interacting simulations per-form ascent, entry, descent, landing, surface travel, or atmospheric flight. The dynamics of surface-interacting simulations are influenced by the modeling of gravity. Gravity is the sum of gravitation and the centrifugal acceleration due to the world s rotation. Both components are functions of position relative to the world s center and that position for a given set of geodetic coordinates (latitude, longitude, and altitude) depends on the world model (world shape and dynamics). Thus, gravity fidelity depends on the fidelities of the gravitation model and the world model and on the interaction of these two models. A surface-interacting simulation cannot treat gravitation separately from the world model. This paper examines the actual performance of different pairs of world and gravitation models (or direct gravity models) on the travel of a supersonic aircraft in level flight under various start-ing conditions.

Multiple component end-member mixing model of dilution: hydrochemical effects of construction water at Yucca Mountain, Nevada, USA

NASA Astrophysics Data System (ADS)

Lu, Guoping; Sonnenthal, Eric L.; Bodvarsson, Gudmundur S.

2008-12-01

The standard dual-component and two-member linear mixing model is often used to quantify water mixing of different sources. However, it is no longer applicable whenever actual mixture concentrations are not exactly known because of dilution. For example, low-water-content (low-porosity) rock samples are leached for pore-water chemical compositions, which therefore are diluted in the leachates. A multicomponent, two-member mixing model of dilution has been developed to quantify mixing of water sources and multiple chemical components experiencing dilution in leaching. This extended mixing model was used to quantify fracture-matrix interaction in construction-water migration tests along the Exploratory Studies Facility (ESF) tunnel at Yucca Mountain, Nevada, USA. The model effectively recovers the spatial distribution of water and chemical compositions released from the construction water, and provides invaluable data on the matrix fracture interaction. The methodology and formulations described here are applicable to many sorts of mixing-dilution problems, including dilution in petroleum reservoirs, hydrospheres, chemical constituents in rocks and minerals, monitoring of drilling fluids, and leaching, as well as to environmental science studies.

[An ADAA model and its analysis method for agronomic traits based on the double-cross mating design].

PubMed

Xu, Z C; Zhu, J

2000-01-01

According to the double-cross mating design and using principles of Cockerham's general genetic model, a genetic model with additive, dominance and epistatic effects (ADAA model) was proposed for the analysis of agronomic traits. Components of genetic effects were derived for different generations. Monte Carlo simulation was conducted for analyzing the ADAA model and its reduced AD model by using different generations. It was indicated that genetic variance components could be estimated without bias by MINQUE(1) method and genetic effects could be predicted effectively by AUP method; at least three generations (including parent, F1 of single cross and F1 of double-cross) were necessary for analyzing the ADAA model and only two generations (including parent and F1 of double-cross) were enough for the reduced AD model. When epistatic effects were taken into account, a new approach for predicting the heterosis of agronomic traits of double-crosses was given on the basis of unbiased prediction of genotypic merits of parents and their crosses. In addition, genotype x environment interaction effects and interaction heterosis due to G x E interaction were discussed briefly.

Users matter : multi-agent systems model of high performance computing cluster users.

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

North, M. J.; Hood, C. S.; Decision and Information Sciences

2005-01-01

High performance computing clusters have been a critical resource for computational science for over a decade and have more recently become integral to large-scale industrial analysis. Despite their well-specified components, the aggregate behavior of clusters is poorly understood. The difficulties arise from complicated interactions between cluster components during operation. These interactions have been studied by many researchers, some of whom have identified the need for holistic multi-scale modeling that simultaneously includes network level, operating system level, process level, and user level behaviors. Each of these levels presents its own modeling challenges, but the user level is the most complex duemore » to the adaptability of human beings. In this vein, there are several major user modeling goals, namely descriptive modeling, predictive modeling and automated weakness discovery. This study shows how multi-agent techniques were used to simulate a large-scale computing cluster at each of these levels.« less

Propulsion and airframe aerodynamic interactions of supersonic V/STOL configurations, phase 1

NASA Technical Reports Server (NTRS)

Mraz, M. R.; Hiley, P. E.

1985-01-01

A wind tunnel model of a supersonic V/STOL fighter configuration has been tested to measure the aerodynamic interaction effects which can result from geometrically close-coupled propulsion system/airframe components. The approach was to configure the model to present two different test techniques. One was a coventional test technique composed of two test modes. In the Flow-Through mode, absolute configuration aerodynamics are measured, including inlet/airframe interactions. In the Jet-Effects mode, incremental nozzle/airframe interactions are measured. The other test technique is a propulsion simulator approach, where a subscale, externally powered engine is mounted in the model. This allows proper measurement of inlet/airframe and nozzle/airframe interactions simultaneously.

Cytoskeletal dynamics in fission yeast: a review of models for polarization and division

PubMed Central

Drake, Tyler; Vavylonis, Dimitrios

2010-01-01

We review modeling studies concerning cytoskeletal activity of fission yeast. Recent models vary in length and time scales, describing a range of phenomena from cellular morphogenesis to polymer assembly. The components of cytoskeleton act in concert to mediate cell-scale events and interactions such as polarization. The mathematical models reduce these events and interactions to their essential ingredients, describing the cytoskeleton by its bulk properties. On a smaller scale, models describe cytoskeletal subcomponents and how bulk properties emerge. PMID:21119765

Interactions between Flight Dynamics and Propulsion Systems of Air-Breathing Hypersonic Vehicles

DTIC Science & Technology

2013-01-01

coupled with combustor – Combustor, component for subsonic or supersonic combustion – Nozzle , expands flow for high thrust and may provide lift... supersonic solution method that is used for both the inlet and nozzle components. The supersonic model SAMURI is a substantial improvement over previous models...purely supersonic inviscid flow. As a result, the model is also appropriate for other applications, including the nozzle , which is important 19 Figure

Investigation of Fully Three-Dimensional Helical RF Field Effects on TWT Beam/Circuit Interaction

NASA Technical Reports Server (NTRS)

Kory, Carol L.

2000-01-01

A fully three-dimensional (3D), time-dependent, helical traveling wave-tube (TWT) interaction model has been developed using the electromagnetic particle-in-cell (PIC) code MAFIA. The model includes a short section of helical slow-wave circuit with excitation fed by RF input/output couplers, and electron beam contained by periodic permanent magnet (PPM) focusing. All components of the model are simulated in three dimensions allowing the effects of the fully 3D helical fields on RF circuit/beam interaction to be investigated for the first time. The development of the interaction model is presented, and predicted TWT performance using 2.5D and 3D models is compared to investigate the effect of conventional approximations used in TWT analyses.

Strategy and model building in the fourth dimension: a null model for genotype x age interaction as a Gaussian stationary stochastic process.

PubMed

Diego, Vincent P; Almasy, Laura; Dyer, Thomas D; Soler, Júlia M P; Blangero, John

2003-12-31

Using univariate and multivariate variance components linkage analysis methods, we studied possible genotype x age interaction in cardiovascular phenotypes related to the aging process from the Framingham Heart Study. We found evidence for genotype x age interaction for fasting glucose and systolic blood pressure. There is polygenic genotype x age interaction for fasting glucose and systolic blood pressure and quantitative trait locus x age interaction for a linkage signal for systolic blood pressure phenotypes located on chromosome 17 at 67 cM.

Climate change amplifies the interactions between wind and bark beetle disturbances in forest landscapes.

PubMed

Seidl, Rupert; Rammer, Werner

2017-07-01

Growing evidence suggests that climate change could substantially alter forest disturbances. Interactions between individual disturbance agents are a major component of disturbance regimes, yet how interactions contribute to their climate sensitivity remains largely unknown. Here, our aim was to assess the climate sensitivity of disturbance interactions, focusing on wind and bark beetle disturbances. We developed a process-based model of bark beetle disturbance, integrated into the dynamic forest landscape model iLand (already including a detailed model of wind disturbance). We evaluated the integrated model against observations from three wind events and a subsequent bark beetle outbreak, affecting 530.2 ha (3.8 %) of a mountain forest landscape in Austria between 2007 and 2014. Subsequently, we conducted a factorial experiment determining the effect of changes in climate variables on the area disturbed by wind and bark beetles separately and in combination. iLand was well able to reproduce observations with regard to area, temporal sequence, and spatial pattern of disturbance. The observed disturbance dynamics was strongly driven by interactions, with 64.3 % of the area disturbed attributed to interaction effects. A +4 °C warming increased the disturbed area by +264.7 % and the area-weighted mean patch size by +1794.3 %. Interactions were found to have a ten times higher sensitivity to temperature changes than main effects, considerably amplifying the climate sensitivity of the disturbance regime. Disturbance interactions are a key component of the forest disturbance regime. Neglecting interaction effects can lead to a substantial underestimation of the climate change sensitivity of disturbance regimes.

Engineering Breast Cancer Microenvironments and 3D Bioprinting

PubMed Central

Belgodere, Jorge A.; King, Connor T.; Bursavich, Jacob B.; Burow, Matthew E.; Martin, Elizabeth C.; Jung, Jangwook P.

2018-01-01

The extracellular matrix (ECM) is a critical cue to direct tumorigenesis and metastasis. Although two-dimensional (2D) culture models have been widely employed to understand breast cancer microenvironments over the past several decades, the 2D models still exhibit limited success. Overwhelming evidence supports that three dimensional (3D), physiologically relevant culture models are required to better understand cancer progression and develop more effective treatment. Such platforms should include cancer-specific architectures, relevant physicochemical signals, stromal–cancer cell interactions, immune components, vascular components, and cell-ECM interactions found in patient tumors. This review briefly summarizes how cancer microenvironments (stromal component, cell-ECM interactions, and molecular modulators) are defined and what emerging technologies (perfusable scaffold, tumor stiffness, supporting cells within tumors and complex patterning) can be utilized to better mimic native-like breast cancer microenvironments. Furthermore, this review emphasizes biophysical properties that differ between primary tumor ECM and tissue sites of metastatic lesions with a focus on matrix modulation of cancer stem cells, providing a rationale for investigation of underexplored ECM proteins that could alter patient prognosis. To engineer breast cancer microenvironments, we categorized technologies into two groups: (1) biochemical factors modulating breast cancer cell-ECM interactions and (2) 3D bioprinting methods and its applications to model breast cancer microenvironments. Biochemical factors include matrix-associated proteins, soluble factors, ECMs, and synthetic biomaterials. For the application of 3D bioprinting, we discuss the transition of 2D patterning to 3D scaffolding with various bioprinting technologies to implement biophysical cues to model breast cancer microenvironments. PMID:29881724

Operational coupled atmosphere - ocean - ice forecast system for the Gulf of St. Lawrence, Canada

NASA Astrophysics Data System (ADS)

Faucher, M.; Roy, F.; Desjardins, S.; Fogarty, C.; Pellerin, P.; Ritchie, H.; Denis, B.

2009-09-01

A fully interactive coupled atmosphere-ocean-ice forecasting system for the Gulf of St. Lawrence (GSL) has been running in experimental mode at the Canadian Meteorological Centre (CMC) for the last two winter seasons. The goal of this project is to provide more accurate weather and sea ice forecasts over the GSL and adjacent coastal areas by including atmosphere-oceanice interactions in the CMC operational forecast system using a formal coupling strategy between two independent modeling components. The atmospheric component is the Canadian operational GEM model (Côté et al. 1998) and the oceanic component is the ocean-ice model for the Gulf of St. Lawrence developed at the Maurice Lamontagne Institute (IML) (Saucier et al. 2003, 2004). The coupling between those two models is achieved by exchanging surface fluxes and variables through MPI communication. The re-gridding of the variables is done with a package developed at the Recherche en Prevision Numerique centre (RPN, Canada). Coupled atmosphere - ocean - ice forecasts are issued once a day based on 00GMT data. Results for the past two years have demonstrated that the coupled system produces improved forecasts in and around the GSL during all seasons, proving that atmosphere-ocean-ice interactions are indeed important even for short-term Canadian weather forecasts. This has important implications for other coupled modeling and data assimilation partnerships that are in progress involving EC, the Department of Fisheries and Oceans (DFO) and the National Defense (DND). Following this experimental phase, it is anticipated that this GSL system will be the first fully interactive coupled system to be implemented at CMC.

Using a Modular Construction Kit for the Realization of an Interactive Computer Graphics Course.

ERIC Educational Resources Information Center

Klein, Reinhard; Hanisch, Frank

Recently, platform independent software components, like JavaBeans, have appeared that allow writing reusable components and composing them in a visual builder tool into new applications. This paper describes the use of such models to transform an existing course into a modular construction kit consisting of components of teaching text and program…

MoCha: Molecular Characterization of Unknown Pathways.

PubMed

Lobo, Daniel; Hammelman, Jennifer; Levin, Michael

2016-04-01

Automated methods for the reverse-engineering of complex regulatory networks are paving the way for the inference of mechanistic comprehensive models directly from experimental data. These novel methods can infer not only the relations and parameters of the known molecules defined in their input datasets, but also unknown components and pathways identified as necessary by the automated algorithms. Identifying the molecular nature of these unknown components is a crucial step for making testable predictions and experimentally validating the models, yet no specific and efficient tools exist to aid in this process. To this end, we present here MoCha (Molecular Characterization), a tool optimized for the search of unknown proteins and their pathways from a given set of known interacting proteins. MoCha uses the comprehensive dataset of protein-protein interactions provided by the STRING database, which currently includes more than a billion interactions from over 2,000 organisms. MoCha is highly optimized, performing typical searches within seconds. We demonstrate the use of MoCha with the characterization of unknown components from reverse-engineered models from the literature. MoCha is useful for working on network models by hand or as a downstream step of a model inference engine workflow and represents a valuable and efficient tool for the characterization of unknown pathways using known data from thousands of organisms. MoCha and its source code are freely available online under the GPLv3 license.

Vestibular coriolis effect differences modeled with three-dimensional linear-angular interactions.

PubMed

Holly, Jan E

2004-01-01

The vestibular coriolis (or "cross-coupling") effect is traditionally explained by cross-coupled angular vectors, which, however, do not explain the differences in perceptual disturbance under different acceleration conditions. For example, during head roll tilt in a rotating chair, the magnitude of perceptual disturbance is affected by a number of factors, including acceleration or deceleration of the chair rotation or a zero-g environment. Therefore, it has been suggested that linear-angular interactions play a role. The present research investigated whether these perceptual differences and others involving linear coriolis accelerations could be explained under one common framework: the laws of motion in three dimensions, which include all linear-angular interactions among all six components of motion (three angular and three linear). The results show that the three-dimensional laws of motion predict the differences in perceptual disturbance. No special properties of the vestibular system or nervous system are required. In addition, simulations were performed with angular, linear, and tilt time constants inserted into the model, giving the same predictions. Three-dimensional graphics were used to highlight the manner in which linear-angular interaction causes perceptual disturbance, and a crucial component is the Stretch Factor, which measures the "unexpected" linear component.

Search for a Scalar Component in the Weak Interaction

NASA Astrophysics Data System (ADS)

Zakoucky, Dalibor; Baczyk, Pavel; Ban, Gilles; Beck, Marcus; Breitenfeldt, Martin; Couratin, Claire; Fabian, Xavier; Finlay, Paul; Flechard, Xavier; Friedag, Peter; Glück, Ferenc; Herlert, Alexander; Knecht, Andreas; Kozlov, Valentin; Lienard, Etienne; Porobic, Tomica; Soti, Gergelj; Tandecki, Michael; Vangorp, Simon; Weinheimer, Christian; Wursten, Elise; Severijns, Nathal

Weak interactions are described by the Standard Model which uses the basic assumption of a pure "V(ector)-A(xial vector)" character for the interaction. However, after more than half a century of model development and experimental testing of its fundamental ingredients, experimental limits for possible admixtures of scalar and/or tensor interactions are still as high as 7%. The WITCH project (Weak Interaction Trap for CHarged particles) at the isotope separator ISOLDE at CERN is trying to probe the structure of the weak interaction in specific low energy β-decays in order to look for possible scalar or tensor components or at least significantly improve the current experimental limits. This worldwide unique experimental setup consisting of a combination of two Penning ion traps and a retardation spectrometer allows to catch, trap and cool the radioactive nuclei provided by the ISOLDE separator, form a cooled and scattering-free radioactive source of β-decaying nuclei and let these nuclei decay at rest. The precise measurement of the shape of the energy spectrum of the recoiling nuclei, the shape of which is very sensitive to the character of the weak interaction, enables searching for a possible admixture of a scalar/tensor component in the dominant vector/axial vector mode. First online measurements with the isotope 35Ar were performed in 2011 and 2012. The current status of the experiment, the data analysis and results as well as extensive simulations will be presented and discussed.

Placing Students at the Heart of the Iron Triangle and the Interaction Equivalence Theorem Models

ERIC Educational Resources Information Center

Lane, Andy

2014-01-01

A number of visual models have been proposed to help explain the interplay and interactions between specified components of higher education systems at different levels and to take account of emerging trends towards open education systems. At sector and institutional levels the notion of an iron triangle has been posited, linking firstly access,…

GEOS S2S-2_1: GMAO's New High Resolution Seasonal Prediction System

NASA Technical Reports Server (NTRS)

Molod, Andrea; Akella, Santha; Andrews, Lauren; Barahona, Donifan; Borovikov, Anna; Chang, Yehui; Cullather, Richard; Hackert, Eric; Kovach, Robin; Koster, Randal;

Novel use of UV broad-band excitation and stretched exponential function in the analysis of fluorescent dissolved organic matter: study of interaction between protein and humic-like components

NASA Astrophysics Data System (ADS)

Panigrahi, Suraj Kumar; Mishra, Ashok Kumar

2017-09-01

A combination of broad-band UV radiation (UV A and UV B; 250-400 nm) and a stretched exponential function (StrEF) has been utilised in efforts towards convenient and sensitive detection of fluorescent dissolved organic matter (FDOM). This approach enables accessing the gross fluorescence spectral signature of both protein-like and humic-like components in a single measurement. Commercial FDOM components are excited with the broad-band UV excitation; the variation of spectral profile as a function of varying component ratio is analysed. The underlying fluorescence dynamics and non-linear quenching of amino acid moieties are studied with the StrEF (exp(-V[Q] β )). The complex quenching pattern reflects the inner filter effect (IFE) as well as inter-component interactions. The inter-component interactions are essentially captured through the ‘sphere of action’ and ‘dark complex’ models. The broad-band UV excitation ascertains increased excitation energy, resulting in increased population density in the excited state and thereby resulting in enhanced sensitivity.

Improving our fundamental understanding of the role of aerosol-cloud interactions in the climate system.

PubMed

Seinfeld, John H; Bretherton, Christopher; Carslaw, Kenneth S; Coe, Hugh; DeMott, Paul J; Dunlea, Edward J; Feingold, Graham; Ghan, Steven; Guenther, Alex B; Kahn, Ralph; Kraucunas, Ian; Kreidenweis, Sonia M; Molina, Mario J; Nenes, Athanasios; Penner, Joyce E; Prather, Kimberly A; Ramanathan, V; Ramaswamy, Venkatachalam; Rasch, Philip J; Ravishankara, A R; Rosenfeld, Daniel; Stephens, Graeme; Wood, Robert

2016-05-24

The effect of an increase in atmospheric aerosol concentrations on the distribution and radiative properties of Earth's clouds is the most uncertain component of the overall global radiative forcing from preindustrial time. General circulation models (GCMs) are the tool for predicting future climate, but the treatment of aerosols, clouds, and aerosol-cloud radiative effects carries large uncertainties that directly affect GCM predictions, such as climate sensitivity. Predictions are hampered by the large range of scales of interaction between various components that need to be captured. Observation systems (remote sensing, in situ) are increasingly being used to constrain predictions, but significant challenges exist, to some extent because of the large range of scales and the fact that the various measuring systems tend to address different scales. Fine-scale models represent clouds, aerosols, and aerosol-cloud interactions with high fidelity but do not include interactions with the larger scale and are therefore limited from a climatic point of view. We suggest strategies for improving estimates of aerosol-cloud relationships in climate models, for new remote sensing and in situ measurements, and for quantifying and reducing model uncertainty.

Improving Our Fundamental Understanding of the Role of Aerosol Cloud Interactions in the Climate System

NASA Technical Reports Server (NTRS)

Seinfeld, John H.; Bretherton, Christopher; Carslaw, Kenneth S.; Coe, Hugh; DeMott, Paul J.; Dunlea, Edward J.; Feingold, Graham; Ghan, Steven; Guenther, Alex B.; Kahn, Ralph;

Modelling indirect interactions during failure spreading in a project activity network.

PubMed

Ellinas, Christos

2018-03-12

Spreading broadly refers to the notion of an entity propagating throughout a networked system via its interacting components. Evidence of its ubiquity and severity can be seen in a range of phenomena, from disease epidemics to financial systemic risk. In order to understand the dynamics of these critical phenomena, computational models map the probability of propagation as a function of direct exposure, typically in the form of pairwise interactions between components. By doing so, the important role of indirect interactions remains unexplored. In response, we develop a simple model that accounts for the effect of both direct and subsequent exposure, which we deploy in the novel context of failure propagation within a real-world engineering project. We show that subsequent exposure has a significant effect in key aspects, including the: (a) final spreading event size, (b) propagation rate, and (c) spreading event structure. In addition, we demonstrate the existence of 'hidden influentials' in large-scale spreading events, and evaluate the role of direct and subsequent exposure in their emergence. Given the evidence of the importance of subsequent exposure, our findings offer new insight on particular aspects that need to be included when modelling network dynamics in general, and spreading processes specifically.

Improving our fundamental understanding of the role of aerosol-cloud interactions in the climate system

DOE PAGES

Seinfeld, John H.; Bretherton, Christopher; Carslaw, Kenneth S.; ...

2016-05-24

The effect of an increase in atmospheric aerosol concentrations on the distribution and radiative properties of Earth’s clouds is the most uncertain component of the overall global radiative forcing from pre-industrial time. General Circulation Models (GCMs) are the tool for predicting future climate, but the treatment of aerosols, clouds, and aerosol-cloud radiative effects carries large uncertainties that directly affect GCM predictions, such as climate sensitivity. Predictions are hampered by the large range of scales of interaction between various components that need to be captured. Observation systems (remote sensing, in situ) are increasingly being used to constrain predictions but significant challengesmore » exist, to some extent because of the large range of scales and the fact that the various measuring systems tend to address different scales. Fine-scale models represent clouds, aerosols, and aerosol-cloud interactions with high fidelity but do not include interactions with the larger scale and are therefore limited from a climatic point of view. Lastly, we suggest strategies for improving estimates of aerosol-cloud relationships in climate models, for new remote sensing and in situ measurements, and for quantifying and reducing model uncertainty.« less

3D Virtual Environment Used to Support Lighting System Management in a Building

NASA Astrophysics Data System (ADS)

Sampaio, A. Z.; Ferreira, M. M.; Rosário, D. P.

The main aim of the research project, which is in progress at the UTL, is to develop a virtual interactive model as a tool to support decision-making in the planning of construction maintenance and facilities management. The virtual model gives the capacity to allow the user to transmit, visually and interactively, information related to the components of a building, defined as a function of the time variable. In addition, the analysis of solutions for repair work/substitution and inherent cost are predicted, the results being obtained interactively and visualized in the virtual environment itself. The first component of the virtual prototype concerns the management of lamps in a lighting system. It was applied in a study case. The interactive application allows the examination of the physical model, visualizing, for each element modeled in 3D and linked to a database, the corresponding technical information concerned with the use of the material, calculated for different points in time during their life. The control of a lamp stock, the constant updating of lifetime information and the planning of periodical local inspections are attended on the prototype. This is an important mean of cooperation between collaborators involved in the building management.

Improving our fundamental understanding of the role of aerosol−cloud interactions in the climate system

PubMed Central

Seinfeld, John H.; Bretherton, Christopher; Carslaw, Kenneth S.; Coe, Hugh; DeMott, Paul J.; Dunlea, Edward J.; Feingold, Graham; Ghan, Steven; Guenther, Alex B.; Kraucunas, Ian; Molina, Mario J.; Nenes, Athanasios; Penner, Joyce E.; Prather, Kimberly A.; Ramanathan, V.; Ramaswamy, Venkatachalam; Rasch, Philip J.; Ravishankara, A. R.; Rosenfeld, Daniel; Stephens, Graeme; Wood, Robert

2016-01-01

The effect of an increase in atmospheric aerosol concentrations on the distribution and radiative properties of Earth’s clouds is the most uncertain component of the overall global radiative forcing from preindustrial time. General circulation models (GCMs) are the tool for predicting future climate, but the treatment of aerosols, clouds, and aerosol−cloud radiative effects carries large uncertainties that directly affect GCM predictions, such as climate sensitivity. Predictions are hampered by the large range of scales of interaction between various components that need to be captured. Observation systems (remote sensing, in situ) are increasingly being used to constrain predictions, but significant challenges exist, to some extent because of the large range of scales and the fact that the various measuring systems tend to address different scales. Fine-scale models represent clouds, aerosols, and aerosol−cloud interactions with high fidelity but do not include interactions with the larger scale and are therefore limited from a climatic point of view. We suggest strategies for improving estimates of aerosol−cloud relationships in climate models, for new remote sensing and in situ measurements, and for quantifying and reducing model uncertainty. PMID:27222566

Interaction in the dark sector

NASA Astrophysics Data System (ADS)

del Campo, Sergio; Herrera, Ramón; Pavón, Diego

2015-06-01

It may well happen that the two main components of the dark sector of the Universe, dark matter and dark energy, do not evolve separately but interact nongravitationally with one another. However, given our current lack of knowledge of the microscopic nature of these two components, there is no clear theoretical path to determine their interaction. Yet, over the years, phenomenological interaction terms have been proposed on mathematical simplicity and heuristic arguments. In this paper, based on the likely evolution of the ratio between the energy densities of these dark components, we lay down reasonable criteria to obtain phenomenological, useful, expressions of the said term independent of any gravity theory. We illustrate this with different proposals which seem compatible with the known evolution of the Universe at the background level. Likewise, we show that two possible degeneracies with noninteracting models are only apparent as they can be readily broken at the background level. Further, we analyze some interaction terms that appear in the literature.

The triel bond: a potential force for tuning anion-π interactions

NASA Astrophysics Data System (ADS)

Esrafili, Mehdi D.; Mousavian, Parisasadat

2018-02-01

Using ab-initio calculations, the mutual influence between anion-π and B···N or B···C triel bond interactions is investigated in some model complexes. The properties of these complexes are studied by molecular electrostatic potential, noncovalent interaction index, quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) analyses. According to the results, the formation of B···N or B···C triel bond interactions in the multi-component systems makes a significant shortening of anion-π distance. Such remarkable variation in the anion-π distances has not been reported previously. The strengthening of the anion-π bonding in the multi-component systems depend significantly on the nature of the anion, and it becomes larger in the order Br- > Cl- > F-. The parameters derived from the QTAIM and NBO methodologies are used to study the mechanism of the cooperativity between the anion-π and triel bond interactions in the multi-component complexes.

Initial analyses of the relationship between 'Thresholds' of toxicity for individual chemicals and 'Interaction Thresholds' for chemical mixtures

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

Yang, Raymond S.H.; Dennison, James E.

2007-09-01

The inter-relationship of 'Thresholds' between chemical mixtures and their respective component single chemicals was studied using three sets of data and two types of analyses. Two in vitro data sets involve cytotoxicity in human keratinocytes from treatment of metals and a metal mixture [Bae, D.S., Gennings, C., Carter, Jr., W.H., Yang, R.S.H., Campain, J.A., 2001. Toxicological interactions among arsenic, cadmium, chromium, and lead in human keratinocytes. Toxicol. Sci. 63, 132-142; Gennings, C., Carter, Jr., W.H., Campain, J.A., Bae, D.S., Yang, R.S.H., 2002. Statistical analysis of interactive cytotoxicity in human epidermal keratinocytes following exposure to a mixture of four metals. J.more » Agric. Biol. Environ. Stat. 7, 58-73], and induction of estrogen receptor alpha (ER-{alpha}) reporter gene in MCF-7 human breast cancer cells by estrogenic xenobiotics [Gennings, C., Carter, Jr., W.H., Carney, E.W., Charles, G.D., Gollapudi, B.B., Carchman, R.A., 2004. A novel flexible approach for evaluating fixed ratio mixtures of full and partial agonists. Toxicol. Sci. 80, 134-150]. The third data set came from PBPK modeling of gasoline and its components in the human. For in vitro cellular responses, we employed Benchmark Dose Software (BMDS) to obtain BMD{sub 01}, BMD{sub 05}, and BMD{sub 10}. We then plotted these BMDs against exposure concentrations for the chemical mixture and its components to assess the ranges and slopes of these BMD-concentration lines. In doing so, we consider certain BMDs to be 'Interaction Thresholds' or 'Thresholds' for mixtures and their component single chemicals and the slope of the line must be a reflection of the potency of the biological effects. For in vivo PBPK modeling, we used 0.1x TLVs, TLVs, and 10x TLVs for gasoline and six component markers as input dosing for PBPK modeling. In this case, the venous blood levels under the hypothetical exposure conditions become our designated 'Interaction Thresholds' or 'Thresholds' for gasoline and its component single chemicals. Our analyses revealed that the mixture 'Interaction Thresholds' appear to stay within the bounds of the 'Thresholds' of its respective component single chemicals. Although such a trend appears to be emerging, nevertheless, it should be emphasized that our analyses are based on limited data sets and further analyses on data sets, preferably the more comprehensive experimental data sets, are needed before a definitive conclusion can be drawn.« less

Lattice model for water-solute mixtures.

PubMed

Furlan, A P; Almarza, N G; Barbosa, M C

2016-10-14

A lattice model for the study of mixtures of associating liquids is proposed. Solvent and solute are modeled by adapting the associating lattice gas (ALG) model. The nature of interaction of solute/solvent is controlled by tuning the energy interactions between the patches of ALG model. We have studied three set of parameters, resulting in, hydrophilic, inert, and hydrophobic interactions. Extensive Monte Carlo simulations were carried out, and the behavior of pure components and the excess properties of the mixtures have been studied. The pure components, water (solvent) and solute, have quite similar phase diagrams, presenting gas, low density liquid, and high density liquid phases. In the case of solute, the regions of coexistence are substantially reduced when compared with both the water and the standard ALG models. A numerical procedure has been developed in order to attain series of results at constant pressure from simulations of the lattice gas model in the grand canonical ensemble. The excess properties of the mixtures, volume and enthalpy as the function of the solute fraction, have been studied for different interaction parameters of the model. Our model is able to reproduce qualitatively well the excess volume and enthalpy for different aqueous solutions. For the hydrophilic case, we show that the model is able to reproduce the excess volume and enthalpy of mixtures of small alcohols and amines. The inert case reproduces the behavior of large alcohols such as propanol, butanol, and pentanol. For the last case (hydrophobic), the excess properties reproduce the behavior of ionic liquids in aqueous solution.

Hierarchical graphs for rule-based modeling of biochemical systems

PubMed Central

2011-01-01

Background In rule-based modeling, graphs are used to represent molecules: a colored vertex represents a component of a molecule, a vertex attribute represents the internal state of a component, and an edge represents a bond between components. Components of a molecule share the same color. Furthermore, graph-rewriting rules are used to represent molecular interactions. A rule that specifies addition (removal) of an edge represents a class of association (dissociation) reactions, and a rule that specifies a change of a vertex attribute represents a class of reactions that affect the internal state of a molecular component. A set of rules comprises an executable model that can be used to determine, through various means, the system-level dynamics of molecular interactions in a biochemical system. Results For purposes of model annotation, we propose the use of hierarchical graphs to represent structural relationships among components and subcomponents of molecules. We illustrate how hierarchical graphs can be used to naturally document the structural organization of the functional components and subcomponents of two proteins: the protein tyrosine kinase Lck and the T cell receptor (TCR) complex. We also show that computational methods developed for regular graphs can be applied to hierarchical graphs. In particular, we describe a generalization of Nauty, a graph isomorphism and canonical labeling algorithm. The generalized version of the Nauty procedure, which we call HNauty, can be used to assign canonical labels to hierarchical graphs or more generally to graphs with multiple edge types. The difference between the Nauty and HNauty procedures is minor, but for completeness, we provide an explanation of the entire HNauty algorithm. Conclusions Hierarchical graphs provide more intuitive formal representations of proteins and other structured molecules with multiple functional components than do the regular graphs of current languages for specifying rule-based models, such as the BioNetGen language (BNGL). Thus, the proposed use of hierarchical graphs should promote clarity and better understanding of rule-based models. PMID:21288338

A finite element model of the human head for auditory bone conduction simulation.

PubMed

Taschke, Henning; Hudde, Herbert

2006-01-01

In order to investigate the mechanisms of bone conduction, a finite element model of the human head was developed. The most important steps of the modelling process are described. The model was excited by means of percutaneously applied forces in order to get a deeper insight into the way the parts of the peripheral hearing organ and the surrounding tissue vibrate. The analysis is done based on the division of the bone conduction mechanisms into components. The frequency-dependent patterns of vibration of the components are analyzed. Furthermore, the model allows for the calculation of the contribution of each component to the overall bone-conducted sound. The components interact in a complicated way, which strongly depends on the nature of the excitation and the spatial region to which it is applied.

Chaotic universe model.

PubMed

Aydiner, Ekrem

2018-01-15

In this study, we consider nonlinear interactions between components such as dark energy, dark matter, matter and radiation in the framework of the Friedman-Robertson-Walker space-time and propose a simple interaction model based on the time evolution of the densities of these components. By using this model we show that these interactions can be given by Lotka-Volterra type equations. We numerically solve these coupling equations and show that interaction dynamics between dark energy-dark matter-matter or dark energy-dark matter-matter-radiation has a strange attractor for 0 > w de  >-1, w dm  ≥ 0, w m  ≥ 0 and w r  ≥ 0 values. These strange attractors with the positive Lyapunov exponent clearly show that chaotic dynamics appears in the time evolution of the densities. These results provide that the time evolution of the universe is chaotic. The present model may have potential to solve some of the cosmological problems such as the singularity, cosmic coincidence, big crunch, big rip, horizon, oscillation, the emergence of the galaxies, matter distribution and large-scale organization of the universe. The model also connects between dynamics of the competing species in biological systems and dynamics of the time evolution of the universe and offers a new perspective and a new different scenario for the universe evolution.

Gender and the Development of Wisdom.

ERIC Educational Resources Information Center

Orwoll, Lucinda; Achenbaum, W. Andrew

1993-01-01

Drawing on a model of wisdom that includes components in three domains (personality, cognition, and conation) and across three levels (intrapersonal, interpersonal, and transpersonal), highlights potential differences in the ways women and men attain and express wisdom; and examines interactive patterns across the components of wisdom. (BC)

Critical point of gas-liquid type phase transition and phase equilibrium functions in developed two-component plasma model

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

Butlitsky, M. A.; Zelener, B. V.; Zelener, B. B.

A two-component plasma model, which we called a “shelf Coulomb” model has been developed in this work. A Monte Carlo study has been undertaken to calculate equations of state, pair distribution functions, internal energies, and other thermodynamics properties. A canonical NVT ensemble with periodic boundary conditions was used. The motivation behind the model is also discussed in this work. The “shelf Coulomb” model can be compared to classical two-component (electron-proton) model where charges with zero size interact via a classical Coulomb law. With important difference for interaction of opposite charges: electrons and protons interact via the Coulomb law for largemore » distances between particles, while interaction potential is cut off on small distances. The cut off distance is defined by an arbitrary ε parameter, which depends on system temperature. All the thermodynamics properties of the model depend on dimensionless parameters ε and γ = βe{sup 2}n{sup 1/3} (where β = 1/k{sub B}T, n is the particle's density, k{sub B} is the Boltzmann constant, and T is the temperature) only. In addition, it has been shown that the virial theorem works in this model. All the calculations were carried over a wide range of dimensionless ε and γ parameters in order to find the phase transition region, critical point, spinodal, and binodal lines of a model system. The system is observed to undergo a first order gas-liquid type phase transition with the critical point being in the vicinity of ε{sub crit}≈13(T{sub crit}{sup *}≈0.076),γ{sub crit}≈1.8(v{sub crit}{sup *}≈0.17),P{sub crit}{sup *}≈0.39, where specific volume v* = 1/γ{sup 3} and reduced temperature T{sup *} = ε{sup −1}.« less

Three Big Hands-On Noncomputer Models for the Biology Classroom.

ERIC Educational Resources Information Center

Miller, James E.

1998-01-01

Proposes models for the lichen symbiosis, genomic, and plasmid DNA and fluid mosaic membrane structure. The models operate at the classroom level with the classroom becoming the cell in a DNA exercise with students as interactive components. (DDR)

Propulsion and airframe aerodynamic interactions of supersonic V/STOL configurations. Volume 4: Summary

NASA Technical Reports Server (NTRS)

Zilz, D. E.; Wallace, H. W.; Hiley, P. E.

1985-01-01

A wind tunnel model of a supersonic V/STOL fighter configuration has been tested to measure the aerodynamic interaction effects which can result from geometrically close-coupled propulsion system/airframe components. The approach was to configure the model to represent two different test techniques. One was a conventional test technique composed of two test modes. In the Flow-Through mode, absolute configuration aerodynamics are measured, including inlet/airframe interactions. In the Jet-Effects mode, incremental nozzle/airframe interactions are measured. The other test technique is a propulsion simulator approach, where a sub-scale, externally powered engine is mounted in the model. This allows proper measurement of inlet/airframe and nozzle/airframe interactions simultaneously. This is Volume 4 of 4: Final Report- Summary.

Four-component numerical simulation model of radiative convective interactions in large-scale oxygen-hydrogen turbulent fire balls

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

Surzhikov, S.T.

1996-12-31

Two-dimensional radiative gas dynamics model for numerical simulation of oxygen-hydrogen fire ball which may be generated by an explosion of a launch vehicle with cryogenic (LO{sub 2}-LH{sub 2}) fuel components is presented. The following physical-chemical processes are taken into account in the numerical model: and effective chemical reaction between the gaseous components (O{sub 2}-H{sub 2}) of the propellant, turbulent mixing and diffusion of the components, and radiative heat transfer. The results of numerical investigations of the following problems are presented: The influence of radiative heat transfer on fire ball gas dynamics during the first 13 sec after explosion, the effectmore » of the fuel gaseous components afterburning on fire ball gas dynamics, and the effect of turbulence on fire ball gas dynamics (in a framework of algebraic model of turbulent mixing).« less

Cortical subnetwork dynamics during human language tasks.

PubMed

Collard, Maxwell J; Fifer, Matthew S; Benz, Heather L; McMullen, David P; Wang, Yujing; Milsap, Griffin W; Korzeniewska, Anna; Crone, Nathan E

2016-07-15

Language tasks require the coordinated activation of multiple subnetworks-groups of related cortical interactions involved in specific components of task processing. Although electrocorticography (ECoG) has sufficient temporal and spatial resolution to capture the dynamics of event-related interactions between cortical sites, it is difficult to decompose these complex spatiotemporal patterns into functionally discrete subnetworks without explicit knowledge of each subnetwork's timing. We hypothesized that subnetworks corresponding to distinct components of task-related processing could be identified as groups of interactions with co-varying strengths. In this study, five subjects implanted with ECoG grids over language areas performed word repetition and picture naming. We estimated the interaction strength between each pair of electrodes during each task using a time-varying dynamic Bayesian network (tvDBN) model constructed from the power of high gamma (70-110Hz) activity, a surrogate for population firing rates. We then reduced the dimensionality of this model using principal component analysis (PCA) to identify groups of interactions with co-varying strengths, which we term functional network components (FNCs). This data-driven technique estimates both the weight of each interaction's contribution to a particular subnetwork, and the temporal profile of each subnetwork's activation during the task. We found FNCs with temporal and anatomical features consistent with articulatory preparation in both tasks, and with auditory and visual processing in the word repetition and picture naming tasks, respectively. These FNCs were highly consistent between subjects with similar electrode placement, and were robust enough to be characterized in single trials. Furthermore, the interaction patterns uncovered by FNC analysis correlated well with recent literature suggesting important functional-anatomical distinctions between processing external and self-produced speech. Our results demonstrate that subnetwork decomposition of event-related cortical interactions is a powerful paradigm for interpreting the rich dynamics of large-scale, distributed cortical networks during human cognitive tasks. Copyright © 2016 Elsevier Inc. All rights reserved.

A High Performance Computing Approach to the Simulation of Fluid Solid Interaction Problems with Rigid and Flexible Components (Open Access Publisher’s Version)

DTIC Science & Technology

2014-08-01

performance computing, smoothed particle hydrodynamics, rigid body dynamics, flexible body dynamics ARMAN PAZOUKI ∗, RADU SERBAN ∗, DAN NEGRUT ∗ A...HIGH PERFORMANCE COMPUTING APPROACH TO THE SIMULATION OF FLUID-SOLID INTERACTION PROBLEMS WITH RIGID AND FLEXIBLE COMPONENTS This work outlines a unified...are implemented to model rigid and flexible multibody dynamics. The two- way coupling of the fluid and solid phases is supported through use of

GEOS S2S-2_1: The GMAO new high resolution Seasonal Prediction System

NASA Astrophysics Data System (ADS)

Molod, A.; Vikhliaev, Y. V.; Hackert, E. C.; Kovach, R. M.; Zhao, B.; Cullather, R. I.; Marshak, J.; Borovikov, A.; Li, Z.; Barahona, D.; Andrews, L. C.; Chang, Y.; Schubert, S. D.; Koster, R. D.; Suarez, M.; Akella, S.

2017-12-01

A new version of the modeling and analysis system used to produce subseasonalto seasonal forecasts has just been released by the NASA/Goddard GlobalModeling and Assimilation Office. The new version runs at higher atmospheric resolution (approximately 1/2 degree globally), contains a subtantially improvedmodel description of the cryosphere, and includes additional interactive earth system model components (aerosol model). In addition, the Ocean data assimilationsystem has been replaced with a Local Ensemble Transform Kalman Filter.Here will describe the new system, along with the plans for the future (GEOS S2S-3_0) which will include a higher resolution ocean model and more interactive earth system model components (interactive vegetation, biomass burning from fires). We will alsopresent results from a free-running coupled simulation with the new system and resultsfrom a series of retrospective seasonal forecasts.Results from retrospective forecasts show significant improvements in surface temperaturesover much of the northern hemisphere and a much improved prediction of sea ice extent in bothhemispheres. The precipitation forecast skill is comparable to previous S2S systems, andthe only tradeoff is an increased "double ITCZ", which is expected as we go to higher atmospheric resolution.

A topological multilayer model of the human body.

PubMed

Barbeito, Antonio; Painho, Marco; Cabral, Pedro; O'Neill, João

2015-11-04

Geographical information systems deal with spatial databases in which topological models are described with alphanumeric information. Its graphical interfaces implement the multilayer concept and provide powerful interaction tools. In this study, we apply these concepts to the human body creating a representation that would allow an interactive, precise, and detailed anatomical study. A vector surface component of the human body is built using a three-dimensional (3-D) reconstruction methodology. This multilayer concept is implemented by associating raster components with the corresponding vector surfaces, which include neighbourhood topology enabling spatial analysis. A root mean square error of 0.18 mm validated the three-dimensional reconstruction technique of internal anatomical structures. The expansion of the identification and the development of a neighbourhood analysis function are the new tools provided in this model.

Astronomical bounds on a cosmological model allowing a general interaction in the dark sector

NASA Astrophysics Data System (ADS)

Pan, Supriya; Mukherjee, Ankan; Banerjee, Narayan

2018-06-01

Non-gravitational interaction between two barotropic dark fluids, namely the pressureless dust and the dark energy in a spatially flat Friedmann-Lemaître-Robertson-Walker model, has been discussed. It is shown that for the interactions that are linear in terms the energy densities of the dark components and their first order derivatives, the net energy density is governed by a second-order differential equation with constant coefficients. Taking a generalized interaction, which includes a number of already known interactions as special cases, the dynamics of the universe is described for three types of the dark energy equation of state, namely that of interacting quintessence, interacting vacuum energy density, and interacting phantom. The models have been constrained using the standard cosmological probes, Supernovae Type Ia data from joint light curve analysis and the observational Hubble parameter data. Two geometric tests, the cosmographic studies, and the Om diagnostic have been invoked so as to ascertain the behaviour of the present model vis-a-vis the Λ-cold dark matter model. We further discussed the interacting scenarios taking into account the thermodynamic considerations.

Fast trimers in a one-dimensional extended Fermi-Hubbard model

NASA Astrophysics Data System (ADS)

Dhar, A.; Törmä, P.; Kinnunen, J. J.

2018-04-01

We consider a one-dimensional two-component extended Fermi-Hubbard model with nearest-neighbor interactions and mass imbalance between the two species. We study the binding energy of trimers, various observables for detecting them, and expansion dynamics. We generalize the definition of the trimer gap to include the formation of different types of clusters originating from nearest-neighbor interactions. Expansion dynamics reveal rapidly propagating trimers, with speeds exceeding doublon propagation in the strongly interacting regime. We present a simple model for understanding this unique feature of the movement of the trimers, and we discuss the potential for experimental realization.

Robust Weak Chimeras in Oscillator Networks with Delayed Linear and Quadratic Interactions

NASA Astrophysics Data System (ADS)

Bick, Christian; Sebek, Michael; Kiss, István Z.

2017-10-01

We present an approach to generate chimera dynamics (localized frequency synchrony) in oscillator networks with two populations of (at least) two elements using a general method based on a delayed interaction with linear and quadratic terms. The coupling design yields robust chimeras through a phase-model-based design of the delay and the ratio of linear and quadratic components of the interactions. We demonstrate the method in the Brusselator model and experiments with electrochemical oscillators. The technique opens the way to directly bridge chimera dynamics in phase models and real-world oscillator networks.

Modeling joint restoration strategies for interdependent infrastructure systems.

PubMed

Zhang, Chao; Kong, Jingjing; Simonovic, Slobodan P

2018-01-01

Life in the modern world depends on multiple critical services provided by infrastructure systems which are interdependent at multiple levels. To effectively respond to infrastructure failures, this paper proposes a model for developing optimal joint restoration strategy for interdependent infrastructure systems following a disruptive event. First, models for (i) describing structure of interdependent infrastructure system and (ii) their interaction process, are presented. Both models are considering the failure types, infrastructure operating rules and interdependencies among systems. Second, an optimization model for determining an optimal joint restoration strategy at infrastructure component level by minimizing the economic loss from the infrastructure failures, is proposed. The utility of the model is illustrated using a case study of electric-water systems. Results show that a small number of failed infrastructure components can trigger high level failures in interdependent systems; the optimal joint restoration strategy varies with failure occurrence time. The proposed models can help decision makers to understand the mechanisms of infrastructure interactions and search for optimal joint restoration strategy, which can significantly enhance safety of infrastructure systems.

Marine mammals' influence on ecosystem processes affecting fisheries in the Barents Sea is trivial.

PubMed

Corkeron, Peter J

2009-04-23

Some interpretations of ecosystem-based fishery management include culling marine mammals as an integral component. The current Norwegian policy on marine mammal management is one example. Scientific support for this policy includes the Scenario Barents Sea (SBS) models. These modelled interactions between cod, Gadus morhua, herring, Clupea harengus, capelin, Mallotus villosus and northern minke whales, Balaenoptera acutorostrata. Adding harp seals Phoca groenlandica into this top-down modelling approach resulted in unrealistic model outputs. Another set of models of the Barents Sea fish-fisheries system focused on interactions within and between the three fish populations, fisheries and climate. These model key processes of the system successfully. Continuing calls to support the SBS models despite their failure suggest a belief that marine mammal predation must be a problem for fisheries. The best available scientific evidence provides no justification for marine mammal culls as a primary component of an ecosystem-based approach to managing the fisheries of the Barents Sea.

Exploring agricultural production systems and their fundamental components with system dynamics modeling

USDA-ARS?s Scientific Manuscript database

Agricultural production in the United States is undergoing marked changes due to rapid shifts in consumer demands, input costs, and concerns for food safety and environmental impact. Agricultural production systems are comprised of multidimensional components and drivers that interact in complex wa...

CFD: A Castle in the Sand?

NASA Technical Reports Server (NTRS)

Kleb, William L.; Wood, William A.

2004-01-01

The computational simulation community is not routinely publishing independently verifiable tests to accompany new models or algorithms. A survey reveals that only 22% of new models published are accompanied by tests suitable for independently verifying the new model. As the community develops larger codes with increased functionality, and hence increased complexity in terms of the number of building block components and their interactions, it becomes prohibitively expensive for each development group to derive the appropriate tests for each component. Therefore, the computational simulation community is building its collective castle on a very shaky foundation of components with unpublished and unrepeatable verification tests. The computational simulation community needs to begin publishing component level verification tests before the tide of complexity undermines its foundation.

Collapse and coexistence for a molecular braid with an attractive interaction component subject to mechanical forces.

PubMed

Lee, Dominic J O'

2015-04-15

Dual mechanical braiding experiments provide a useful tool with which to investigate the nature of interactions between rod-like molecules, for instance actin and DNA. In conditions close to molecular condensation, one would expect an appearance of a local minimum in the interaction potential between the two molecules. We investigate this situation, introducing an attractive component into the interaction potential, using a model developed for describing such experiments. We consider both attractive interactions that do not depend on molecular structure and those which depend on a DNA-like helix structure. In braiding experiments, an attractive term may lead to certain effects. A local minimum may cause molecules to collapse from a loosely braided configuration into a tight one, occurring at a critical value of the moment applied about the axis of the braid. For a fixed number of braid pitches, this may lead to coexistence between the two braiding states, tight and loose. Coexistence implies certain proportions of the braid are in each state, their relative size depending on the number of braid pitches. This manifests itself as a linear dependence in numerically calculated quantities as functions of the number of braid pitches. Also, in the collapsed state, the braid radius stays roughly constant. Furthermore, if the attractive interaction is helix dependent, the left-right handed braid symmetry is broken. For a DNA like charge distribution, using the Kornyshev-Leikin interaction model, our results suggest that significant braid collapse and coexistence only occurs for left handed braids. Regardless of the interaction model, the study highlights the possible qualitative physics of braid collapse and coexistence; and the role helix specific forces might play, if important. The model could be used to connect other microscopic theories of interaction with braiding experiments.

Genetic and environmental (physical fitness and sedentary activity) interaction effects on cardiometabolic risk factors in Mexican American children and adolescents.

PubMed

Arya, Rector; Farook, Vidya S; Fowler, Sharon P; Puppala, Sobha; Chittoor, Geetha; Resendez, Roy G; Mummidi, Srinivas; Vanamala, Jairam; Almasy, Laura; Curran, Joanne E; Comuzzie, Anthony G; Lehman, Donna M; Jenkinson, Christopher P; Lynch, Jane L; DeFronzo, Ralph A; Blangero, John; Hale, Daniel E; Duggirala, Ravindranath; Diego, Vincent P

2018-06-01

Knowledge on genetic and environmental (G × E) interaction effects on cardiometabolic risk factors (CMRFs) in children is limited.  The purpose of this study was to examine the impact of G × E interaction effects on CMRFs in Mexican American (MA) children (n = 617, ages 6-17 years). The environments examined were sedentary activity (SA), assessed by recalls from "yesterday" (SAy) and "usually" (SAu) and physical fitness (PF) assessed by Harvard PF scores (HPFS). CMRF data included body mass index (BMI), waist circumference (WC), fat mass (FM), fasting insulin (FI), homeostasis model of assessment-insulin resistance (HOMA-IR), high-density lipoprotein cholesterol (HDL-C), triglycerides (TG), systolic (SBP) and diastolic (DBP) blood pressure, and number of metabolic syndrome components (MSC). We examined potential G × E interaction in the phenotypic expression of CMRFs using variance component models and likelihood-based statistical inference. Significant G × SA interactions were identified for six CMRFs: BMI, WC, FI, HOMA-IR, MSC, and HDL, and significant G × HPFS interactions were observed for four CMRFs: BMI, WC, FM, and HOMA-IR. However, after correcting for multiple hypothesis testing, only WC × SAy, FM × SAy, and FI × SAu interactions became marginally significant. After correcting for multiple testing, most of CMRFs exhibited significant G × E interactions (Reduced G × E model vs. Constrained model). These findings provide evidence that genetic factors interact with SA and PF to influence variation in CMRFs, and underscore the need for better understanding of these relationships to develop strategies and interventions to effectively reduce or prevent cardiometabolic risk in children. © 2018 WILEY PERIODICALS, INC.

Probabilistic Structural Analysis Methods (PSAM) for select space propulsion system components, part 2

NASA Technical Reports Server (NTRS)

1991-01-01

The technical effort and computer code enhancements performed during the sixth year of the Probabilistic Structural Analysis Methods program are summarized. Various capabilities are described to probabilistically combine structural response and structural resistance to compute component reliability. A library of structural resistance models is implemented in the Numerical Evaluations of Stochastic Structures Under Stress (NESSUS) code that included fatigue, fracture, creep, multi-factor interaction, and other important effects. In addition, a user interface was developed for user-defined resistance models. An accurate and efficient reliability method was developed and was successfully implemented in the NESSUS code to compute component reliability based on user-selected response and resistance models. A risk module was developed to compute component risk with respect to cost, performance, or user-defined criteria. The new component risk assessment capabilities were validated and demonstrated using several examples. Various supporting methodologies were also developed in support of component risk assessment.

Building Quantitative Hydrologic Storylines from Process-based Models for Managing Water Resources in the U.S. Under Climate-changed Futures

NASA Astrophysics Data System (ADS)

Arnold, J.; Gutmann, E. D.; Clark, M. P.; Nijssen, B.; Vano, J. A.; Addor, N.; Wood, A.; Newman, A. J.; Mizukami, N.; Brekke, L. D.; Rasmussen, R.; Mendoza, P. A.

2016-12-01

Climate change narratives for water-resource applications must represent the change signals contextualized by hydroclimatic process variability and uncertainty at multiple scales. Building narratives of plausible change includes assessing uncertainties across GCM structure, internal climate variability, climate downscaling methods, and hydrologic models. Work with this linked modeling chain has dealt mostly with GCM sampling directed separately to either model fidelity (does the model correctly reproduce the physical processes in the world?) or sensitivity (of different model responses to CO2 forcings) or diversity (of model type, structure, and complexity). This leaves unaddressed any interactions among those measures and with other components in the modeling chain used to identify water-resource vulnerabilities to specific climate threats. However, time-sensitive, real-world vulnerability studies typically cannot accommodate a full uncertainty ensemble across the whole modeling chain, so a gap has opened between current scientific knowledge and most routine applications for climate-changed hydrology. To close that gap, the US Army Corps of Engineers, the Bureau of Reclamation, and the National Center for Atmospheric Research are working on techniques to subsample uncertainties objectively across modeling chain components and to integrate results into quantitative hydrologic storylines of climate-changed futures. Importantly, these quantitative storylines are not drawn from a small sample of models or components. Rather, they stem from the more comprehensive characterization of the full uncertainty space for each component. Equally important from the perspective of water-resource practitioners, these quantitative hydrologic storylines are anchored in actual design and operations decisions potentially affected by climate change. This talk will describe part of our work characterizing variability and uncertainty across modeling chain components and their interactions using newly developed observational data, models and model outputs, and post-processing tools for making the resulting quantitative storylines most useful in practical hydrology applications.

A numerical study on the effects of wave-current-surge interactions on the height and propagation of sea surface waves in Charleston Harbor during Hurricane Hugo 1989

NASA Astrophysics Data System (ADS)

Liu, Huiqing; Xie, Lian

2009-06-01

The effects of wave-current interactions on ocean surface waves induced by Hurricane Hugo in and around the Charleston Harbor and its adjacent coastal waters are examined by using a three-dimensional (3D) wave-current coupled modeling system. The 3D storm surge modeling component of the coupled system is based on the Princeton Ocean Model (POM), the wave modeling component is based on the third generation wave model, Simulating WAves Nearshore (SWAN), and the inundation model is adopted from [Xie, L., Pietrafesa, L. J., Peng, M., 2004. Incorporation of a mass-conserving inundation scheme into a three-dimensional storm surge model. J. Coastal Res., 20, 1209-1223]. The results indicate that the change of water level associated with the storm surge is the primary cause for wave height changes due to wave-surge interaction. Meanwhile, waves propagating on top of surge cause a feedback effect on the surge height by modulating the surface wind stress and bottom stress. This effect is significant in shallow coastal waters, but relatively small in offshore deep waters. The influence of wave-current interaction on wave propagation is relatively insignificant, since waves generally propagate in the direction of the surface currents driven by winds. Wave-current interactions also affect the surface waves as a result of inundation and drying induced by the storm. Waves break as waters retreat in regions of drying, whereas waves are generated in flooded regions where no waves would have occurred without the flood water.

Additive effects in high-voltage layered-oxide cells: A statistics of mixtures approach

DOE PAGES

Sahore, Ritu; Peebles, Cameron; Abraham, Daniel P.; ...

2017-07-20

Li 1.03(Ni 0.5Mn 0.3Co 0.2) 0.97O 2 (NMC)-based coin cells containing the electrolyte additives vinylene carbonate (VC) and tris(trimethylsilyl)phosphite (TMSPi) in the range of 0-2 wt% were cycled between 3.0 and 4.4 V. The changes in capacity at rates of C/10 and C/1 and resistance at 60% state of charge were found to follow linear-with-time kinetic rate laws. Further, the C/10 capacity and resistance data were amenable to modeling by a statistics of mixtures approach. Applying physical meaning to the terms in the empirical models indicated that the interactions between the electrolyte and additives were not simple. For example, theremore » were strong, synergistic interactions between VC and TMSPi affecting C/10 capacity loss, as expected, but there were other, more subtle interactions between the electrolyte components. In conclusion, the interactions between these components controlled the C/10 capacity decline and resistance increase.« less

ARTEMIS: Ares Real Time Environments for Modeling, Integration, and Simulation

NASA Technical Reports Server (NTRS)

Hughes, Ryan; Walker, David

2009-01-01

This slide presentation reviews the use of ARTEMIS in the development and testing of the ARES launch vehicles. Ares Real Time Environment for Modeling, Simulation and Integration (ARTEMIS) is the real time simulation supporting Ares I hardware-in-the-loop (HWIL) testing. ARTEMIS accurately models all Ares/Orion/Ground subsystems which interact with Ares avionics components from pre-launch through orbit insertion The ARTEMIS System integration Lab, and the STIF architecture is reviewed. The functional components of ARTEMIS are outlined. An overview of the models and a block diagram is presented.

Image-based 3D reconstruction and virtual environmental walk-through

NASA Astrophysics Data System (ADS)

Sun, Jifeng; Fang, Lixiong; Luo, Ying

2001-09-01

We present a 3D reconstruction method, which combines geometry-based modeling, image-based modeling and rendering techniques. The first component is an interactive geometry modeling method which recovery of the basic geometry of the photographed scene. The second component is model-based stereo algorithm. We discus the image processing problems and algorithms of walking through in virtual space, then designs and implement a high performance multi-thread wandering algorithm. The applications range from architectural planning and archaeological reconstruction to virtual environments and cinematic special effects.

Nonlinear Dynamics of Turbulent Thermals in Shear Flow

NASA Astrophysics Data System (ADS)

Ingel, L. Kh.

2018-03-01

The nonlinear integral model of a turbulent thermal is extended to the case of the horizontal component of its motion relative to the medium (e.g., thermal floating-up in shear flow). In contrast to traditional models, the possibility of a heat source in the thermal is taken into account. For a piecewise constant vertical profile of the horizontal velocity of the medium and a constant vertical velocity shear, analytical solutions are obtained which describe different modes of dynamics of thermals. The nonlinear interaction between the horizontal and vertical components of thermal motion is studied because each of the components influences the rate of entrainment of the surrounding medium, i.e., the growth rate of the thermal size and, hence, its mobility. It is shown that the enhancement of the entrainment of the medium due to the interaction between the thermal and the cross flow can lead to a significant decrease in the mobility of the thermal.

AIM for Allostery: Using the Ising Model to Understand Information Processing and Transmission in Allosteric Biomolecular Systems.

PubMed

LeVine, Michael V; Weinstein, Harel

2015-05-01

In performing their biological functions, molecular machines must process and transmit information with high fidelity. Information transmission requires dynamic coupling between the conformations of discrete structural components within the protein positioned far from one another on the molecular scale. This type of biomolecular "action at a distance" is termed allostery . Although allostery is ubiquitous in biological regulation and signal transduction, its treatment in theoretical models has mostly eschewed quantitative descriptions involving the system's underlying structural components and their interactions. Here, we show how Ising models can be used to formulate an approach to allostery in a structural context of interactions between the constitutive components by building simple allosteric constructs we termed Allosteric Ising Models (AIMs). We introduce the use of AIMs in analytical and numerical calculations that relate thermodynamic descriptions of allostery to the structural context, and then show that many fundamental properties of allostery, such as the multiplicative property of parallel allosteric channels, are revealed from the analysis of such models. The power of exploring mechanistic structural models of allosteric function in more complex systems by using AIMs is demonstrated by building a model of allosteric signaling for an experimentally well-characterized asymmetric homodimer of the dopamine D2 receptor.

Elliptic-cylindrical analytical flux-rope model for ICMEs

NASA Astrophysics Data System (ADS)

Nieves-Chinchilla, T.; Linton, M.; Hidalgo, M. A. U.; Vourlidas, A.

2016-12-01

We present an analytical flux-rope model for realistic magnetic structures embedded in Interplanetary Coronal Mass Ejections. The framework of this model was established by Nieves-Chinchilla et al. (2016) with the circular-cylindrical analytical flux rope model and under the concept developed by Hidalgo et al. (2002). Elliptic-cylindrical geometry establishes the first-grade of complexity of a series of models. The model attempts to describe the magnetic flux rope topology with distorted cross-section as a possible consequence of the interaction with the solar wind. In this model, the flux rope is completely described in the non-euclidean geometry. The Maxwell equations are solved using tensor calculus consistently with the geometry chosen, invariance along the axial component, and with the only assumption of no radial current density. The model is generalized in terms of the radial dependence of the poloidal current density component and axial current density component. The misalignment between current density and magnetic field is studied in detail for the individual cases of different pairs of indexes for the axial and poloidal current density components. This theoretical analysis provides a map of the force distribution inside of the flux-rope. The reconstruction technique has been adapted to the model and compared with in situ ICME set of events with different in situ signatures. The successful result is limited to some cases with clear in-situ signatures of distortion. However, the model adds a piece in the puzzle of the physical-analytical representation of these magnetic structures. Other effects such as axial curvature, expansion and/or interaction could be incorporated in the future to fully understand the magnetic structure. Finally, the mathematical formulation of this model opens the door to the next model: toroidal flux rope analytical model.

Non-linear Min protein interactions generate harmonics that signal mid-cell division in Escherichia coli

PubMed Central

Walsh, James C.; Angstmann, Christopher N.; Duggin, Iain G.

2017-01-01

The Min protein system creates a dynamic spatial pattern in Escherichia coli cells where the proteins MinD and MinE oscillate from pole to pole. MinD positions MinC, an inhibitor of FtsZ ring formation, contributing to the mid-cell localization of cell division. In this paper, Fourier analysis is used to decompose experimental and model MinD spatial distributions into time-dependent harmonic components. In both experiment and model, the second harmonic component is responsible for producing a mid-cell minimum in MinD concentration. The features of this harmonic are robust in both experiment and model. Fourier analysis reveals a close correspondence between the time-dependent behaviour of the harmonic components in the experimental data and model. Given this, each molecular species in the model was analysed individually. This analysis revealed that membrane-bound MinD dimer shows the mid-cell minimum with the highest contrast when averaged over time, carrying the strongest signal for positioning the cell division ring. This concurs with previous data showing that the MinD dimer binds to MinC inhibiting FtsZ ring formation. These results show that non-linear interactions of Min proteins are essential for producing the mid-cell positioning signal via the generation of second-order harmonic components in the time-dependent spatial protein distribution. PMID:29040283

Detecting epistasis with the marginal epistasis test in genetic mapping studies of quantitative traits

PubMed Central

Zeng, Ping; Mukherjee, Sayan; Zhou, Xiang

2017-01-01

Epistasis, commonly defined as the interaction between multiple genes, is an important genetic component underlying phenotypic variation. Many statistical methods have been developed to model and identify epistatic interactions between genetic variants. However, because of the large combinatorial search space of interactions, most epistasis mapping methods face enormous computational challenges and often suffer from low statistical power due to multiple test correction. Here, we present a novel, alternative strategy for mapping epistasis: instead of directly identifying individual pairwise or higher-order interactions, we focus on mapping variants that have non-zero marginal epistatic effects—the combined pairwise interaction effects between a given variant and all other variants. By testing marginal epistatic effects, we can identify candidate variants that are involved in epistasis without the need to identify the exact partners with which the variants interact, thus potentially alleviating much of the statistical and computational burden associated with standard epistatic mapping procedures. Our method is based on a variance component model, and relies on a recently developed variance component estimation method for efficient parameter inference and p-value computation. We refer to our method as the “MArginal ePIstasis Test”, or MAPIT. With simulations, we show how MAPIT can be used to estimate and test marginal epistatic effects, produce calibrated test statistics under the null, and facilitate the detection of pairwise epistatic interactions. We further illustrate the benefits of MAPIT in a QTL mapping study by analyzing the gene expression data of over 400 individuals from the GEUVADIS consortium. PMID:28746338

Exploring component-based approaches in forest landscape modeling

Treesearch

H. S. He; D. R. Larsen; D. J. Mladenoff

2002-01-01

Forest management issues are increasingly required to be addressed in a spatial context, which has led to the development of spatially explicit forest landscape models. The numerous processes, complex spatial interactions, and diverse applications in spatial modeling make the development of forest landscape models difficult for any single research group. New...

Effect of interaction between dynapenic component of the European working group on sarcopenia in older people sarcopenia criteria and obesity on activities of daily living in the elderly.

PubMed

Kim, Yeon-Pyo; Kim, Sun; Joh, Ju-Youn; Hwang, Hwan-Sik

2014-05-01

To examine the effects of interaction between dynapenic component of the European Working Group on Sarcopenia in Older People (EWGSOP) sarcopenia and obesity (dynapenia × obesity) on activities of daily living (ADL) in older participants. Cross-sectional analysis of the Validity and Reliability of Korean Frailty Index and the Validity and Reliability of the Kaigo-Yobo Checklist in Korean Elderly studies. Six welfare facilities operated by government in South Korea. Four hundred eighty-seven community-dwelling individuals (157 males, 330 females) >65 years of age. Dynapenic component of the EWGSOP sarcopenia was defined as usual gait speed <0.8 m/s or grip strength lower than cut-off value (male <25.3 kg, female <12.0 kg). Obesity was defined as body mass index ≥27.5 kg/m(2). ADL were assessed using the Barthel index. There were 14 obese with dynapenic component cases (2 males, 12 females) of the 487 participants. Interaction of dynapenia and obesity was significant on multivariate generalized linear model analysis (P = .015). Dynapenic component of the EWGSOP sarcopenia and obesity in the elderly is associated with multiplicative interactions rather than additive interactions in ADL. Copyright © 2014 American Medical Directors Association, Inc. Published by Elsevier Inc. All rights reserved.

Variable selection and model choice in geoadditive regression models.

PubMed

Kneib, Thomas; Hothorn, Torsten; Tutz, Gerhard

2009-06-01

Model choice and variable selection are issues of major concern in practical regression analyses, arising in many biometric applications such as habitat suitability analyses, where the aim is to identify the influence of potentially many environmental conditions on certain species. We describe regression models for breeding bird communities that facilitate both model choice and variable selection, by a boosting algorithm that works within a class of geoadditive regression models comprising spatial effects, nonparametric effects of continuous covariates, interaction surfaces, and varying coefficients. The major modeling components are penalized splines and their bivariate tensor product extensions. All smooth model terms are represented as the sum of a parametric component and a smooth component with one degree of freedom to obtain a fair comparison between the model terms. A generic representation of the geoadditive model allows us to devise a general boosting algorithm that automatically performs model choice and variable selection.

Contrasting single and multi-component working-memory systems in dual tasking.

PubMed

Nijboer, Menno; Borst, Jelmer; van Rijn, Hedderik; Taatgen, Niels

2016-05-01

Working memory can be a major source of interference in dual tasking. However, there is no consensus on whether this interference is the result of a single working memory bottleneck, or of interactions between different working memory components that together form a complete working-memory system. We report a behavioral and an fMRI dataset in which working memory requirements are manipulated during multitasking. We show that a computational cognitive model that assumes a distributed version of working memory accounts for both behavioral and neuroimaging data better than a model that takes a more centralized approach. The model's working memory consists of an attentional focus, declarative memory, and a subvocalized rehearsal mechanism. Thus, the data and model favor an account where working memory interference in dual tasking is the result of interactions between different resources that together form a working-memory system. Copyright © 2016 Elsevier Inc. All rights reserved.

The Research Dynamic: A Professional Development Model for Secondary School Science Teachers

PubMed Central

2009-01-01

This essay summarizes the author's 10 years of experience at the Oklahoma Medical Research Foundation mentoring secondary school science teachers during 8-wk Summer Research Institutes. The summary is presented as a learning model, which we call the research dynamic. This model consists of three interlocked components: specified ignorance, peer interactions, and gateway experiments. Specified ignorance is based on the work of the sociologist Robert K. Merton. It is essentially the art of highlighting what is not known about a phenomenon but must become known for further progress. In practice, specified ignorance is framed as a hypothesis, a prediction, or a question. It is commonly the outcome of peer interactions, which are the second essential component of the research dynamic. Peer interactions are the inevitable outcome of having teachers work together in the same laboratory on related research topics. These topics are introduced as gateway experiments, the third component. The most important attribute of gateway experiments is their authenticity. These experiments, when first carried out, opened new scientific vistas. They are also technically, conceptually, and logically simple. We illustrate the research dynamic with a line of seminal experiments in biochemical genetics. We provide evidence that the research dynamic produced significantly positive effects on teachers' confidence in their professional preparedness. PMID:19487501

Dynamic NMR Study of Model CMP Slurry Containing Silica Particles as Abrasives

NASA Astrophysics Data System (ADS)

Odeh, F.; Al-Bawab, A.; Li, Y.

2018-02-01

Chemical mechanical planarization (CMP) should provide a good surface planarity with minimal surface defectivity. Since CMP slurries are multi-component systems, it is very important to understand the various processes and interactions taking place in such slurries. Several techniques have been employed for such task, however, most of them lack the molecular recognition to investigate molecular interactions without adding probes which in turn increase complexity and might alter the microenvironment of the slurry. Nuclear magnetic resonance (NMR) is a powerful technique that can be employed in such study. The longitudinal relaxation times (T1) of the different components of CMP slurries were measured using Spin Echo-NMR (SE-NMR) at a constant temperature. The fact that NMR is non-invasive and gives information on the molecular level gives more advantage to the technique. The model CMP slurry was prepared in D2O to enable monitoring of T1 for the various components' protons. SE-NMR provide a very powerful tool to study the various interactions and adsorption processes that take place in a model CMP silica based slurry which contains BTA and/or glycine and/or Cu+2 ions. It was found that BTA is very competitive towards complexation with Cu+2 ions and BTA-Cu complex adsorbs on silica surface.

Two-component quantum Hall effects in topological flat bands

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

Zeng, Tian-Sheng; Zhu, Wei; Sheng, D. N.

2017-03-27

Here in this paper, we study quantum Hall states for two-component particles (hardcore bosons and fermions) loading in topological lattice models. By tuning the interplay of interspecies and intraspecies interactions, we demonstrate that two-component fractional quantum Hall states emerge at certain fractional filling factors ν = 1/2 for fermions (ν = 2/3 for bosons) in the lowest Chern band, classified by features from ground states including the unique Chern number matrix (inverse of the K matrix), the fractional charge and spin pumpings, and two parallel propagating edge modes. Moreover, we also apply our strategy to two-component fermions at integer fillingmore » factor ν = 2 , where a possible topological Neel antiferromagnetic phase is under intense debate very recently. For the typical π -flux checkerboard lattice, by tuning the onsite Hubbard repulsion, we establish a first-order phase transition directly from a two-component fermionic ν = 2 quantum Hall state at weak interaction to a topologically trivial antiferromagnetic insulator at strong interaction, and therefore exclude the possibility of an intermediate topological phase for our system.« less

Hydrological modeling in forested systems

Treesearch

H.E. Golden; G.R. Evenson; S. Tian; Devendra Amatya; Ge Sun

2015-01-01

Characterizing and quantifying interactions among components of the forest hydrological cycle is complex and usually requires a combination of field monitoring and modelling approaches (Weiler and McDonnell, 2004; National Research Council, 2008). Models are important tools for testing hypotheses, understanding hydrological processes and synthesizing experimental data...

Modeling of the Global Water Cycle - Analytical Models

Treesearch

Yongqiang Liu; Roni Avissar

2005-01-01

Both numerical and analytical models of coupled atmosphere and its underlying ground components (land, ocean, ice) are useful tools for modeling the global and regional water cycle. Unlike complex three-dimensional climate models, which need very large computing resources and involve a large number of complicated interactions often difficult to interpret, analytical...

The effect of wave current interactions on the storm surge and inundation in Charleston Harbor during Hurricane Hugo 1989

NASA Astrophysics Data System (ADS)

Xie, Lian; Liu, Huiqing; Peng, Machuan

The effects of wave-current interactions on the storm surge and inundation induced by Hurricane Hugo in and around the Charleston Harbor and its adjacent coastal regions are examined by using a three-dimensional (3-D) wave-current coupled modeling system. The 3-D storm surge and inundation modeling component of the coupled system is based on the Princeton ocean model (POM), whereas the wave modeling component is based on the third-generation wave model, simulating waves nearshore (SWAN). The results indicate that the effects of wave-induced surface, bottom, and radiation stresses can separately or in combination produce significant changes in storm surge and inundation. The effects of waves vary spatially. In some areas, the contribution of waves to peak storm surge during Hurricane Hugo reached as high as 0.76 m which led to substantial changes in the inundation and drying areas simulated by the storm surge model.

DEVELOPMENT OF A MODEL THAT CONTAINS BOTH MULTIPOLE MOMENTS AND GAUSSIANS FOR THE CALCULATION OF MOLECULAR ELECTROSTATIC POTENTIALS

EPA Science Inventory

The electrostatic interaction is a critical component of intermolecular interactions in biological processes. Rapid methods for the computation and characterization of the molecular electrostatic potential (MEP) that segment the molecular charge distribution and replace this cont...

Graph-theoretic quantum system modelling for neuronal microtubules as hierarchical clustered quantum Hopfield networks

NASA Astrophysics Data System (ADS)

Srivastava, D. P.; Sahni, V.; Satsangi, P. S.

2014-08-01

Graph-theoretic quantum system modelling (GTQSM) is facilitated by considering the fundamental unit of quantum computation and information, viz. a quantum bit or qubit as a basic building block. Unit directional vectors "ket 0" and "ket 1" constitute two distinct fundamental quantum across variable orthonormal basis vectors, for the Hilbert space, specifying the direction of propagation of information, or computation data, while complementary fundamental quantum through, or flow rate, variables specify probability parameters, or amplitudes, as surrogates for scalar quantum information measure (von Neumann entropy). This paper applies GTQSM in continuum of protein heterodimer tubulin molecules of self-assembling polymers, viz. microtubules in the brain as a holistic system of interacting components representing hierarchical clustered quantum Hopfield network, hQHN, of networks. The quantum input/output ports of the constituent elemental interaction components, or processes, of tunnelling interactions and Coulombic bidirectional interactions are in cascade and parallel interconnections with each other, while the classical output ports of all elemental components are interconnected in parallel to accumulate micro-energy functions generated in the system as Hamiltonian, or Lyapunov, energy function. The paper presents an insight, otherwise difficult to gain, for the complex system of systems represented by clustered quantum Hopfield network, hQHN, through the application of GTQSM construct.

Position-dependent interactions between cysteine residues and the helix dipole

PubMed Central

Miranda, JJ L.

2003-01-01

A protein model was developed for studying the interaction between cysteine residues and the helix dipole. Site-directed mutagenesis was used to introduce cysteine residues at the N-terminus of helix H in recombinant sperm whale myoglobin. Based on the difference in thiol pKa between folded proteins and an unfolded peptide, the energy of interaction between the thiolate and the helix dipole was determined. Thiolates at the N1 and N2 positions of the helix were stabilized by 0.3 kcal/mole and 0.7 kcal/mole, respectively. A thiolate at the Ncap position was stabilized by 2.8 kcal/mole, and may involve a hydrogen bond. In context with other studies, an experimentally observed helix dipole effect may be defined in terms of two distinct components. A charge-dipole component involves electrostatic interactions with peptide bond dipoles in the first two turns of the helix and affects residues at all positions of the terminus; a hydrogen bond component involves one or more backbone amide groups and is only possible at the capping position due to conformational restraints elsewhere. The nature and magnitude of the helix dipole effect is, therefore, position-dependent. Results from this model system were used to interpret cysteine reactivity in rodent hemoglobins and the thioredoxin family. PMID:12493830

Rhythmic behavior in a two-population mean-field Ising model

NASA Astrophysics Data System (ADS)

Collet, Francesca; Formentin, Marco; Tovazzi, Daniele

2016-10-01

Many real systems composed of a large number of interacting components, as, for instance, neural networks, may exhibit collective periodic behavior even though single components have no natural tendency to behave periodically. Macroscopic oscillations are indeed one of the most common self-organized behavior observed in living systems. In the present paper we study some dynamical features of a two-population generalization of the mean-field Ising model with the scope of investigating simple mechanisms capable to generate rhythms in large groups of interacting individuals. We show that the system may undergo a transition from a disordered phase, where the magnetization of each population fluctuates closely around zero, to a phase in which they both display a macroscopic regular rhythm. In particular, there exists a region in the parameter space where having two groups of spins with inter- and intrapopulation interactions of different strengths suffices for the emergence of a robust periodic behavior.

OFMspert: An architecture for an operator's associate that evolves to an intelligent tutor

NASA Technical Reports Server (NTRS)

Mitchell, Christine M.

1991-01-01

With the emergence of new technology for both human-computer interaction and knowledge-based systems, a range of opportunities exist which enhance the effectiveness and efficiency of controllers of high-risk engineering systems. The design of an architecture for an operator's associate is described. This associate is a stand-alone model-based system designed to interact with operators of complex dynamic systems, such as airplanes, manned space systems, and satellite ground control systems in ways comparable to that of a human assistant. The operator function model expert system (OFMspert) architecture and the design and empirical validation of OFMspert's understanding component are described. The design and validation of OFMspert's interactive and control components are also described. A description of current work in which OFMspert provides the foundation in the development of an intelligent tutor that evolves to an assistant, as operator expertise evolves from novice to expert, is provided.

Modeling the mechanics of cells in the cell-spreading process driven by traction forces

NASA Astrophysics Data System (ADS)

Fang, Yuqiang; Lai, King W. C.

2016-04-01

Mechanical properties of cells and their mechanical interaction with the extracellular environments are main factors influencing cellular function, thus indicating the progression of cells in different disease states. By considering the mechanical interactions between cell adhesion molecules and the extracellular environment, we developed a cell mechanical model that can characterize the mechanical changes in cells during cell spreading. A cell model was established that consisted of various main subcellular components, including cortical cytoskeleton, nuclear envelope, actin filaments, intermediate filaments, and microtubules. We demonstrated the structural changes in subcellular components and the changes in spreading areas during cell spreading driven by traction forces. The simulation of nanoindentation tests was conducted by integrating the indenting force to the cell model. The force-indentation curve of the cells at different spreading states was simulated, and the results showed that cell stiffness increased with increasing traction forces, which were consistent with the experimental results. The proposed cell mechanical model provides a strategy to investigate the mechanical interactions of cells with the extracellular environments through the adhesion molecules and to reveal the cell mechanical properties at the subcellular level as cells shift from the suspended state to the adherent state.

Modeling the mechanics of cells in the cell-spreading process driven by traction forces.

PubMed

Fang, Yuqiang; Lai, King W C

2016-04-01

Mechanical properties of cells and their mechanical interaction with the extracellular environments are main factors influencing cellular function, thus indicating the progression of cells in different disease states. By considering the mechanical interactions between cell adhesion molecules and the extracellular environment, we developed a cell mechanical model that can characterize the mechanical changes in cells during cell spreading. A cell model was established that consisted of various main subcellular components, including cortical cytoskeleton, nuclear envelope, actin filaments, intermediate filaments, and microtubules. We demonstrated the structural changes in subcellular components and the changes in spreading areas during cell spreading driven by traction forces. The simulation of nanoindentation tests was conducted by integrating the indenting force to the cell model. The force-indentation curve of the cells at different spreading states was simulated, and the results showed that cell stiffness increased with increasing traction forces, which were consistent with the experimental results. The proposed cell mechanical model provides a strategy to investigate the mechanical interactions of cells with the extracellular environments through the adhesion molecules and to reveal the cell mechanical properties at the subcellular level as cells shift from the suspended state to the adherent state.

Propulsion and airframe aerodynamic interactions of supersonic V/STOL configurations. Volume 1: Wind tunnel test pressure data report

NASA Technical Reports Server (NTRS)

Zilz, D. E.; Devereaux, P. A.

1985-01-01

A wind tunnel model of a supersonic V/STOL fighter configuration has been tested to measure the aerodynamic interaction effects which can result from geometrically close-coupled propulsion system/airframe components. The approach was to configure the model to represent two different test techniques. One was a conventional test technique composed of two test modes. In the Flow-Through mode, absolute configuration aerodynamics are measured, including inlet/airframe interactions. In the Jet-Effects mode, incremental nozzle/airframe interactions are measured. The other test technique is a propulsion simulator approach, where a sub-scale, externally powered engine is mounted in the model. This allows proper measurement of inlet/airframe and nozzle/airframe interactions simultaneously. This is Volume 1 of 2: Wind Tunnel Test Pressure Data Report.

Primary Cosmic-Ray Spectra in the Knee Region

NASA Astrophysics Data System (ADS)

Ter-Antonyan, Samvel V.; Biermann, P. L.

2003-07-01

Using EAS inverse approach and KASCADE EAS data the primary energy spectra for different primary nuclei at energies 1015 - 1017 eV are obtained in the framework of multi-comp onent model of primary cosmic ray origin and QGSJET and SIBYLL interaction models. The rigidity-dep endent behavior of spectra is the same for two interaction models. The extrap olation of the obtained primary spectra in a 1017 - 1018 eV energy range displays a presence of the extragalactic component of primary cosmic rays.

Interacting dark energy: Dynamical system analysis

NASA Astrophysics Data System (ADS)

Golchin, Hanif; Jamali, Sara; Ebrahimi, Esmaeil

We investigate the impacts of interaction between dark matter (DM) and dark energy (DE) in the context of two DE models, holographic (HDE) and ghost dark energy (GDE). In fact, using the dynamical system analysis, we obtain the cosmological consequence of several interactions, considering all relevant component of universe, i.e. matter (dark and luminous), radiation and DE. Studying the phase space for all interactions in detail, we show the existence of unstable matter-dominated and stable DE-dominated phases. We also show that linear interactions suffer from the absence of standard radiation-dominated epoch. Interestingly, this failure resolved by adding the nonlinear interactions to the models. We find an upper bound for the value of the coupling constant of the interaction between DM and DE as b < 0.57in the case of holographic model, and b < 0.61 in the case of GDE model, to result in a cosmological viable matter-dominated epoch. More specifically, this bound is vital to satisfy instability and deceleration of matter-dominated epoch.

Infinite Systems of Interacting Chains with Memory of Variable Length—A Stochastic Model for Biological Neural Nets

NASA Astrophysics Data System (ADS)

Galves, A.; Löcherbach, E.

2013-06-01

We consider a new class of non Markovian processes with a countable number of interacting components. At each time unit, each component can take two values, indicating if it has a spike or not at this precise moment. The system evolves as follows. For each component, the probability of having a spike at the next time unit depends on the entire time evolution of the system after the last spike time of the component. This class of systems extends in a non trivial way both the interacting particle systems, which are Markovian (Spitzer in Adv. Math. 5:246-290, 1970) and the stochastic chains with memory of variable length which have finite state space (Rissanen in IEEE Trans. Inf. Theory 29(5):656-664, 1983). These features make it suitable to describe the time evolution of biological neural systems. We construct a stationary version of the process by using a probabilistic tool which is a Kalikow-type decomposition either in random environment or in space-time. This construction implies uniqueness of the stationary process. Finally we consider the case where the interactions between components are given by a critical directed Erdös-Rényi-type random graph with a large but finite number of components. In this framework we obtain an explicit upper-bound for the correlation between successive inter-spike intervals which is compatible with previous empirical findings.

Fourier decomposition of payoff matrix for symmetric three-strategy games.

PubMed

Szabó, György; Bodó, Kinga S; Allen, Benjamin; Nowak, Martin A

2014-10-01

In spatial evolutionary games the payoff matrices are used to describe pair interactions among neighboring players located on a lattice. Now we introduce a way how the payoff matrices can be built up as a sum of payoff components reflecting basic symmetries. For the two-strategy games this decomposition reproduces interactions characteristic to the Ising model. For the three-strategy symmetric games the Fourier components can be classified into four types representing games with self-dependent and cross-dependent payoffs, variants of three-strategy coordinations, and the rock-scissors-paper (RSP) game. In the absence of the RSP component the game is a potential game. The resultant potential matrix has been evaluated. The general features of these systems are analyzed when the game is expressed by the linear combinations of these components.

Towards an Automated Full-Turbofan Engine Numerical Simulation

NASA Technical Reports Server (NTRS)

Reed, John A.; Turner, Mark G.; Norris, Andrew; Veres, Joseph P.

2003-01-01

The objective of this study was to demonstrate the high-fidelity numerical simulation of a modern high-bypass turbofan engine. The simulation utilizes the Numerical Propulsion System Simulation (NPSS) thermodynamic cycle modeling system coupled to a high-fidelity full-engine model represented by a set of coupled three-dimensional computational fluid dynamic (CFD) component models. Boundary conditions from the balanced, steady-state cycle model are used to define component boundary conditions in the full-engine model. Operating characteristics of the three-dimensional component models are integrated into the cycle model via partial performance maps generated automatically from the CFD flow solutions using one-dimensional meanline turbomachinery programs. This paper reports on the progress made towards the full-engine simulation of the GE90-94B engine, highlighting the generation of the high-pressure compressor partial performance map. The ongoing work will provide a system to evaluate the steady and unsteady aerodynamic and mechanical interactions between engine components at design and off-design operating conditions.

Controlling Microbial Safety Challenges of Meat Using High Voltage Atmospheric Cold Plasma

PubMed Central

Han, Lu; Ziuzina, Dana; Heslin, Caitlin; Boehm, Daniela; Patange, Apurva; Sango, David M.; Valdramidis, Vasilis P.; Cullen, Patrick J.; Bourke, Paula

2016-01-01

Atmospheric cold plasma (ACP) is a non-thermal technology, effective against a wide range of pathogenic microorganisms. Inactivation efficacy results from plasma generated reactive species. These may interact with any organic components in a test matrix including the target microorganism, thus food components may exert a protective effect against the antimicrobial mode of action. The effect of an in-package high voltage ACP process applied in conjunction with common meat processing MAP gas compositions as well as bacteria type and meat model media composition have been investigated to determine the applicability of this technology for decontamination of safety challenges associated with meat products. E. coli, L. monocytogenes, and S. aureus in PBS were undetectable after 60 s of treatment at 80 kVRMS in air, while ACP treatment of the contaminated meat model required post-treatment refrigeration to retain antimicrobial effect. The nutritive components in the meat model exerted a protective effect during treatment, where 300 s ACP exposure yielded a maximum reduction of 1.5 log using a high oxygen atmosphere, whilst using air and high nitrogen atmospheres yielded lower antimicrobial efficacy. Furthermore, an ROS assay was performed to understand the protective effects observed using the meat model. This revealed that nutritive components inhibited penetration of ROS into bacterial cells. This knowledge can assist the optimization of meat decontamination using ACP technology where interactions with all components of the food matrix require evaluation. PMID:27446018

Examining protein-lipid interactions in model systems with a new squarylium fluorescent dye.

PubMed

Ioffe, Valeriya M; Gorbenko, Galyna P; Tatarets, Anatoliy L; Patsenker, Leonid D; Terpechnig, Ewald A

2006-07-01

The applicability of newly synthesized squarylium dye Sq to probing the changes in physical characteristics of lipid bilayer on the formation of protein-lipid complexes has been evaluated. Lipid vesicles composed of zwitterionic phospholipid phosphatidylcholine (PC) and its mixtures with positively charged detergent cetyltrimethylammonium bromide (CTAB), anionic phospholipid cardiolipin (CL), and cholesterol (Chol) were employed as lipid component of model membrane systems while protein constituent was represented by lysozyme (Lz). Fluorescence intensity of Sq was found to decrease on Lz association with lipid bilayer. This effect was observed in all kinds of model systems suggesting that Sq is sensitive to modification of lipid bilayer physical properties on hydrophobic protein-lipid interactions. It was found that Sq spectral response to variations in Chol content depends on relative contributions of electrostatic and hydrophobic components of Lz-membrane binding.

Tire-soil interaction model for turning (steered) tires

NASA Astrophysics Data System (ADS)

Karafiath, L. L.

1985-07-01

A review of the experimental information on the development of lateral forces on tires traveling at an angle to their center plane is presented and the usefulness of the consideration of the lateral forces for the development of an analytical model is evaluated. Major components of the lateral force have been identified as the forces required to balance the tractive force and the drawbar pull vectorially. These are the shear stresses developing in the contact area and the horizontal component of the normal stresses acting on the in-ground portion or the curved side walls of the tire. The tire-soil interaction model for steady state straight travel has been expanded to include the necessary algorithms for the calculation of these lateral forces. The pattern of tractive force-slip and longitudinal-lateral force relationships is in general agreement with experiments.

A new synoptic scale resolving global climate simulation using the Community Earth System Model

NASA Astrophysics Data System (ADS)

Small, R. Justin; Bacmeister, Julio; Bailey, David; Baker, Allison; Bishop, Stuart; Bryan, Frank; Caron, Julie; Dennis, John; Gent, Peter; Hsu, Hsiao-ming; Jochum, Markus; Lawrence, David; Muñoz, Ernesto; diNezio, Pedro; Scheitlin, Tim; Tomas, Robert; Tribbia, Joseph; Tseng, Yu-heng; Vertenstein, Mariana

2014-12-01

High-resolution global climate modeling holds the promise of capturing planetary-scale climate modes and small-scale (regional and sometimes extreme) features simultaneously, including their mutual interaction. This paper discusses a new state-of-the-art high-resolution Community Earth System Model (CESM) simulation that was performed with these goals in mind. The atmospheric component was at 0.25° grid spacing, and ocean component at 0.1°. One hundred years of "present-day" simulation were completed. Major results were that annual mean sea surface temperature (SST) in the equatorial Pacific and El-Niño Southern Oscillation variability were well simulated compared to standard resolution models. Tropical and southern Atlantic SST also had much reduced bias compared to previous versions of the model. In addition, the high resolution of the model enabled small-scale features of the climate system to be represented, such as air-sea interaction over ocean frontal zones, mesoscale systems generated by the Rockies, and Tropical Cyclones. Associated single component runs and standard resolution coupled runs are used to help attribute the strengths and weaknesses of the fully coupled run. The high-resolution run employed 23,404 cores, costing 250 thousand processor-hours per simulated year and made about two simulated years per day on the NCAR-Wyoming supercomputer "Yellowstone."

Synthesis of benthic flux components in the Patos Lagoon coastal zone, Rio Grande do Sul, Brazil

NASA Astrophysics Data System (ADS)

King, J. N.

2012-12-01

The primary objective of this work is to synthesize components of benthic flux in the Patos Lagoon coastal zone, Rio Grande do Sul, Brazil. Specifically, the component of benthic discharge flux forced by the terrestrial hydraulic gradient is 0.8 m3 d-1; components of benthic discharge and recharge flux associated with the groundwater tidal prism are both 2.1 m3 d-1; components of benthic discharge and recharge flux forced by surface-gravity wave setup are both 6.3 m3 d-1; the component of benthic discharge flux that transports radium-228 is 350 m3 d-1; and components of benthic discharge and recharge flux forced by surface-gravity waves propagating over a porous medium are both 1400 m3 d-1. (All models are normalized per meter shoreline.) Benthic flux is a function of components forced by individual mechanisms and nonlinear interactions that exist between components. Constructive and destructive interference may enhance or diminish the contribution of benthic flux components. It may not be possible to model benthic flux by summing component magnitudes. Geochemical tracer techniques may not accurately model benthic discharge flux or submarine groundwater discharge (SGD). A conceptual model provides a framework on which to quantitatively characterize benthic discharge flux and SGD with a multifaceted approach.

Synthesis of benthic flux components in the Patos Lagooncoastal zone, Rio Grande do Sul, Brazil

USGS Publications Warehouse

King, Jeffrey N.

2012-01-01

The primary objective of this work is to synthesize components of benthic flux in the Patos Lagoon coastal zone, Rio Grande do Sul, Brazil. Specifically, the component of benthic discharge flux forced by the terrestrial hydraulic gradient is 0.8 m3 d-1; components of benthic discharge and recharge flux associated with the groundwater tidal prism are both 2.1 m3 d-1; components of benthic discharge and recharge flux forced by surface-gravity wave setup are both 6.3 m3 d-1; the component of benthic discharge flux that transports radium-228 is 350 m3 d-1; and components of benthic discharge and recharge flux forced by surface-gravity waves propagating over a porous medium are both 1400 m3 d-1. (All models are normalized per meter shoreline.) Benthic flux is a function of components forced by individual mechanisms and nonlinear interactions that exist between components. Constructive and destructive interference may enhance or diminish the contribution of benthic flux components. It may not be possible to model benthic flux by summing component magnitudes. Geochemical tracer techniques may not accurately model benthic discharge flux or submarine groundwater discharge (SGD). A conceptual model provides a framework on which to quantitatively characterize benthic discharge flux and SGD with a multifaceted approach.

Interactive Multimedia Learning: Innovating Classroom Education in a Malaysian University

ERIC Educational Resources Information Center

Leow, Fui-Theng; Neo, Mai

2014-01-01

This research study was conducted at INTI International University, and aimed at enhancing the quality of classroom learning for University students with three important emphases: Gagne's instructional model, multimedia, and student-centred learning. An Interactive Learning Module (ILM) was developed as the core component in forming the…

Storytelling: An Important Component of Successful Training.

ERIC Educational Resources Information Center

Siegel, Mark

1996-01-01

The director of production at Interactive Media Communications discusses its multimedia training models that address health and safety issues. Their purpose is to create entertaining instructional designs to guide the student in an interactive approach. The article describes two CD-ROM products (on hazardous chemicals and safe driving),…

Gravitational collapse and the vacuum energy

NASA Astrophysics Data System (ADS)

Campos, M.

2014-03-01

To explain the accelerated expansion of the universe, models with interacting dark components (dark energy and dark matter) have been considered recently in the literature. Generally, the dark energy component is physically interpreted as the vacuum energy of the all fields that fill the universe. As the other side of the same coin, the influence of the vacuum energy on the gravitational collapse is of great interest. We study such collapse adopting different parameterizations for the evolution of the vacuum energy. We discuss the homogeneous collapsing star fluid, that interacts with a vacuum energy component, using the stiff matter case as example. We conclude this work with a discussion of the Cahill-McVittie mass for the collapsed object.

A component-based software environment for visualizing large macromolecular assemblies.

PubMed

Sanner, Michel F

2005-03-01

The interactive visualization of large biological assemblies poses a number of challenging problems, including the development of multiresolution representations and new interaction methods for navigating and analyzing these complex systems. An additional challenge is the development of flexible software environments that will facilitate the integration and interoperation of computational models and techniques from a wide variety of scientific disciplines. In this paper, we present a component-based software development strategy centered on the high-level, object-oriented, interpretive programming language: Python. We present several software components, discuss their integration, and describe some of their features that are relevant to the visualization of large molecular assemblies. Several examples are given to illustrate the interoperation of these software components and the integration of structural data from a variety of experimental sources. These examples illustrate how combining visual programming with component-based software development facilitates the rapid prototyping of novel visualization tools.

Biophysical markers of the peripheral vasoconstriction response to pain in sickle cell disease

PubMed Central

Khaleel, Maha; Sunwoo, John; Shah, Payal; Detterich, Jon A.; Kato, Roberta M.; Thuptimdang, Wanwara; Meiselman, Herbert J.; Sposto, Richard; Tsao, Jennie; Wood, John C.; Zeltzer, Lonnie; Coates, Thomas D.; Khoo, Michael C. K.

2017-01-01

Painful vaso-occlusive crisis (VOC), a complication of sickle cell disease (SCD), occurs when sickled red blood cells obstruct flow in the microvasculature. We postulated that exaggerated sympathetically mediated vasoconstriction, endothelial dysfunction and the synergistic interaction between these two factors act together to reduce microvascular flow, promoting regional vaso-occlusions, setting the stage for VOC. We previously found that SCD subjects had stronger vasoconstriction response to pulses of heat-induced pain compared to controls but the relative degrees to which autonomic dysregulation, peripheral vascular dysfunction and their interaction are present in SCD remain unknown. In the present study, we employed a mathematical model to decompose the total vasoconstriction response to pain into: 1) the neurogenic component, 2) the vascular response to blood pressure, 3) respiratory coupling and 4) neurogenic-vascular interaction. The model allowed us to quantify the contribution of each component to the total vasoconstriction response. The most salient features of the components were extracted to represent biophysical markers of autonomic and vascular impairment in SCD and controls. These markers provide a means of phenotyping severity of disease in sickle-cell anemia that is based more on underlying physiology than on genotype. The marker of the vascular component (BMv) showed stronger contribution to vasoconstriction in SCD than controls (p = 0.0409), suggesting a dominant myogenic response in the SCD subjects as a consequence of endothelial dysfunction. The marker of neurogenic-vascular interaction (BMn-v) revealed that the interaction reinforced vasoconstriction in SCD but produced vasodilatory response in controls (p = 0.0167). This marked difference in BMn-v suggests that it is the most sensitive marker for quantifying combined alterations in autonomic and vascular function in SCD in response to heat-induced pain. PMID:28542469

Cross-correlation spin noise spectroscopy of heterogeneous interacting spin systems

DOE PAGES

Roy, Dibyendu; Yang, Luyi; Crooker, Scott A.; ...

2015-04-30

Interacting multi-component spin systems are ubiquitous in nature and in the laboratory. As such, investigations of inter-species spin interactions are of vital importance. Traditionally, they are studied by experimental methods that are necessarily perturbative: e.g., by intentionally polarizing or depolarizing one spin species while detecting the response of the other(s). Here, we describe and demonstrate an alternative approach based on multi-probe spin noise spectroscopy, which can reveal inter-species spin interactions - under conditions of strict thermal equilibrium - by detecting and cross-correlating the stochastic fluctuation signals exhibited by each of the constituent spin species. Specifically, we consider a two-component spinmore » ensemble that interacts via exchange coupling, and we determine cross-correlations between their intrinsic spin fluctuations. The model is experimentally confirmed using “two-color” optical spin noise spectroscopy on a mixture of interacting Rb and Cs vapors. Noise correlations directly reveal the presence of inter-species spin exchange, without ever perturbing the system away from thermal equilibrium. These non-invasive and noise-based techniques should be generally applicable to any heterogeneous spin system in which the fluctuations of the constituent components are detectable.« less

Microstructure from ferroelastic transitions using strain pseudospin clock models in two and three dimensions: A local mean-field analysis

NASA Astrophysics Data System (ADS)

Vasseur, Romain; Lookman, Turab; Shenoy, Subodh R.

2010-09-01

We show how microstructure can arise in first-order ferroelastic structural transitions, in two and three spatial dimensions, through a local mean-field approximation of their pseudospin Hamiltonians, that include anisotropic elastic interactions. Such transitions have symmetry-selected physical strains as their NOP -component order parameters, with Landau free energies that have a single zero-strain “austenite” minimum at high temperatures, and spontaneous-strain “martensite” minima of NV structural variants at low temperatures. The total free energy also has gradient terms, and power-law anisotropic effective interactions, induced by “no-dislocation” St Venant compatibility constraints. In a reduced description, the strains at Landau minima induce temperature dependent, clocklike ZNV+1 Hamiltonians, with NOP -component strain-pseudospin vectors S⃗ pointing to NV+1 discrete values (including zero). We study elastic texturing in five such first-order structural transitions through a local mean-field approximation of their pseudospin Hamiltonians, that include the power-law interactions. As a prototype, we consider the two-variant square/rectangle transition, with a one-component pseudospin taking NV+1=3 values of S=0,±1 , as in a generalized Blume-Capel model. We then consider transitions with two-component (NOP=2) pseudospins: the equilateral to centered rectangle (NV=3) ; the square to oblique polygon (NV=4) ; the triangle to oblique (NV=6) transitions; and finally the three-dimensional (3D) cubic to tetragonal transition (NV=3) . The local mean-field solutions in two-dimensional and 3D yield oriented domain-wall patterns as from continuous-variable strain dynamics, showing the discrete-variable models capture the essential ferroelastic texturings. Other related Hamiltonians illustrate that structural transitions in materials science can be the source of interesting spin models in statistical mechanics.

Modeling understory vegetation and its response to fire [Chapter 15

Treesearch

Donald McKenzie; Crystal L. Raymond; Samuel A. Cushman

2008-01-01

The understory is an oft-neglected element in landscape modeling. Most landscape models focus on the dominant vegetation and how it responds over successional time to climate, competitive interactions, and disturbance (Keane et al. 2004, Cary et al. 2006). Even forest stand-level models rarely consider understory components other than seedlings, saplings, and...

Review of forest landscape models: types, methods, development and applications

Treesearch

Weimin Xi; Robert N. Coulson; Andrew G. Birt; Zong-Bo Shang; John D. Waldron; Charles W. Lafon; David M. Cairns; Maria D. Tchakerian; Kier D. Klepzig

2009-01-01

Forest landscape models simulate forest change through time using spatially referenced data across a broad spatial scale (i.e. landscape scale) generally larger than a single forest stand. Spatial interactions between forest stands are a key component of such models. These models can incorporate other spatio-temporal processes such as...

Hierarchical graphs for better annotations of rule-based models of biochemical systems

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

Hu, Bin; Hlavacek, William

2009-01-01

In the graph-based formalism of the BioNetGen language (BNGL), graphs are used to represent molecules, with a colored vertex representing a component of a molecule, a vertex label representing the internal state of a component, and an edge representing a bond between components. Components of a molecule share the same color. Furthermore, graph-rewriting rules are used to represent molecular interactions, with a rule that specifies addition (removal) of an edge representing a class of association (dissociation) reactions and with a rule that specifies a change of vertex label representing a class of reactions that affect the internal state of amore » molecular component. A set of rules comprises a mathematical/computational model that can be used to determine, through various means, the system-level dynamics of molecular interactions in a biochemical system. Here, for purposes of model annotation, we propose an extension of BNGL that involves the use of hierarchical graphs to represent (1) relationships among components and subcomponents of molecules and (2) relationships among classes of reactions defined by rules. We illustrate how hierarchical graphs can be used to naturally document the structural organization of the functional components and subcomponents of two proteins: the protein tyrosine kinase Lck and the T cell receptor (TCR)/CD3 complex. Likewise, we illustrate how hierarchical graphs can be used to document the similarity of two related rules for kinase-catalyzed phosphorylation of a protein substrate. We also demonstrate how a hierarchical graph representing a protein can be encoded in an XML-based format.« less

A multi-level model of emerging technology: An empirical study of the evolution of biotechnology from 1976 to 2003

PubMed Central

van Witteloostuijn, Arjen

2018-01-01

In this paper, we develop an ecological, multi-level model that can be used to study the evolution of emerging technology. More specifically, by defining technology as a system composed of a set of interacting components, we can build upon the argument of multi-level density dependence from organizational ecology to develop a distribution-independent model of technological evolution. This allows us to distinguish between different stages of component development, which provides more insight into the emergence of stable component configurations, or dominant designs. We validate our hypotheses in the biotechnology industry by using patent data from the USPTO from 1976 to 2003. PMID:29795575

Towards a Theory-Based Design Framework for an Effective E-Learning Computer Programming Course

ERIC Educational Resources Information Center

McGowan, Ian S.

2016-01-01

Built on Dabbagh (2005), this paper presents a four component theory-based design framework for an e-learning session in introductory computer programming. The framework, driven by a body of exemplars component, emphasizes the transformative interaction between the knowledge building community (KBC) pedagogical model, a mixed instructional…

Energy transfer dynamics and kinetics of elementary processes (promoted) by gas-phase CO2 -N2 collisions: Selectivity control by the anisotropy of the interaction.

PubMed

Lombardi, Andrea; Pirani, Fernando; Laganà, Antonio; Bartolomei, Massimiliano

2016-06-15

In this work, we exploit a new formulation of the potential energy and of the related computational procedures, which embodies the coupling between the intra and intermolecular components, to characterize possible propensities of the collision dynamics in energy transfer processes of interest for simulation and control of phenomena occurring in a variety of equilibrium and nonequilibrium environments. The investigation reported in the paper focuses on the prototype CO2 -N2 system, whose intramolecular component of the interaction is modeled in terms of a many body expansion while the intermolecular component is modeled in terms of a recently developed bonds-as-interacting-molecular-centers' approach. The main advantage of this formulation of the potential energy surface is that of being (a) truly full dimensional (i.e., all the variations of the coordinates associated with the molecular vibrations and rotations on the geometrical and electronic structure of the monomers, are explicitly taken into account without freezing any bonds or angles), (b) more flexible than other usual formulations of the interaction and (c) well suited for fitting procedures better adhering to accurate ab initio data and sensitive to experimental arrangement dependent information. Specific attention has been given to the fact that a variation of vibrational and rotational energy has a higher (both qualitative and quantitative) impact on the energy transfer when a more accurate formulation of the intermolecular interaction (with respect to that obtained when using rigid monomers) is adopted. This makes the potential energy surface better suited for the kinetic modeling of gaseous mixtures in plasma, combustion and atmospheric chemistry computational applications. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Kinetics of the inhibitory interaction of organophosphorus neuropathy inducers and non-inducers in soluble esterases in the avian nervous system

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

Mangas, Iris; Vilanova, Eugenio; Estevez, Jorge, E-mail: jorge.estevez@umh.es

2011-11-15

Some published studies suggest that low level exposure to organophosphorus esters (OPs) may cause neurological and neurobehavioral effects at long term exposure. These effects cannot be explained by action on known targets. In this work, the interactions (inhibition, spontaneous reactivation and 'ongoing inhibition') of two model OPs (paraoxon, non neuropathy-inducer, and mipafox, neuropathy-inducer) with the chicken brain soluble esterases were evaluated. The best-fitting kinetic model with both inhibitors was compatible with three enzymatic components. The amplitudes (proportions) of the components detected with mipafox were similar to those obtained with paraoxon. These observations confirm the consistency of the results and themore » model applied and may be considered an external validation. The most sensitive component (E{alpha}) for paraoxon (11-23% of activity, I{sub 50} (30 min) = 9-11 nM) is also the most sensitive for mipafox (I{sub 50} (30 min) = 4 nM). This component is spontaneously reactivated after inhibition with paraoxon. The second sensitive component to paraoxon (E{beta}, 71-84% of activity; I{sub 50} (30 min) = 1216 nM) is practically resistant to mipafox. The third component (E{gamma}, 5-8% of activity) is paraoxon resistant and has I{sub 50} (30 min) of 3.4 {mu}M with mipafox, similar to NTE (neuropathy target esterase). The role of these esterases remains unknown. Their high sensitivity suggests that they may either play a role in toxicity in low-level long-term exposure of organophosphate compounds or have a protective effect related with the spontaneous reactivation. They will have to be considered in further metabolic and toxicological studies. -- Research Highlights: Black-Right-Pointing-Pointer Paraoxon and mipafox interactions have been evaluated with chicken soluble brain esterases. Black-Right-Pointing-Pointer The paraoxon inhibition was analyzed considering the simultaneous spontaneous reactivation. Black-Right-Pointing-Pointer The best-fitting kinetic models were compatible with a three enzymatic components. Black-Right-Pointing-Pointer The amplitudes of the components were similar in paraoxon and mipafox experiments. Black-Right-Pointing-Pointer It is suggested they may play a role in toxicity in low-level long-term exposure of these compounds.« less

Effects of septum and pericardium on heart-lung interactions in a cardiopulmonary simulation model.

PubMed

Karamolegkos, Nikolaos; Albanese, Antonio; Chbat, Nicolas W

2017-07-01

Mechanical heart-lung interactions are often overlooked in clinical settings. However, their impact on cardiac function can be quite significant. Mechanistic physiology-based models can provide invaluable insights into such cardiorespiratory interactions, which occur not only under external mechanical ventilatory support but in normal physiology as well. In this work, we focus on the cardiac component of a previously developed mathematical model of the human cardiopulmonary system, aiming to improve the model's response to the intrathoracic pressure variations that are associated with the respiratory cycle. Interventricular septum and pericardial membrane are integrated into the existing model. Their effect on the overall cardiac response is explained by means of comparison against simulation results from the original model as well as experimental data from literature.

Simulations of galaxy cluster collisions with a dark plasma component

NASA Astrophysics Data System (ADS)

Spethmann, Christian; Veermäe, Hardi; Sepp, Tiit; Heikinheimo, Matti; Deshev, Boris; Hektor, Andi; Raidal, Martti

2017-12-01

Context. Dark plasma is an intriguing form of self-interacting dark matter with an effective fluid-like behavior, which is well motivated by various theoretical particle physics models. Aims: We aim to find an explanation for an isolated mass clump in the Abell 520 system, which cannot be explained by traditional models of dark matter, but has been detected in weak lensing observations. Methods: We performed N-body smoothed particle hydrodynamics simulations of galaxy cluster collisions with a two component model of dark matter, which is assumed to consist of a predominant non-interacting dark matter component and a 10-40% mass fraction of dark plasma. Results: The mass of a possible dark clump was calculated for each simulation in a parameter scan over the underlying model parameters. In two higher resolution simulations shock-waves and Mach cones were observed to form in the dark plasma halos. Conclusions: By choosing suitable simulation parameters, the observed distributions of dark matter in both the Bullet cluster (1E 0657-558) and Abell 520 (MS 0451.5+0250) can be qualitatively reproduced. Movies associated to Figs. A.1 and A.2 are available at http://www.aanda.org

Characterization of the pharmacokinetics of gasoline using PBPK modeling with a complex mixtures chemical lumping approach.

PubMed

Dennison, James E; Andersen, Melvin E; Yang, Raymond S H

2003-09-01

Gasoline consists of a few toxicologically significant components and a large number of other hydrocarbons in a complex mixture. By using an integrated, physiologically based pharmacokinetic (PBPK) modeling and lumping approach, we have developed a method for characterizing the pharmacokinetics (PKs) of gasoline in rats. The PBPK model tracks selected target components (benzene, toluene, ethylbenzene, o-xylene [BTEX], and n-hexane) and a lumped chemical group representing all nontarget components, with competitive metabolic inhibition between all target compounds and the lumped chemical. PK data was acquired by performing gas uptake PK studies with male F344 rats in a closed chamber. Chamber air samples were analyzed every 10-20 min by gas chromatography/flame ionization detection and all nontarget chemicals were co-integrated. A four-compartment PBPK model with metabolic interactions was constructed using the BTEX, n-hexane, and lumped chemical data. Target chemical kinetic parameters were refined by studies with either the single chemical alone or with all five chemicals together. o-Xylene, at high concentrations, decreased alveolar ventilation, consistent with respiratory irritation. A six-chemical interaction model with the lumped chemical group was used to estimate lumped chemical partitioning and metabolic parameters for a winter blend of gasoline with methyl t-butyl ether and a summer blend without any oxygenate. Computer simulation results from this model matched well with experimental data from single chemical, five-chemical mixture, and the two blends of gasoline. The PBPK model analysis indicated that metabolism of individual components was inhibited up to 27% during the 6-h gas uptake experiments of gasoline exposures.

Parallel Optimization of an Earth System Model (100 Gigaflops and Beyond?)

NASA Technical Reports Server (NTRS)

Drummond, L. A.; Farrara, J. D.; Mechoso, C. R.; Spahr, J. A.; Chao, Y.; Katz, S.; Lou, J. Z.; Wang, P.

1997-01-01

We are developing an Earth System Model (ESM) to be used in research aimed to better understand the interactions between the components of the Earth System and to eventually predict their variations. Currently, our ESM includes models of the atmosphere, oceans and the important chemical tracers therein.

Description of the NCAR Community Climate Model (CCM3). Technical note

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

Kiehl, J.T.; Hack, J.J.; Bonan, G.B.

This repor presents the details of the governing equations, physical parameterizations, and numerical algorithms defining the version of the NCAR Community Climate Model designated CCM3. The material provides an overview of the major model components, and the way in which they interact as the numerical integration proceeds. This version of the CCM incorporates significant improvements to the physic package, new capabilities such as the incorporation of a slab ocean component, and a number of enhancements to the implementation (e.g., the ability to integrate the model on parallel distributed-memory computational platforms).

A simple model for solvation in mixed solvents. Applications to the stabilization and destabilization of macromolecular structures.

PubMed

Schellman, J A

1990-08-31

The properties of a simple model for solvation in mixed solvents are explored in this paper. The model is based on the supposition that solvent replacement is a simple one-for-one substitution reaction at macromolecular sites which are independent of one another. This leads to a new form for the binding polynomial in which all terms are associated with ligand interchange rather than ligand addition. The principal solvent acts as one of the ligands. Thermodynamic analysis then shows that thermodynamic binding (i.e., selective interaction) depends on the properties of K'-1, whereas stoichiometric binding (site occupation) depends on K'. K' is a 'practical' interchange equilibrium constant given by (f3/f1)K, where K is the true equilibrium constant for the interchange of components 3 and 1 on the site and f3 and f4 denote their respective activity coefficients on the mole fraction scale. Values of K' less than unity lead to negative selective interaction. It is selective interaction and not occupation number which determines the thermodynamic effects of solvation. When K' greater than 100 on the mole fraction scale or K' greater than 2 on the molality scale (in water), the differences between stoichiometric binding and selective interaction become less than 1%. The theory of this paper is therefore necessary only for very weak binding constants. When K'-1 is small, large concentrations of the added solvent component are required to produce a thermodynamic effect. Under these circumstances the isotherms for the selective interaction and for the excess (or transfer) free energy are strongly dependent on the behavior of the activity coefficients of both solvent components. Two classes of behavior are described depending on whether the components display positive or negative deviations from Raoult's law. Examples which are discussed are aqueous solutions of urea and guanidinium chloride for positive deviations and of sucrose and glucose for negative deviations. Examination of the few studies which have been reported in the literature shows that most of the qualitative features of the stabilization of proteins by sugars and their destabilization by urea and guanidinium chloride are faithfully represented with the model. This includes maxima in the free energy of stabilization and destabilization, decreased and zero selective interaction at high concentrations, etc. These phenomena had no prior explanation. Deficiencies in the model as a representation of solvation in aqueous solution are discussed in the appendix.

Thomson scattering from a three-component plasma.

PubMed

Johnson, W R; Nilsen, J

2014-02-01

A model for a three-component plasma consisting of two distinct ionic species and electrons is developed and applied to study x-ray Thomson scattering. Ions of a specific type are assumed to be identical and are treated in the average-atom approximation. Given the plasma temperature and density, the model predicts mass densities, effective ionic charges, and cell volumes for each ionic type, together with the plasma chemical potential and free-electron density. Additionally, the average-atom treatment of individual ions provides a quantum-mechanical description of bound and continuum electrons. The model is used to obtain parameters needed to determine the dynamic structure factors for x-ray Thomson scattering from a three-component plasma. The contribution from inelastic scattering by free electrons is evaluated in the random-phase approximation. The contribution from inelastic scattering by bound electrons is evaluated using the bound-state and scattering wave functions obtained from the average-atom calculations. Finally, the partial static structure factors for elastic scattering by ions are evaluated using a two-component version of the Ornstein-Zernike equations with hypernetted chain closure, in which electron-ion interactions are accounted for using screened ion-ion interaction potentials. The model is used to predict the x-ray Thomson scattering spectrum from a CH plasma and the resulting spectrum is compared with experimental results obtained by Feltcher et al. [Phys. Plasmas 20, 056316 (2013)].

Effect of perforation on flow past a conic cylinder at \\varvec{Re} = 100 : wavy vortex and sign laws

NASA Astrophysics Data System (ADS)

Lin, L. M.; Zhong, X. F.; Wu, Y. X.

2018-04-01

In order to find the intrinsic physical mechanism of the original Kármán vortex wavily distorted across the span due to the introduction of three-dimensional (3-D) geometric disturbances, a flow past a peak-perforated conic shroud is numerically simulated at a Reynolds number of 100. Based on previous work by Meiburg and Lasheras (1988), the streamwise and vertical interactions with spanwise vortices are introduced and analyzed. Then vortex-shedding patterns in the near wake for different flow regimes are reinspected and illustrated from the view of these two interactions. Generally, in regime I, spanwise vortices are a little distorted due to the weak interaction. Then in regime II, spanwise vortices, even though curved obviously, are still shed synchronously with moderate streamwise and vertical interactions. But in regime III, violently wavy spanwise vortices in some vortex-shedding patterns, typically an Ω -type vortex, are mainly attributed to the strong vertical interactions, while other cases, such as multiple vortex-shedding patterns in sub-regime III-D, are resulted from complex streamwise and vertical interactions. A special phenomenon, spacial distribution of streamwise and vertical components of vorticity with specific signs in the near wake, is analyzed based on two models of streamwise and vertical vortices in explaining physical reasons of top and bottom shear layers wavily varied across the span. Then these two models and above two interactions are unified. Finally two sign laws are summarized: the first sign law for streamwise and vertical components of vorticity is positive in the upper shear layer, but negative in the lower shear layer, while the second sign law for three vorticity components is always negative in the wake.

An integrative top-down and bottom-up qualitative model construction framework for exploration of biochemical systems.

PubMed

Wu, Zujian; Pang, Wei; Coghill, George M

Computational modelling of biochemical systems based on top-down and bottom-up approaches has been well studied over the last decade. In this research, after illustrating how to generate atomic components by a set of given reactants and two user pre-defined component patterns, we propose an integrative top-down and bottom-up modelling approach for stepwise qualitative exploration of interactions among reactants in biochemical systems. Evolution strategy is applied to the top-down modelling approach to compose models, and simulated annealing is employed in the bottom-up modelling approach to explore potential interactions based on models constructed from the top-down modelling process. Both the top-down and bottom-up approaches support stepwise modular addition or subtraction for the model evolution. Experimental results indicate that our modelling approach is feasible to learn the relationships among biochemical reactants qualitatively. In addition, hidden reactants of the target biochemical system can be obtained by generating complex reactants in corresponding composed models. Moreover, qualitatively learned models with inferred reactants and alternative topologies can be used for further web-lab experimental investigations by biologists of interest, which may result in a better understanding of the system.

Propulsion and airframe aerodynamic interactions of supersonic V/STOL configurations. Volume 2: Wind tunnel test force and moment data report

NASA Technical Reports Server (NTRS)

Zilz, D. E.

1985-01-01

A wind tunnel model of a supersonic V/STOL fighter configuration has been tested to measure the aerodynamic interaction effects which can result from geometrically close-coupled propulsion system/airframe components. The approach was to configure the model to represent two different test techniques. One was a conventional test technique composed of two test modes. In the Flow-Through mode, absolute configuration aerodynamics are measured, including inlet/airframe interactions. In the Jet-Effects mode, incremental nozzle/airframe interactions are measured. The other test technique is a propulsion simulator approach, where a sub-scale, externally powered engine is mounted in the model. This allows proper measurement of inlet/airframe and nozzle/airframe interactions simultaneously. This is Volume 2 of 2: Wind Tunnel Test Force and Moment Data Report.

Assessing the performance of dispersionless and dispersion-accounting methods: helium interaction with cluster models of the TiO2(110) surface.

PubMed

de Lara-Castells, María Pilar; Stoll, Hermann; Mitrushchenkov, Alexander O

2014-08-21

As a prototypical dispersion-dominated physisorption problem, we analyze here the performance of dispersionless and dispersion-accounting methodologies on the helium interaction with cluster models of the TiO2(110) surface. A special focus has been given to the dispersionless density functional dlDF and the dlDF+Das construction for the total interaction energy (K. Pernal, R. Podeswa, K. Patkowski, and K. Szalewicz, Phys. Rev. Lett. 2009, 109, 263201), where Das is an effective interatomic pairwise functional form for the dispersion. Likewise, the performance of symmetry-adapted perturbation theory (SAPT) method is evaluated, where the interacting monomers are described by density functional theory (DFT) with the dlDF, PBE, and PBE0 functionals. Our benchmarks include CCSD(T)-F12b calculations and comparative analysis on the nuclear bound states supported by the He-cluster potentials. Moreover, intra- and intermonomer correlation contributions to the physisorption interaction are analyzed through the method of increments (H. Stoll, J. Chem. Phys. 1992, 97, 8449) at the CCSD(T) level of theory. This method is further applied in conjunction with a partitioning of the Hartree-Fock interaction energy to estimate individual interaction energy components, comparing them with those obtained using the different SAPT(DFT) approaches. The cluster size evolution of dispersionless and dispersion-accounting energy components is then discussed, revealing the reduced role of the dispersionless interaction and intramonomer correlation when the extended nature of the surface is better accounted for. On the contrary, both post-Hartree-Fock and SAPT(DFT) results clearly demonstrate the high-transferability character of the effective pairwise dispersion interaction whatever the cluster model is. Our contribution also illustrates how the method of increments can be used as a valuable tool not only to achieve the accuracy of CCSD(T) calculations using large cluster models but also to evaluate the performance of SAPT(DFT) methods for the physically well-defined contributions to the total interaction energy. Overall, our work indicates the excellent performance of a dlDF+Das approach in which the parameters are optimized using the smallest cluster model of the target surface to treat van der Waals adsorbate-surface interactions.

Modeling joint restoration strategies for interdependent infrastructure systems

PubMed Central

Simonovic, Slobodan P.

2018-01-01

Life in the modern world depends on multiple critical services provided by infrastructure systems which are interdependent at multiple levels. To effectively respond to infrastructure failures, this paper proposes a model for developing optimal joint restoration strategy for interdependent infrastructure systems following a disruptive event. First, models for (i) describing structure of interdependent infrastructure system and (ii) their interaction process, are presented. Both models are considering the failure types, infrastructure operating rules and interdependencies among systems. Second, an optimization model for determining an optimal joint restoration strategy at infrastructure component level by minimizing the economic loss from the infrastructure failures, is proposed. The utility of the model is illustrated using a case study of electric-water systems. Results show that a small number of failed infrastructure components can trigger high level failures in interdependent systems; the optimal joint restoration strategy varies with failure occurrence time. The proposed models can help decision makers to understand the mechanisms of infrastructure interactions and search for optimal joint restoration strategy, which can significantly enhance safety of infrastructure systems. PMID:29649300

Water's Interfacial Hydrogen Bonding Structure Reveals the Effective Strength of Surface-Water Interactions.

PubMed

Shin, Sucheol; Willard, Adam P

2018-06-05

We combine all-atom molecular dynamics simulations with a mean field model of interfacial hydrogen bonding to analyze the effect of surface-water interactions on the structural and energetic properties of the liquid water interface. We show that the molecular structure of water at a weakly interacting ( i.e., hydrophobic) surface is resistant to change unless the strength of surface-water interactions are above a certain threshold. We find that below this threshold water's interfacial structure is homogeneous and insensitive to the details of the disordered surface, however, above this threshold water's interfacial structure is heterogeneous. Despite this heterogeneity, we demonstrate that the equilibrium distribution of molecular orientations can be used to quantify the energetic component of the surface-water interactions that contribute specifically to modifying the interfacial hydrogen bonding network. We identify this specific energetic component as a new measure of hydrophilicity, which we refer to as the intrinsic hydropathy.

How self-organization can guide evolution.

PubMed

Glancy, Jonathan; Stone, James V; Wilson, Stuart P

2016-11-01

Self-organization and natural selection are fundamental forces that shape the natural world. Substantial progress in understanding how these forces interact has been made through the study of abstract models. Further progress may be made by identifying a model system in which the interaction between self-organization and selection can be investigated empirically. To this end, we investigate how the self-organizing thermoregulatory huddling behaviours displayed by many species of mammals might influence natural selection of the genetic components of metabolism. By applying a simple evolutionary algorithm to a well-established model of the interactions between environmental, morphological, physiological and behavioural components of thermoregulation, we arrive at a clear, but counterintuitive, prediction: rodents that are able to huddle together in cold environments should evolve a lower thermal conductance at a faster rate than animals reared in isolation. The model therefore explains how evolution can be accelerated as a consequence of relaxed selection , and it predicts how the effect may be exaggerated by an increase in the litter size, i.e. by an increase in the capacity to use huddling behaviours for thermoregulation. Confirmation of these predictions in future experiments with rodents would constitute strong evidence of a mechanism by which self-organization can guide natural selection.

PACS/information systems interoperability using Enterprise Communication Framework.

PubMed

alSafadi, Y; Lord, W P; Mankovich, N J

1998-06-01

Interoperability among healthcare applications goes beyond connectivity to allow components to exchange structured information and work together in a predictable, coordinated fashion. To facilitate building an interoperability infrastructure, an Enterprise Communication Framework (ECF) was developed by the members of the Andover Working Group for Healthcare Interoperability (AWG-OHI). The ECF consists of four models: 1) Use Case Model, 2) Domain Information Model (DIM), 3) Interaction Model, and 4) Message Model. To realize this framework, a software component called the Enterprise Communicator (EC) is used. In this paper, we will demonstrate the use of the framework in interoperating a picture archiving and communication system (PACS) with a radiology information system (RIS).

Corolla Is a Novel Protein That Contributes to the Architecture of the Synaptonemal Complex of Drosophila

PubMed Central

Collins, Kimberly A.; Unruh, Jay R.; Slaughter, Brian D.; Yu, Zulin; Lake, Cathleen M.; Nielsen, Rachel J.; Box, Kimberly S.; Miller, Danny E.; Blumenstiel, Justin P.; Perera, Anoja G.; Malanowski, Kathryn E.; Hawley, R. Scott

2014-01-01

In most organisms the synaptonemal complex (SC) connects paired homologs along their entire length during much of meiotic prophase. To better understand the structure of the SC, we aim to identify its components and to determine how each of these components contributes to SC function. Here, we report the identification of a novel SC component in Drosophila melanogaster female oocytes, which we have named Corolla. Using structured illumination microscopy, we demonstrate that Corolla is a component of the central region of the SC. Consistent with its localization, we show by yeast two-hybrid analysis that Corolla strongly interacts with Cona, a central element protein, demonstrating the first direct interaction between two inner-synaptonemal complex proteins in Drosophila. These observations help provide a more complete model of SC structure and function in Drosophila females. PMID:24913682

Insight to the Interaction of the Dihydrolipoamide Acetyltransferase (E2) Core with the Peripheral Components in the Escherichia coli Pyruvate Dehydrogenase Complex via Multifaceted Structural Approaches*

PubMed Central

Chandrasekhar, Krishnamoorthy; Wang, Junjie; Arjunan, Palaniappa; Sax, Martin; Park, Yun-Hee; Nemeria, Natalia S.; Kumaran, Sowmini; Song, Jaeyoung; Jordan, Frank; Furey, William

2013-01-01

Multifaceted structural approaches were undertaken to investigate interaction of the E2 component with E3 and E1 components from the Escherichia coli pyruvate dehydrogenase multienzyme complex (PDHc), as a representative of the PDHc from Gram-negative bacteria. The crystal structure of E3 at 2.5 Å resolution reveals similarity to other E3 structures and was an important starting point for understanding interaction surfaces between E3 and E2. Biochemical studies revealed that R129E-E2 and R150E-E2 substitutions in the peripheral subunit-binding domain (PSBD) of E2 greatly diminished PDHc activity, affected interactions with E3 and E1 components, and affected reductive acetylation of E2. Because crystal structures are unavailable for any complete E2-containing complexes, peptide-specific hydrogen/deuterium exchange mass spectrometry was used to identify loci of interactions between 3-lipoyl E2 and E3. Two peptides from the PSBD, including Arg-129, and three peptides from E3 displayed statistically significant reductions in deuterium uptake resulting from interaction between E3 and E2. Of the peptides identified on E3, two were from the catalytic site, and the third was from the interface domain, which for all known E3 structures is believed to interact with the PSBD. NMR clearly demonstrates that there is no change in the lipoyl domain structure on complexation with E3. This is the first instance where the entire wild-type E2 component was employed to understand interactions with E3. A model for PSBD-E3 binding was independently constructed and found to be consistent with the importance of Arg-129, as well as revealing other electrostatic interactions likely stabilizing this complex. PMID:23580650

Insight to the interaction of the dihydrolipoamide acetyltransferase (E2) core with the peripheral components in the Escherichia coli pyruvate dehydrogenase complex via multifaceted structural approaches.

PubMed

Chandrasekhar, Krishnamoorthy; Wang, Junjie; Arjunan, Palaniappa; Sax, Martin; Park, Yun-Hee; Nemeria, Natalia S; Kumaran, Sowmini; Song, Jaeyoung; Jordan, Frank; Furey, William

2013-05-24

Multifaceted structural approaches were undertaken to investigate interaction of the E2 component with E3 and E1 components from the Escherichia coli pyruvate dehydrogenase multienzyme complex (PDHc), as a representative of the PDHc from Gram-negative bacteria. The crystal structure of E3 at 2.5 Å resolution reveals similarity to other E3 structures and was an important starting point for understanding interaction surfaces between E3 and E2. Biochemical studies revealed that R129E-E2 and R150E-E2 substitutions in the peripheral subunit-binding domain (PSBD) of E2 greatly diminished PDHc activity, affected interactions with E3 and E1 components, and affected reductive acetylation of E2. Because crystal structures are unavailable for any complete E2-containing complexes, peptide-specific hydrogen/deuterium exchange mass spectrometry was used to identify loci of interactions between 3-lipoyl E2 and E3. Two peptides from the PSBD, including Arg-129, and three peptides from E3 displayed statistically significant reductions in deuterium uptake resulting from interaction between E3 and E2. Of the peptides identified on E3, two were from the catalytic site, and the third was from the interface domain, which for all known E3 structures is believed to interact with the PSBD. NMR clearly demonstrates that there is no change in the lipoyl domain structure on complexation with E3. This is the first instance where the entire wild-type E2 component was employed to understand interactions with E3. A model for PSBD-E3 binding was independently constructed and found to be consistent with the importance of Arg-129, as well as revealing other electrostatic interactions likely stabilizing this complex.

Biomathematical modeling of pulsatile hormone secretion: a historical perspective.

PubMed

Evans, William S; Farhy, Leon S; Johnson, Michael L

2009-01-01

Shortly after the recognition of the profound physiological significance of the pulsatile nature of hormone secretion, computer-based modeling techniques were introduced for the identification and characterization of such pulses. Whereas these earlier approaches defined perturbations in hormone concentration-time series, deconvolution procedures were subsequently employed to separate such pulses into their secretion event and clearance components. Stochastic differential equation modeling was also used to define basal and pulsatile hormone secretion. To assess the regulation of individual components within a hormone network, a method that quantitated approximate entropy within hormone concentration-times series was described. To define relationships within coupled hormone systems, methods including cross-correlation and cross-approximate entropy were utilized. To address some of the inherent limitations of these methods, modeling techniques with which to appraise the strength of feedback signaling between and among hormone-secreting components of a network have been developed. Techniques such as dynamic modeling have been utilized to reconstruct dose-response interactions between hormones within coupled systems. A logical extension of these advances will require the development of mathematical methods with which to approximate endocrine networks exhibiting multiple feedback interactions and subsequently reconstruct their parameters based on experimental data for the purpose of testing regulatory hypotheses and estimating alterations in hormone release control mechanisms.

A locomotive-track coupled vertical dynamics model with gear transmissions

NASA Astrophysics Data System (ADS)

Chen, Zaigang; Zhai, Wanming; Wang, Kaiyun

2017-02-01

A gear transmission system is a key element in a locomotive for the transmission of traction or braking forces between the motor and the wheel-rail interface. Its dynamic performance has a direct effect on the operational reliability of the locomotive and its components. This paper proposes a comprehensive locomotive-track coupled vertical dynamics model, in which the locomotive is driven by axle-hung motors. In this coupled dynamics model, the dynamic interactions between the gear transmission system and the other components, e.g. motor and wheelset, are considered based on the detailed analysis of its structural properties and working mechanism. Thus, the mechanical transmission system for power delivery from the motor to the wheelset via gear transmission is coupled with a traditional locomotive-track dynamics system via the wheel-rail contact interface and the gear mesh interface. This developed dynamics model enables investigations of the dynamic performance of the entire dynamics system under the excitations from the wheel-rail contact interface and/or the gear mesh interface. Dynamic interactions are demonstrated by numerical simulations using this dynamics model. The results indicate that both of the excitations from the wheel-rail contact interface and the gear mesh interface have a significant effect on the dynamic responses of the components in this coupled dynamics system.

Effects of calcium carbonate, magnesium oxide and sodium citrate bicarbonate health supplements on the urinary risk factors for kidney stone formation.

PubMed

Allie, Shameez; Rodgers, Allen

2003-01-01

We describe a model to illustrate different chemical interactions that can occur in urine following ingestion of individual and combined health supplements. Two types of interactions are defined: synergism and addition. The model was applied to eight healthy males who participated in a study to investigate the chemical interactions between calcium carbonate, magnesium oxide and sodium citrate-bicarbonate health supplements on calcium oxalate urinary stone risk factors. Subjects ingested these components individually and in combination for 7 days. Twenty-four-hour urines were collected at baseline and during the final day of supplementation. These were analysed using standard laboratory techniques. Three different chemical interactions, all involving citrate, were identified: magnesium and citrate exerted a synergistic effect on lowering the relative superaturation (RS) of brushite; the same two components produced a synergistic effect on raising pH; finally, calcium and citrate exerted an additive effect on lowering the RS of uric acid. We propose that the novel approach described in this paper allows for the evaluation of individual, additive and synergistic interactions in the assessment of the efficacy of stone-risk reducing preparations.

Language Program as Ecology: A Perspective for Leadership

ERIC Educational Resources Information Center

Pennington, Martha C.; Hoekje, Barbara J.

2010-01-01

A language program is a delicate and intricate system of interacting resources or components, which, like a biological ecology, is in a constant state of evolution and change. The interactive system making up the program's internal culture is connected ecologically to the external environment. The ecological model is introduced as a useful…

A Kinesthetic Model Demonstrating Molecular Interactions Involved in Anterior-Posterior Pattern Formation in "Drosophila"

ERIC Educational Resources Information Center

Douglas, Kristin R.

2008-01-01

Prerequisites for the Developmental Biology course at Augustana College are introductory courses in zoology and cell biology. After introductory courses students appreciate the fact that proteins have three-dimensional structures; however, they often fail to recognize how protein interactions with other cellular components can lead to specific…

Dark degeneracy and interacting cosmic components

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

Aviles, Alejandro; Cervantes-Cota, Jorge L.

2011-10-15

We study some properties of the dark degeneracy, which is the fact that what we measure in gravitational experiments is the energy-momentum tensor of the total dark sector, and any split into components (as in dark matter and dark energy) is arbitrary. In fact, just one dark fluid is necessary to obtain exactly the same cosmological and astrophysical phenomenology as the {Lambda}CDM model. We work explicitly the first-order perturbation theory and show that beyond the linear order the dark degeneracy is preserved under some general assumptions. Then we construct the dark fluid from a collection of interacting fluids. Finally, wemore » try to break the degeneracy with a general class of couplings to baryonic matter. Nonetheless, we show that these interactions can also be understood in the context of the {Lambda}CDM model as between dark matter and baryons. For this last investigation we choose two independent parametrizations for the interactions, one inspired by electromagnetism and the other by chameleon theories. Then, we constrain them with a joint analysis of CMB and supernovae observational data.« less

Application of Molecular Interaction Volume Model for Phase Equilibrium of Sn-Based Binary System in Vacuum Distillation

NASA Astrophysics Data System (ADS)

Kong, Lingxin; Yang, Bin; Xu, Baoqiang; Li, Yifu

2014-09-01

Based on the molecular interaction volume model (MIVM), the activities of components of Sn-Sb, Sb-Bi, Sn-Zn, Sn-Cu, and Sn-Ag alloys were predicted. The predicted values are in good agreement with the experimental data, which indicate that the MIVM is of better stability and reliability due to its good physical basis. A significant advantage of the MIVM lies in its ability to predict the thermodynamic properties of liquid alloys using only two parameters. The phase equilibria of Sn-Sb and Sn-Bi alloys were calculated based on the properties of pure components and the activity coefficients, which indicates that Sn-Sb and Sn-Bi alloys can be separated thoroughly by vacuum distillation. This study extends previous investigations and provides an effective and convenient model on which to base refining simulations for Sn-based alloys.

Enhancements to the Water Erosion Prediction Project (WEPP) for modeling large snow-dominated mountainous forest watersheds

Treesearch

Anurag Srivastava; Joan Q. Wu; William J. Elliot; Erin S. Brooks

2015-01-01

The Water Erosion Prediction Project (WEPP) model, originally developed for hillslope and small watershed applications, simulates complex interactive processes influencing erosion. Recent incorporations to the model have improved the subsurface hydrology components for forest applications. Incorporation of channel routing has made the WEPP model well suited for large...

Integrative Analysis of Subcellular Quantitative Proteomics Studies Reveals Functional Cytoskeleton Membrane-Lipid Raft Interactions in Cancer.

PubMed

Shah, Anup D; Inder, Kerry L; Shah, Alok K; Cristino, Alexandre S; McKie, Arthur B; Gabra, Hani; Davis, Melissa J; Hill, Michelle M

2016-10-07

Lipid rafts are dynamic membrane microdomains that orchestrate molecular interactions and are implicated in cancer development. To understand the functions of lipid rafts in cancer, we performed an integrated analysis of quantitative lipid raft proteomics data sets modeling progression in breast cancer, melanoma, and renal cell carcinoma. This analysis revealed that cancer development is associated with increased membrane raft-cytoskeleton interactions, with ∼40% of elevated lipid raft proteins being cytoskeletal components. Previous studies suggest a potential functional role for the raft-cytoskeleton in the action of the putative tumor suppressors PTRF/Cavin-1 and Merlin. To extend the observation, we examined lipid raft proteome modulation by an unrelated tumor suppressor opioid binding protein cell-adhesion molecule (OPCML) in ovarian cancer SKOV3 cells. In agreement with the other model systems, quantitative proteomics revealed that 39% of OPCML-depleted lipid raft proteins are cytoskeletal components, with microfilaments and intermediate filaments specifically down-regulated. Furthermore, protein-protein interaction network and simulation analysis showed significantly higher interactions among cancer raft proteins compared with general human raft proteins. Collectively, these results suggest increased cytoskeleton-mediated stabilization of lipid raft domains with greater molecular interactions as a common, functional, and reversible feature of cancer cells.

Modeling of DNA and Protein Organization Levels with Cn3D Software

ERIC Educational Resources Information Center

Stasinakis, Panagiotis K.; Nicolaou, Despoina

2017-01-01

The molecular structure of living organisms and the complex interactions amongst its components are the basis for the diversity observed at the macroscopic level. Proteins and nucleic acids are some of the major molecular components, and play a key role in several biological functions, such as those of development and evolution. This article…

Analytic model for academic research productivity having factors, interactions and implications

PubMed Central

2011-01-01

Financial support is dear in academia and will tighten further. How can the research mission be accomplished within new restraints? A model is presented for evaluating source components of academic research productivity. It comprises six factors: funding; investigator quality; efficiency of the research institution; the research mix of novelty, incremental advancement, and confirmatory studies; analytic accuracy; and passion. Their interactions produce output and patterned influences between factors. Strategies for optimizing output are enabled. PMID:22130145

Point sources from dissipative dark matter

NASA Astrophysics Data System (ADS)

Agrawal, Prateek; Randall, Lisa

2017-12-01

If a component of dark matter has dissipative interactions, it can cool to form compact astrophysical objects with higher density than that of conventional cold dark matter (sub)haloes. Dark matter annihilations might then appear as point sources, leading to novel morphology for indirect detection. We explore dissipative models where interaction with the Standard Model might provide visible signals, and show how such objects might give rise to the observed excess in gamma rays arising from the galactic center.

The autophagy interaction network of the aging model Podospora anserina.

PubMed

Philipp, Oliver; Hamann, Andrea; Osiewacz, Heinz D; Koch, Ina

2017-03-27

Autophagy is a conserved molecular pathway involved in the degradation and recycling of cellular components. It is active either as response to starvation or molecular damage. Evidence is emerging that autophagy plays a key role in the degradation of damaged cellular components and thereby affects aging and lifespan control. In earlier studies, it was found that autophagy in the aging model Podospora anserina acts as a longevity assurance mechanism. However, only little is known about the individual components controlling autophagy in this aging model. Here, we report a biochemical and bioinformatics study to detect the protein-protein interaction (PPI) network of P. anserina combining experimental and theoretical methods. We constructed the PPI network of autophagy in P. anserina based on the corresponding networks of yeast and human. We integrated PaATG8 interaction partners identified in an own yeast two-hybrid analysis using ATG8 of P. anserina as bait. Additionally, we included age-dependent transcriptome data. The resulting network consists of 89 proteins involved in 186 interactions. We applied bioinformatics approaches to analyze the network topology and to prove that the network is not random, but exhibits biologically meaningful properties. We identified hub proteins which play an essential role in the network as well as seven putative sub-pathways, and interactions which are likely to be evolutionary conserved amongst species. We confirmed that autophagy-associated genes are significantly often up-regulated and co-expressed during aging of P. anserina. With the present study, we provide a comprehensive biological network of the autophagy pathway in P. anserina comprising PPI and gene expression data. It is based on computational prediction as well as experimental data. We identified sub-pathways, important hub proteins, and evolutionary conserved interactions. The network clearly illustrates the relation of autophagy to aging processes and enables further specific studies to understand autophagy and aging in P. anserina as well as in other systems.

Frontal–Occipital Connectivity During Visual Search

PubMed Central

Pantazatos, Spiro P.; Yanagihara, Ted K.; Zhang, Xian; Meitzler, Thomas

2012-01-01

Abstract Although expectation- and attention-related interactions between ventral and medial prefrontal cortex and stimulus category-selective visual regions have been identified during visual detection and discrimination, it is not known if similar neural mechanisms apply to other tasks such as visual search. The current work tested the hypothesis that high-level frontal regions, previously implicated in expectation and visual imagery of object categories, interact with visual regions associated with object recognition during visual search. Using functional magnetic resonance imaging, subjects searched for a specific object that varied in size and location within a complex natural scene. A model-free, spatial-independent component analysis isolated multiple task-related components, one of which included visual cortex, as well as a cluster within ventromedial prefrontal cortex (vmPFC), consistent with the engagement of both top-down and bottom-up processes. Analyses of psychophysiological interactions showed increased functional connectivity between vmPFC and object-sensitive lateral occipital cortex (LOC), and results from dynamic causal modeling and Bayesian Model Selection suggested bidirectional connections between vmPFC and LOC that were positively modulated by the task. Using image-guided diffusion-tensor imaging, functionally seeded, probabilistic white-matter tracts between vmPFC and LOC, which presumably underlie this effective interconnectivity, were also observed. These connectivity findings extend previous models of visual search processes to include specific frontal–occipital neuronal interactions during a natural and complex search task. PMID:22708993

A Novel Tool for Simulating Aerosol-cloud Interactions with a Sectional Model Implemented to a Large-Eddy Simulator

NASA Astrophysics Data System (ADS)

Tonttila, J.; Romakkaniemi, S.; Kokkola, H.; Maalick, Z.; Korhonen, H.; Liqing, H.

2015-12-01

A new cloud-resolving model setup for studying aerosol-cloud interactions, with a special emphasis on partitioning and wet deposition of semi-volatile aerosol species, is presented. The model is based on modified versions of two well-established model components: the Large-Eddy Simulator (LES) UCLALES, and the sectional aerosol model SALSA, previously employed in the ECHAM climate model family. Implementation of the UCLALES-SALSA is described in detail. As the basis for this work, SALSA has been extended to include a sectional representation of the size distributions of cloud droplets and precipitation. Microphysical processes operating on clouds and precipitation have also been added. Given our main motivation, the cloud droplet size bins are defined according to the dry particle diameter. The droplet wet diameter is solved dynamically through condensation equations, but represents an average droplet diameter inside each size bin. This approach allows for accurate tracking of the aerosol properties inside clouds, but minimizes the computational cost. Since the actual cloud droplet diameter is not fully resolved inside the size bins, processes such as precipitation formation rely on parameterizations. For realistic growth of drizzle drops to rain, which is critical for the aerosol wet deposition, the precipitation size bins are defined according to the actual drop size. With these additions, the implementation of the SALSA model replaces most of the microphysical and thermodynamical components within the LES. The cloud properties and aerosol-cloud interactions simulated by the model are analysed and evaluated against detailed cloud microphysical boxmodel results and in-situ aerosol-cloud interaction observations from the Puijo measurement station in Kuopio, Finland. The ability of the model to reproduce the impacts of wet deposition on the aerosol population is demonstrated.

Neural Modeling and Imaging of the Cortical Interactions Underlying Syllable Production

ERIC Educational Resources Information Center

Guenther, Frank H.; Ghosh, Satrajit S.; Tourville, Jason A.

2006-01-01

This paper describes a neural model of speech acquisition and production that accounts for a wide range of acoustic, kinematic, and neuroimaging data concerning the control of speech movements. The model is a neural network whose components correspond to regions of the cerebral cortex and cerebellum, including premotor, motor, auditory, and…

Online Professional Development: Combining Best Practices from Teacher, Technology and Distance Education

ERIC Educational Resources Information Center

Signer, Barbara

2008-01-01

This article provides a model of online professional development that is consistent with recommendations from the fields of teacher education, technology staff development and online learning. A graduate mathematics education course designed and implemented using the model is presented to exemplify the model's core components and interactions. The…

Characterization of mediators of microbial virulence and innate immunity using the Caenorhabditis elegans host-pathogen model.

PubMed

Alegado, Rosanna A; Campbell, Marianne C; Chen, Will C; Slutz, Sandra S; Tan, Man-Wah

2003-07-01

The soil-borne nematode, Caenorhabditis elegans, is emerging as a versatile model in which to study host-pathogen interactions. The worm model has shown to be particularly effective in elucidating both microbial and animal genes involved in toxin-mediated killing. In addition, recent work on worm infection by a variety of bacterial pathogens has shown that a number of virulence regulatory genes mediate worm susceptibility. Many of these regulatory genes, including the PhoP/Q two-component regulators in Salmonella and LasR in Pseudomonas aeruginosa, have also been implicated in mammalian models suggesting that findings in the worm model will be relevant to other systems. In keeping with this concept, experiments aimed at identifying host innate immunity genes have also implicated pathways that have been suggested to play a role in plants and animals, such as the p38 MAP kinase pathway. Despite rapid forward progress using this model, much work remains to be done including the design of more sensitive methods to find effector molecules and further characterization of the exact interaction between invading pathogens and C. elegans' cellular components.

[Evaluate drug interaction of multi-components in Morus alba leaves based on α-glucosidase inhibitory activity].

PubMed

Ji, Tao; Su, Shu-Lan; Guo, Sheng; Qian, Da-Wei; Ouyang, Zhen; Duan, Jin-Ao

2016-06-01

Column chromatography was used for enrichment and separation of flavonoids, alkaloids and polysaccharides from the extracts of Morus alba leaves; glucose oxidase method was used with sucrose as the substrate to evaluate the multi-components of M. alba leaves in α-glucosidase inhibitory models; isobole method, Chou-Talalay combination index analysis and isobolographic analysis were used to evaluate the interaction effects and dose-effect characteristics of two components, providing scientific basis for revealing the hpyerglycemic mechanism of M. alba leaves. The components analysis showed that flavonoid content was 5.3%; organic phenolic acids content was 10.8%; DNJ content was 39.4%; and polysaccharide content was 18.9%. Activity evaluation results demonstrated that flavonoids, alkaloids and polysaccharides of M. alba leaves had significant inhibitory effects on α-glucosidase, and the inhibitory rate was increased with the increasing concentration. Alkaloids showed most significant inhibitory effects among these three components. Both compatibility of alkaloids and flavonoids, and the compatibility of alkaloids and polysaccharides demonstrated synergistic effects, but the compatibility of flavonoids and polysaccharides showed no obvious synergistic effects. The results have confirmed the interaction of multi-components from M. alba leaves to regulate blood sugar, and provided scientific basis for revealing hpyerglycemic effectiveness and mechanism of the multi-components from M. alba leaves. Copyright© by the Chinese Pharmaceutical Association.

bioWidgets: data interaction components for genomics.

PubMed

Fischer, S; Crabtree, J; Brunk, B; Gibson, M; Overton, G C

1999-10-01

The presentation of genomics data in a perspicuous visual format is critical for its rapid interpretation and validation. Relatively few public database developers have the resources to implement sophisticated front-end user interfaces themselves. Accordingly, these developers would benefit from a reusable toolkit of user interface and data visualization components. We have designed the bioWidget toolkit as a set of JavaBean components. It includes a wide array of user interface components and defines an architecture for assembling applications. The toolkit is founded on established software engineering design patterns and principles, including componentry, Model-View-Controller, factored models and schema neutrality. As a proof of concept, we have used the bioWidget toolkit to create three extendible applications: AnnotView, BlastView and AlignView.

Modeling of intracerebral interictal epileptic discharges: Evidence for network interactions.

PubMed

Meesters, Stephan; Ossenblok, Pauly; Colon, Albert; Wagner, Louis; Schijns, Olaf; Boon, Paul; Florack, Luc; Fuster, Andrea

2018-06-01

The interictal epileptic discharges (IEDs) occurring in stereotactic EEG (SEEG) recordings are in general abundant compared to ictal discharges, but difficult to interpret due to complex underlying network interactions. A framework is developed to model these network interactions. To identify the synchronized neuronal activity underlying the IEDs, the variation in correlation over time of the SEEG signals is related to the occurrence of IEDs using the general linear model. The interdependency is assessed of the brain areas that reflect highly synchronized neural activity by applying independent component analysis, followed by cluster analysis of the spatial distributions of the independent components. The spatiotemporal interactions of the spike clusters reveal the leading or lagging of brain areas. The analysis framework was evaluated for five successfully operated patients, showing that the spike cluster that was related to the MRI-visible brain lesions coincided with the seizure onset zone. The additional value of the framework was demonstrated for two more patients, who were MRI-negative and for whom surgery was not successful. A network approach is promising in case of complex epilepsies. Analysis of IEDs is considered a valuable addition to routine review of SEEG recordings, with the potential to increase the success rate of epilepsy surgery. Copyright © 2018 International Federation of Clinical Neurophysiology. Published by Elsevier B.V. All rights reserved.

More on the holographic Ricci dark energy model: smoothing Rips through interaction effects?

PubMed

Bouhmadi-López, Mariam; Errahmani, Ahmed; Ouali, Taoufik; Tavakoli, Yaser

2018-01-01

The background cosmological dynamics of the late Universe is analysed on the framework of a dark energy model described by an holographic Ricci dark energy component. Several kind of interactions between the dark energy and the dark matter components are considered herein. We solve the background cosmological dynamics for the different choices of interactions with the aim to analyse not only the current evolution of the universe but also its asymptotic behaviour and, in particular, possible future singularities removal. We show that in most of the cases, the Big Rip singularity, a finger print of this model in absence of an interaction between the dark sectors, is substituted by a de Sitter or a Minkowski state. Most importantly, we found two new future bouncing solutions leading to two possible asymptotic behaviours, we named Little Bang and Little Sibling of the Big Bang. At a Little Bang, as the size of the universe shrinks to zero in an infinite cosmic time, the Hubble rate and its cosmic time derivative blow up. In addition, at a Little sibling of the Big Bang, as the size of the universe shrinks to zero in an infinite cosmic time, the Hubble rate blows up but its cosmic time derivative is finite. These two abrupt events can happen as well in the past.

More on the holographic Ricci dark energy model: smoothing Rips through interaction effects?

NASA Astrophysics Data System (ADS)

Bouhmadi-López, Mariam; Errahmani, Ahmed; Ouali, Taoufik; Tavakoli, Yaser

2018-04-01

The background cosmological dynamics of the late Universe is analysed on the framework of a dark energy model described by an holographic Ricci dark energy component. Several kind of interactions between the dark energy and the dark matter components are considered herein. We solve the background cosmological dynamics for the different choices of interactions with the aim to analyse not only the current evolution of the universe but also its asymptotic behaviour and, in particular, possible future singularities removal. We show that in most of the cases, the Big Rip singularity, a finger print of this model in absence of an interaction between the dark sectors, is substituted by a de Sitter or a Minkowski state. Most importantly, we found two new future bouncing solutions leading to two possible asymptotic behaviours, we named Little Bang and Little Sibling of the Big Bang. At a Little Bang, as the size of the universe shrinks to zero in an infinite cosmic time, the Hubble rate and its cosmic time derivative blow up. In addition, at a Little sibling of the Big Bang, as the size of the universe shrinks to zero in an infinite cosmic time, the Hubble rate blows up but its cosmic time derivative is finite. These two abrupt events can happen as well in the past.

Viscous Dissipation in One-Dimensional Quantum Liquids

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

Matveev, K. A.; Pustilnik, M.

We develop a theory of viscous dissipation in one-dimensional single-component quantum liquids at low temperatures. Such liquids are characterized by a single viscosity coefficient, the bulk viscosity. We show that for a generic interaction between the constituent particles this viscosity diverges in the zerotemperature limit. In the special case of integrable models, the viscosity is infinite at any temperature, which can be interpreted as a breakdown of the hydrodynamic description. In conclusion, our consideration is applicable to all single-component Galilean- invariant one-dimensional quantum liquids, regardless of the statistics of the constituent particles and the interaction strength.

Viscous Dissipation in One-Dimensional Quantum Liquids

DOE PAGES

Matveev, K. A.; Pustilnik, M.

2017-07-20

We develop a theory of viscous dissipation in one-dimensional single-component quantum liquids at low temperatures. Such liquids are characterized by a single viscosity coefficient, the bulk viscosity. We show that for a generic interaction between the constituent particles this viscosity diverges in the zerotemperature limit. In the special case of integrable models, the viscosity is infinite at any temperature, which can be interpreted as a breakdown of the hydrodynamic description. In conclusion, our consideration is applicable to all single-component Galilean- invariant one-dimensional quantum liquids, regardless of the statistics of the constituent particles and the interaction strength.

ILP-2 modeling and virtual screening of an FDA-approved library:a possible anticancer therapy.

PubMed

Khalili, Saeed; Mohammadpour, Hemn; Shokrollahi Barough, Mahideh; Kokhaei, Parviz

2016-06-23

The members of the inhibitors of apoptosis protein (IAP) family inhibit diverse components of the caspase signaling pathway, notably caspase 3, 7, and 9. ILP-2 (BIRC-8) is the most recently identified member of the IAPs, mainly interacting with caspase 9. This interaction would eventually lead to death resistance in the case of cancerous cells. Therefore, structural modeling of ILP-2 and finding applicable inhibitors of its interaction with caspase 9 are a compelling challenge. Three main protein modeling approaches along with various model refinement measures were harnessed to achieve a reliable 3D model, using state-of-the-art software. Thereafter, the selected model was employed to perform virtual screening of an FDA approved library. A model built by a combinatorial approach (homology and ab initio approaches) was chosen as the best model. Model refinement processes successfully bolstered the model quality. Virtual screening of the compound library introduced several high affinity inhibitor candidates that interact with functional residues of ILP2. Given the 3D structure of the ILP2 molecule, we found promising inhibitory molecules. In addition to high affinity towards the ILP2 molecule, these molecules interact with residues that play pivotal rules in ILP2-caspase interaction. These molecules would inhibit ILP2-caspase interaction and consequently would lead to reactivated cell apoptosis through the caspases pathway.

Rule-Based Simulation of Multi-Cellular Biological Systems—A Review of Modeling Techniques

PubMed Central

Hwang, Minki; Garbey, Marc; Berceli, Scott A.; Tran-Son-Tay, Roger

2011-01-01

Emergent behaviors of multi-cellular biological systems (MCBS) result from the behaviors of each individual cells and their interactions with other cells and with the environment. Modeling MCBS requires incorporating these complex interactions among the individual cells and the environment. Modeling approaches for MCBS can be grouped into two categories: continuum models and cell-based models. Continuum models usually take the form of partial differential equations, and the model equations provide insight into the relationship among the components in the system. Cell-based models simulate each individual cell behavior and interactions among them enabling the observation of the emergent system behavior. This review focuses on the cell-based models of MCBS, and especially, the technical aspect of the rule-based simulation method for MCBS is reviewed. How to implement the cell behaviors and the interactions with other cells and with the environment into the computational domain is discussed. The cell behaviors reviewed in this paper are division, migration, apoptosis/necrosis, and differentiation. The environmental factors such as extracellular matrix, chemicals, microvasculature, and forces are also discussed. Application examples of these cell behaviors and interactions are presented. PMID:21369345

Predator diversity and environmental change modify the strengths of trophic and nontrophic interactions.

PubMed

Sentis, Arnaud; Gémard, Charlène; Jaugeon, Baptiste; Boukal, David S

2017-07-01

Understanding the dependence of species interaction strengths on environmental factors and species diversity is crucial to predict community dynamics and persistence in a rapidly changing world. Nontrophic (e.g. predator interference) and trophic components together determine species interaction strengths, but the effects of environmental factors on these two components remain largely unknown. This impedes our ability to fully understand the links between environmental drivers and species interactions. Here, we used a dynamical modelling framework based on measured predator functional responses to investigate the effects of predator diversity, prey density, and temperature on trophic and nontrophic interaction strengths within a freshwater food web. We found that (i) species interaction strengths cannot be predicted from trophic interactions alone, (ii) nontrophic interaction strengths vary strongly among predator assemblages, (iii) temperature has opposite effects on trophic and nontrophic interaction strengths, and (iv) trophic interaction strengths decrease with prey density, whereas the dependence of nontrophic interaction strengths on prey density is concave up. Interestingly, the qualitative impacts of temperature and prey density on the strengths of trophic and nontrophic interactions were independent of predator identity, suggesting a general pattern. Our results indicate that taking multiple environmental factors and the nonlinearity of density-dependent species interactions into account is an important step towards a better understanding of the effects of environmental variations on complex ecological communities. The functional response approach used in this study opens new avenues for (i) the quantification of the relative importance of the trophic and nontrophic components in species interactions and (ii) a better understanding how environmental factors affect these interactions and the dynamics of ecological communities. © 2016 John Wiley & Sons Ltd.

Interactive effects of global change factors on soil respiration and its components: a meta-analysis.

PubMed

Zhou, Lingyan; Zhou, Xuhui; Shao, Junjiong; Nie, Yuanyuan; He, Yanghui; Jiang, Liling; Wu, Zhuoting; Hosseini Bai, Shahla

2016-09-01

As the second largest carbon (C) flux between the atmosphere and terrestrial ecosystems, soil respiration (Rs) plays vital roles in regulating atmospheric CO2 concentration ([CO2 ]) and climatic dynamics in the earth system. Although numerous manipulative studies and a few meta-analyses have been conducted to determine the responses of Rs and its two components [i.e., autotrophic (Ra) and heterotrophic (Rh) respiration] to single global change factors, the interactive effects of the multiple factors are still unclear. In this study, we performed a meta-analysis of 150 multiple-factor (≥2) studies to examine the main and interactive effects of global change factors on Rs and its two components. Our results showed that elevated [CO2 ] (E), nitrogen addition (N), irrigation (I), and warming (W) induced significant increases in Rs by 28.6%, 8.8%, 9.7%, and 7.1%, respectively. The combined effects of the multiple factors, EN, EW, DE, IE, IN, IW, IEW, and DEW, were also significantly positive on Rs to a greater extent than those of the single-factor ones. For all the individual studies, the additive interactions were predominant on Rs (90.6%) and its components (≈70.0%) relative to synergistic and antagonistic ones. However, the different combinations of global change factors (e.g., EN, NW, EW, IW) indicated that the three types of interactions were all important, with two combinations for synergistic effects, two for antagonistic, and five for additive when at least eight independent experiments were considered. In addition, the interactions of elevated [CO2 ] and warming had opposite effects on Ra and Rh, suggesting that different processes may influence their responses to the multifactor interactions. Our study highlights the crucial importance of the interactive effects among the multiple factors on Rs and its components, which could inform regional and global models to assess the climate-biosphere feedbacks and improve predictions of the future states of the ecological and climate systems. © 2016 John Wiley & Sons Ltd.

Modeling complex and multi-component food systems in molecular dynamics simulations on the example of chocolate conching.

PubMed

Greiner, Maximilian; Sonnleitner, Bettina; Mailänder, Markus; Briesen, Heiko

2014-02-01

Additional benefits of foods are an increasing factor in the consumer's purchase. To produce foods with the properties the consumer demands, understanding the micro- and nanostructure is becoming more important in food research today. We present molecular dynamics (MD) simulations as a tool to study complex and multi-component food systems on the example of chocolate conching. The process of conching is chosen because of the interesting challenges it provides: the components (fats, emulsifiers and carbohydrates) contain diverse functional groups, are naturally fluctuating in their chemical composition, and have a high number of internal degrees of freedom. Further, slow diffusion in the non-aqueous medium is expected. All of these challenges are typical to food systems in general. Simulation results show the suitability of present force fields to correctly model the liquid and crystal density of cocoa butter and sucrose, respectively. Amphiphilic properties of emulsifiers are observed by micelle formation in water. For non-aqueous media, pulling simulations reveal high energy barriers for motion in the viscous cocoa butter. The work for detachment of an emulsifier from the sucrose crystal is calculated and matched with detachment of the head and tail groups separately. Hydrogen bonding is shown to be the dominant interaction between the emulsifier and the crystal surface. Thus, MD simulations are suited to model the interaction between the emulsifier and sugar crystal interface in non-aqueous media, revealing detailed information about the structuring and interactions on a molecular level. With interaction parameters being available for a wide variety of chemical groups, MD simulations are a valuable tool to understand complex and multi-component food systems in general. MD simulations provide a substantial benefit to researchers to verify their hypothesis in dynamic simulations with an atomistic resolution. Rapid rise of computational resources successively increases the complexity and the size of the systems that can be studied.

The permeability characteristics and interaction of main components from Si-Ni-San in a MDCK epithelial cell monolayer model.

PubMed

Chen, Ruonan; Shen, Chenlin; Xu, Qingqing; Liu, Yaru; Li, Bo; Huang, Cheng; Ma, Taotao; Meng, Xiaoming; Wu, Maomao; Li, Jun

2017-07-26

1. Si-Ni-San (SNS) possesses extensive therapeutic effects, however, the extent to which main components are absorbed and the mechanisms involved are controversial. 2. In this study, MDCK cell model was used to determine the permeability characteristics and interaction between the major components of Si-Ni-San, including saikosaponin a, paeoniflorin, naringin and glycyrrhizic acid. 3. The transport of the major components was concentration-dependent in both directions. Moreover, the transport of paeoniflorin, naringin and glycyrrhizic acid was significantly reduced at 4°C or in the presence of NaN3. Additionally, the efflux of paeoniflorin and naringin were apparently reduced in the presence of P-gp inhibitor verapamil. The transport of glycyrrhizic acid was clearly inhibited by the inhibitors of MRP2, indicating that MRP2 may be involved in the transport of glycyrrhizic acid. However, the results indicated that saikosaponin a was absorbed mainly by passive diffusion. Furthermore, the combined incubation of four major components had a powerful sorbefacient effect than a single drug used alone which may be regulated by tight junctions. 4. Taken together, our study provides useful information for pharmacological applications of Si-Ni-San and offers new insights into this ancient decoction for further researches, especially in drug synergism.

Phase separation in an exactly solvable model binary solution with three-body interactions and intermolecular bonding.

PubMed

Lungu, Radu P; Huckaby, Dale A; Buzatu, Florin D

2006-02-01

A model is presented in which the bonds of a honeycomb lattice are covered by rodlike molecules of types AA and BB, molecular ends near a common site having both three-body interactions and orientation-dependent bonding between two A molecular ends and between an A and a B molecular end. Phase diagrams corresponding to the separation into AA-rich and BB-rich phases are calculated exactly. Depending on the relative strengths of the interactions, one of several qualitatively different types of phase diagrams can result, including diagrams containing phenomena such as a double critical point or two separate asymmetric closed loops. The model is essentially a limiting case of a previously considered ternary solution model, and it is equivalent to a two-component system of interacting A and B molecules on the sites of a kagomé lattice.

Low Frequency Noise Contamination in Fan Model Testing

NASA Technical Reports Server (NTRS)

Brown, Clifford A.; Schifer, Nicholas A.

2008-01-01

Aircraft engine noise research and development depends on the ability to study and predict the noise created by each engine component in isolation. The presence of a downstream pylon for a model fan test, however, may result in noise contamination through pylon interactions with the free stream and model exhaust airflows. Additionally, there is the problem of separating the fan and jet noise components generated by the model fan. A methodology was therefore developed to improve the data quality for the 9 15 Low Speed Wind Tunnel (LSWT) at the NASA Glenn Research Center that identifies three noise sources: fan noise, jet noise, and rig noise. The jet noise and rig noise were then measured by mounting a scale model of the 9 15 LSWT model fan installation in a jet rig to simulate everything except the rotating machinery and in duct components of fan noise. The data showed that the spectra measured in the LSWT has a strong rig noise component at frequencies as high as 3 kHz depending on the fan and airflow fan exit velocity. The jet noise was determined to be significantly lower than the rig noise (i.e., noise generated by flow interaction with the downstream support pylon). A mathematical model for the rig noise was then developed using a multi-dimensional least squares fit to the rig noise data. This allows the rig noise to be subtracted or removed, depending on the amplitude of the rig noise relative to the fan noise, at any given frequency, observer angle, or nozzle pressure ratio. The impact of isolating the fan noise with this method on spectra, overall power level (OAPWL), and Effective Perceived Noise Level (EPNL) is studied.

Solution to urn models of pairwise interaction with application to social, physical, and biological sciences

NASA Astrophysics Data System (ADS)

Pickering, William; Lim, Chjan

2017-07-01

We investigate a family of urn models that correspond to one-dimensional random walks with quadratic transition probabilities that have highly diverse applications. Well-known instances of these two-urn models are the Ehrenfest model of molecular diffusion, the voter model of social influence, and the Moran model of population genetics. We also provide a generating function method for diagonalizing the corresponding transition matrix that is valid if and only if the underlying mean density satisfies a linear differential equation and express the eigenvector components as terms of ordinary hypergeometric functions. The nature of the models lead to a natural extension to interaction between agents in a general network topology. We analyze the dynamics on uncorrelated heterogeneous degree sequence networks and relate the convergence times to the moments of the degree sequences for various pairwise interaction mechanisms.

Mouse Models for Unraveling the Importance of Diet in Colon Cancer Prevention

PubMed Central

Tammariello, Alexandra E.; Milner, John A.

2010-01-01

Diet and genetics are both considered important risk determinants for colorectal cancer, a leading cause of death worldwide. Several genetically engineered mouse models have been created, including the ApcMin mouse, to aid in the identification of key cancer related processes and to assist with the characterization of environmental factors, including the diet, which influence risk. Current research using these models provides evidence that several bioactive food components can inhibit genetically predisposed colorectal cancer, while others increase risk. Specifically, calorie restriction or increased exposure to n-3 fatty acids, sulforaphane, chafuroside, curcumin, and dibenzoylmethane were reported protective. Total fat, calories and all-trans retinoic acid are associated with an increased risk. Unraveling the importance of specific dietary components in these models is complicated by the basal diet used, the quantity of test components provided, and interactions among food components. Newer models are increasingly available to evaluate fundamental cellular processes, including DNA mismatch repair, immune function and inflammation as markers for colon cancer risk. Unfortunately, these models have been used infrequently to examine the influence of specific dietary components. The enhanced use of these models can shed mechanistic insights about the involvement of specific bioactive food and components and energy as determinants of colon cancer risk. However, the use of available mouse models to exactly represent processes important to human gastrointestinal cancers will remain a continued scientific challenge. PMID:20122631

Evolving hard problems: Generating human genetics datasets with a complex etiology.

PubMed

Himmelstein, Daniel S; Greene, Casey S; Moore, Jason H

2011-07-07

A goal of human genetics is to discover genetic factors that influence individuals' susceptibility to common diseases. Most common diseases are thought to result from the joint failure of two or more interacting components instead of single component failures. This greatly complicates both the task of selecting informative genetic variants and the task of modeling interactions between them. We and others have previously developed algorithms to detect and model the relationships between these genetic factors and disease. Previously these methods have been evaluated with datasets simulated according to pre-defined genetic models. Here we develop and evaluate a model free evolution strategy to generate datasets which display a complex relationship between individual genotype and disease susceptibility. We show that this model free approach is capable of generating a diverse array of datasets with distinct gene-disease relationships for an arbitrary interaction order and sample size. We specifically generate eight-hundred Pareto fronts; one for each independent run of our algorithm. In each run the predictiveness of single genetic variation and pairs of genetic variants have been minimized, while the predictiveness of third, fourth, or fifth-order combinations is maximized. Two hundred runs of the algorithm are further dedicated to creating datasets with predictive four or five order interactions and minimized lower-level effects. This method and the resulting datasets will allow the capabilities of novel methods to be tested without pre-specified genetic models. This allows researchers to evaluate which methods will succeed on human genetics problems where the model is not known in advance. We further make freely available to the community the entire Pareto-optimal front of datasets from each run so that novel methods may be rigorously evaluated. These 76,600 datasets are available from http://discovery.dartmouth.edu/model_free_data/.

Matter rogue waves in an F=1 spinor Bose-Einstein condensate.

PubMed

Qin, Zhenyun; Mu, Gui

2012-09-01

We report new types of matter rogue waves of a spinor (three-component) model of the Bose-Einstein condensate governed by a system of three nonlinearly coupled Gross-Pitaevskii equations. The exact first-order rational solutions containing one free parameter are obtained by means of a Darboux transformation for the integrable system where the mean-field interaction is attractive and the spin-exchange interaction is ferromagnetic. For different choices of the parameter, there exists a variety of different shaped solutions including two peaks in bright rogue waves and four dips in dark rogue waves. Furthermore, by utilizing the relation between the three-component and the one-component versions of the nonlinear Schrödinger equation, we can devise higher-order rational solutions, in which three components have different shapes. In addition, it is noteworthy that dark rogue wave features disappear in the third-order rational solution.

Self-criticism interacts with the affective component of pain to predict depressive symptoms in female patients.

PubMed

Lerman, S F; Shahar, G; Rudich, Z

2012-01-01

This longitudinal study examined the role of the trait of self-criticism as a moderator of the relationship between the affective and sensory components of pain, and depression. One hundred and sixty-three chronic pain patients treated at a specialty pain clinic completed self-report questionnaires at two time points assessing affective and sensory components of pain, depression, and self-criticism. Hierarchical linear regression analysis revealed a significant 3-way interaction between self-criticism, affective pain and gender, whereby women with high affective pain and high self-criticism demonstrated elevated levels of depression. Our findings are the first to show within a broad, comprehensive model, that selfcriticism is activated by the affective, but not sensory component of pain in leading to depressive symptoms, and highlight the need to assess patients' personality as part of an effective treatment plan. © 2011 European Federation of International Association for the Study of Pain Chapters.

A Computer Model of the Cardiovascular System for Effective Learning.

ERIC Educational Resources Information Center

Rothe, Carl F.

1979-01-01

Described is a physiological model which solves a set of interacting, possibly nonlinear, differential equations through numerical integration on a digital computer. Sample printouts are supplied and explained for effects on the components of a cardiovascular system when exercise, hemorrhage, and cardiac failure occur. (CS)

Performance of the AMOEBA Water Model in the Vicinity of QM Solutes: A Diagnosis Using Energy Decomposition Analysis.

PubMed

Mao, Yuezhi; Shao, Yihan; Dziedzic, Jacek; Skylaris, Chris-Kriton; Head-Gordon, Teresa; Head-Gordon, Martin

2017-05-09

The importance of incorporating solvent polarization effects into the modeling of solvation processes has been well-recognized, and therefore a new generation of hybrid quantum mechanics/molecular mechanics (QM/MM) approaches that accounts for this effect is desirable. We present a fully self-consistent, mutually polarizable QM/MM scheme using the AMOEBA force field, in which the total energy of the system is variationally minimized with respect to both the QM electronic density and the MM induced dipoles. This QM/AMOEBA model is implemented through the Q-Chem/LibEFP code interface and then applied to the evaluation of solute-solvent interaction energies for various systems ranging from the water dimer to neutral and ionic solutes (NH 3 , NH 4 + , CN - ) surrounded by increasing numbers of water molecules (up to 100). In order to analyze the resulting interaction energies, we also utilize an energy decomposition analysis (EDA) scheme which identifies contributions from permanent electrostatics, polarization, and van der Waals (vdW) interaction for the interaction between the QM solute and the solvent molecules described by AMOEBA. This facilitates a component-wise comparison against full QM calculations where the corresponding energy components are obtained via a modified version of the absolutely localized molecular orbitals (ALMO)-EDA. The results show that the present QM/AMOEBA model can yield reasonable solute-solvent interaction energies for neutral and cationic species, while further scrutiny reveals that this accuracy highly relies on the delicate balance between insufficiently favorable permanent electrostatics and softened vdW interaction. For anionic solutes where the charge penetration effect becomes more pronounced, the QM/MM interface turns out to be unbalanced. These results are consistent with and further elucidate our findings in a previous study using a slightly different QM/AMOEBA model ( Dziedzic et al. J. Chem. Phys. 2016 , 145 , 124106 ). The implications of these results for further refinement of this model are also discussed.

Evaluation of RCAS Inflow Models for Wind Turbine Analysis

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

Tangler, J.; Bir, G.

The finite element structural modeling in the Rotorcraft Comprehensive Analysis System (RCAS) provides a state-of-the-art approach to aeroelastic analysis. This, coupled with its ability to model all turbine components, results in a methodology that can simulate complex system interactions characteristic of large wind. In addition, RCAS is uniquely capable of modeling advanced control algorithms and the resulting dynamic responses.

Learning Gene Expression through Modelling and Argumentation: A Case Study Exploring the Connections between the Worlds of Knowledge

ERIC Educational Resources Information Center

Puig, Blanca; Ageitos, Noa; Jiménez-Aleixandre, María Pilar

2017-01-01

There is emerging interest on the interactions between modelling and argumentation in specific contexts, such as genetics learning. It has been suggested that modelling might help students understand and argue on genetics. We propose modelling gene expression as a way to learn molecular genetics and diseases with a genetic component. The study is…

Defect modelling in an interactive 3-D CAD environment

NASA Astrophysics Data System (ADS)

Reilly, D.; Potts, A.; McNab, A.; Toft, M.; Chapman, R. K.

2000-05-01

This paper describes enhancement of the NDT Workbench, as presented at QNDE '98, to include theoretical models for the ultrasonic inspection of smooth planar defects, developed by British Energy and BNFL-Magnox Generation. The Workbench is a PC-based software package for the reconstruction, visualization and analysis of 3-D ultrasonic NDT data in an interactive CAD environment. This extension of the Workbeach now provides the user with a well established modelling approach, coupled with a graphical user interface for: a) configuring the model for flaw size, shape, orientation and location; b) flexible specification of probe parameters; c) selection of scanning surface and scan pattern on the CAD component model; d) presentation of the output as a simulated ultrasound image within the component, or as graphical or tabular displays. The defect modelling facilities of the Workbench can be used for inspection procedure assessment and confirmation of data interpretation, by comparison of overlay images generated from real and simulated data. The modelling technique currently implemented is based on the Geometrical Theory of Diffraction, for simulation of strip-like, circular or elliptical crack responses in the time harmonic or time dependent cases. Eventually, the Workbench will also allow modelling using elastodynamic Kirchhoff theory.

A hybridizable discontinuous Galerkin method for modeling fluid-structure interaction

NASA Astrophysics Data System (ADS)

Sheldon, Jason P.; Miller, Scott T.; Pitt, Jonathan S.

2016-12-01

This work presents a novel application of the hybridizable discontinuous Galerkin (HDG) finite element method to the multi-physics simulation of coupled fluid-structure interaction (FSI) problems. Recent applications of the HDG method have primarily been for single-physics problems including both solids and fluids, which are necessary building blocks for FSI modeling. Utilizing these established models, HDG formulations for linear elastostatics, a nonlinear elastodynamic model, and arbitrary Lagrangian-Eulerian Navier-Stokes are derived. The elasticity formulations are written in a Lagrangian reference frame, with the nonlinear formulation restricted to hyperelastic materials. With these individual solid and fluid formulations, the remaining challenge in FSI modeling is coupling together their disparate mathematics on the fluid-solid interface. This coupling is presented, along with the resultant HDG FSI formulation. Verification of the component models, through the method of manufactured solutions, is performed and each model is shown to converge at the expected rate. The individual components, along with the complete FSI model, are then compared to the benchmark problems proposed by Turek and Hron [1]. The solutions from the HDG formulation presented in this work trend towards the benchmark as the spatial polynomial order and the temporal order of integration are increased.

Bayesian Genomic Prediction with Genotype × Environment Interaction Kernel Models

PubMed Central

Cuevas, Jaime; Crossa, José; Montesinos-López, Osval A.; Burgueño, Juan; Pérez-Rodríguez, Paulino; de los Campos, Gustavo

2016-01-01

The phenomenon of genotype × environment (G × E) interaction in plant breeding decreases selection accuracy, thereby negatively affecting genetic gains. Several genomic prediction models incorporating G × E have been recently developed and used in genomic selection of plant breeding programs. Genomic prediction models for assessing multi-environment G × E interaction are extensions of a single-environment model, and have advantages and limitations. In this study, we propose two multi-environment Bayesian genomic models: the first model considers genetic effects (u) that can be assessed by the Kronecker product of variance–covariance matrices of genetic correlations between environments and genomic kernels through markers under two linear kernel methods, linear (genomic best linear unbiased predictors, GBLUP) and Gaussian (Gaussian kernel, GK). The other model has the same genetic component as the first model (u) plus an extra component, f, that captures random effects between environments that were not captured by the random effects u. We used five CIMMYT data sets (one maize and four wheat) that were previously used in different studies. Results show that models with G × E always have superior prediction ability than single-environment models, and the higher prediction ability of multi-environment models with u and f over the multi-environment model with only u occurred 85% of the time with GBLUP and 45% of the time with GK across the five data sets. The latter result indicated that including the random effect f is still beneficial for increasing prediction ability after adjusting by the random effect u. PMID:27793970

Bayesian Genomic Prediction with Genotype × Environment Interaction Kernel Models.

PubMed

Cuevas, Jaime; Crossa, José; Montesinos-López, Osval A; Burgueño, Juan; Pérez-Rodríguez, Paulino; de Los Campos, Gustavo

2017-01-05

The phenomenon of genotype × environment (G × E) interaction in plant breeding decreases selection accuracy, thereby negatively affecting genetic gains. Several genomic prediction models incorporating G × E have been recently developed and used in genomic selection of plant breeding programs. Genomic prediction models for assessing multi-environment G × E interaction are extensions of a single-environment model, and have advantages and limitations. In this study, we propose two multi-environment Bayesian genomic models: the first model considers genetic effects [Formula: see text] that can be assessed by the Kronecker product of variance-covariance matrices of genetic correlations between environments and genomic kernels through markers under two linear kernel methods, linear (genomic best linear unbiased predictors, GBLUP) and Gaussian (Gaussian kernel, GK). The other model has the same genetic component as the first model [Formula: see text] plus an extra component, F: , that captures random effects between environments that were not captured by the random effects [Formula: see text] We used five CIMMYT data sets (one maize and four wheat) that were previously used in different studies. Results show that models with G × E always have superior prediction ability than single-environment models, and the higher prediction ability of multi-environment models with [Formula: see text] over the multi-environment model with only u occurred 85% of the time with GBLUP and 45% of the time with GK across the five data sets. The latter result indicated that including the random effect f is still beneficial for increasing prediction ability after adjusting by the random effect [Formula: see text]. Copyright © 2017 Cuevas et al.

Coarse-grained component concurrency in Earth system modeling: parallelizing atmospheric radiative transfer in the GFDL AM3 model using the Flexible Modeling System coupling framework

NASA Astrophysics Data System (ADS)

Balaji, V.; Benson, Rusty; Wyman, Bruce; Held, Isaac

2016-10-01

Climate models represent a large variety of processes on a variety of timescales and space scales, a canonical example of multi-physics multi-scale modeling. Current hardware trends, such as Graphical Processing Units (GPUs) and Many Integrated Core (MIC) chips, are based on, at best, marginal increases in clock speed, coupled with vast increases in concurrency, particularly at the fine grain. Multi-physics codes face particular challenges in achieving fine-grained concurrency, as different physics and dynamics components have different computational profiles, and universal solutions are hard to come by. We propose here one approach for multi-physics codes. These codes are typically structured as components interacting via software frameworks. The component structure of a typical Earth system model consists of a hierarchical and recursive tree of components, each representing a different climate process or dynamical system. This recursive structure generally encompasses a modest level of concurrency at the highest level (e.g., atmosphere and ocean on different processor sets) with serial organization underneath. We propose to extend concurrency much further by running more and more lower- and higher-level components in parallel with each other. Each component can further be parallelized on the fine grain, potentially offering a major increase in the scalability of Earth system models. We present here first results from this approach, called coarse-grained component concurrency, or CCC. Within the Geophysical Fluid Dynamics Laboratory (GFDL) Flexible Modeling System (FMS), the atmospheric radiative transfer component has been configured to run in parallel with a composite component consisting of every other atmospheric component, including the atmospheric dynamics and all other atmospheric physics components. We will explore the algorithmic challenges involved in such an approach, and present results from such simulations. Plans to achieve even greater levels of coarse-grained concurrency by extending this approach within other components, such as the ocean, will be discussed.

Chapter 15: Potential Surprises: Compound Extremes and Tipping Elements

NASA Technical Reports Server (NTRS)

Kopp, R. E.; Hayhoe, K.; Easterling, D. R.; Hall, T.; Horton, R.; Kunkel, K. E.; LeGrande, A. N.

2017-01-01

The Earth system is made up of many components that interact in complex ways across a broad range of temporal and spatial scales. As a result of these interactions the behavior of the system cannot be predicted by looking at individual components in isolation. Negative feedbacks, or self-stabilizing cycles, within and between components of the Earth system can dampen changes (Ch. 2: Physical Drivers of Climate Change). However, their stabilizing effects render such feedbacks of less concern from a risk perspective than positive feedbacks, or self-reinforcing cycles. Positive feedbacks magnify both natural and anthropogenic changes. Some Earth system components, such as arctic sea ice and the polar ice sheets, may exhibit thresholds beyond which these self-reinforcing cycles can drive the component, or the entire system, into a radically different state. Although the probabilities of these state shifts may be difficult to assess, their consequences could be high, potentially exceeding anything anticipated by climate model projections for the coming century.

Global water cycle

NASA Technical Reports Server (NTRS)

Robertson, Franklin R.; Christy, John R.; Goodman, Steven J.; Miller, Tim L.; Fitzjarrald, Dan; Lapenta, Bill; Wang, Shouping

1991-01-01

The primary objective is to determine the scope and interactions of the global water cycle with all components of the Earth system and to understand how it stimulates and regulates changes on both global and regional scales. The following subject areas are covered: (1) water vapor variability; (2) multi-phase water analysis; (3) diabatic heating; (4) MSU (Microwave Sounding Unit) temperature analysis; (5) Optimal precipitation and streamflow analysis; (6) CCM (Community Climate Model) hydrological cycle; (7) CCM1 climate sensitivity to lower boundary forcing; and (8) mesoscale modeling of atmosphere/surface interaction.

Covariant spectator theory of np scattering: Deuteron quadrupole moment

DOE PAGES

Gross, Franz

2015-01-26

The deuteron quadrupole moment is calculated using two CST model wave functions obtained from the 2007 high precision fits to np scattering data. Included in the calculation are a new class of isoscalar np interaction currents automatically generated by the nuclear force model used in these fits. The prediction for model WJC-1, with larger relativistic P-state components, is 2.5% smaller that the experiential result, in common with the inability of models prior to 2014 to predict this important quantity. However, model WJC-2, with very small P-state components, gives agreement to better than 1%, similar to the results obtained recently frommore » XEFT predictions to order N 3LO.« less

Thought and talk. The intrapersonal component of human communication.

PubMed

Farley, M J

1992-09-01

The intrapersonal component of human communication, self-talk, influences what we say and how we respond to another in interpersonal dialogues. A model of communication that incorporates the notion of self-talk, both that of the speaker and that of the listener, is useful in assisting nurses in making more realistic appraisals of communication interactions and addressing problems in communication failures.

Running vacuum cosmological models: linear scalar perturbations

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

Perico, E.L.D.; Tamayo, D.A., E-mail: elduartep@usp.br, E-mail: tamayo@if.usp.br

In cosmology, phenomenologically motivated expressions for running vacuum are commonly parameterized as linear functions typically denoted by Λ( H {sup 2}) or Λ( R ). Such models assume an equation of state for the vacuum given by P-bar {sub Λ} = - ρ-bar {sub Λ}, relating its background pressure P-bar {sub Λ} with its mean energy density ρ-bar {sub Λ} ≡ Λ/8π G . This equation of state suggests that the vacuum dynamics is due to an interaction with the matter content of the universe. Most of the approaches studying the observational impact of these models only consider the interactionmore » between the vacuum and the transient dominant matter component of the universe. We extend such models by assuming that the running vacuum is the sum of independent contributions, namely ρ-bar {sub Λ} = Σ {sub i} ρ-bar {sub Λ} {sub i} . Each Λ i vacuum component is associated and interacting with one of the i matter components in both the background and perturbation levels. We derive the evolution equations for the linear scalar vacuum and matter perturbations in those two scenarios, and identify the running vacuum imprints on the cosmic microwave background anisotropies as well as on the matter power spectrum. In the Λ( H {sup 2}) scenario the vacuum is coupled with every matter component, whereas the Λ( R ) description only leads to a coupling between vacuum and non-relativistic matter, producing different effects on the matter power spectrum.« less

Problematic Internet use and problematic alcohol use from the cognitive-behavioral model: a longitudinal study among adolescents.

PubMed

Gámez-Guadix, Manuel; Calvete, Esther; Orue, Izaskun; Las Hayas, Carlota

2015-01-01

Problematic Internet use (PIU) and problematic alcohol use are two pervasive problems during adolescence that share similar characteristics and predictors. The first objective of this study was to analyze the temporal and reciprocal relationships among the main components of PIU from the cognitive-behavioral model (preference for online social interaction, mood regulation through the Internet, deficient self-regulation, and negative consequences). The second objective was to examine the temporal and reciprocal relationships between PIU components and problematic alcohol use. We also examined whether these relationships differ between males and females. The sample comprised 801 Spanish adolescents (mean age=14.92, SD=1.01) who completed the measures both at Time 1 (T1) and Time 2 (T2) six months apart. We used structural equation modeling to analyze the relationship among the variables. Results showed that deficient self-regulation at T1 predicted an increase in preference for online interactions, mood regulation, and negative consequences of the Internet at T2. In turn, the emergence of negative consequences of PIU at T1 predicted a rise in problematic alcohol use at T2. Longitudinal relationships between different components of PIU and between the components of PIU and problematic alcohol use were invariant across genders. Deficient self-regulation, consisting of diminished self-control over cognition and behaviors related to the Internet, plays a central role in the maintenance of PIU, increasing the preference for online interactions, mood regulation, and negative consequences from Internet use over time. In turn, adolescents who present negative consequences of PIU are vulnerable targets for problematic alcohol use. Copyright © 2014 Elsevier Ltd. All rights reserved.

Simultaneous determination of intestinal permeability and potential drug interactions of complex mixtures using Caco-2 cells and high-resolution mass spectrometry: Studies with Rauwolfia serpentina extract.

PubMed

Flynn, Thomas J; Vohra, Sanah N

2018-06-25

Caco-2 cells are a commonly used model for estimating the intestinal bioavailability of single chemical entity pharmaceuticals. Caco-2 cells, when induced with calcitriol, also express other biological functions such as phase I (CYP) and phase II (glucuronosyltransferases) drug metabolizing enzymes which are relevant to drug-supplement interactions. Intestinal bioavailability is an important factor in the overall safety assessment of products consumed orally. Foods, including herbal dietary supplements, are complex substances with multiple chemical components. Because of potential interactions between components of complex mixtures, more reliable safety assessments can be obtained by studying the commercial products "as consumed" rather than by testing individual chemical components one at a time. The present study evaluated the apparent intestinal permeability (P app ) of a model herbal extract, Rauwolfia serpentina, using both whole plant extracts and the individual purified Rauwolfia alkaloids. All test compounds, endpoint substrates, and their metabolites were quantified using liquid chromatography and high-resolution mass spectrometry. The P app values for individual Rauwolfia alkaloids were comparable whether measured individually or as components of the complete extract. Both Rauwolfia extract and all individual Rauwolfia alkaloids except yohimbine inhibited CYP3A4 activity (midazolam 1'-hydroxylation). Both Rauwolfia extract and all individual Rauwolfia alkaloids except corynanthine and reserpic acid significantly increased glucuronosyltransferase activity (glucuronidation of 4-methylumbelliferone). The positive control, ketoconazole, significantly inhibited both CYP3A4 and glucuronosyltransferase activities. These findings suggest that the Caco-2 assay is capable of simultaneously identifying both bioavailability and potentially hazardous intestinal drug-supplement interactions in complex mixtures. Published by Elsevier B.V.

A Component-Based Extension Framework for Large-Scale Parallel Simulations in NEURON

PubMed Central

King, James G.; Hines, Michael; Hill, Sean; Goodman, Philip H.; Markram, Henry; Schürmann, Felix

2008-01-01

As neuronal simulations approach larger scales with increasing levels of detail, the neurosimulator software represents only a part of a chain of tools ranging from setup, simulation, interaction with virtual environments to analysis and visualizations. Previously published approaches to abstracting simulator engines have not received wide-spread acceptance, which in part may be to the fact that they tried to address the challenge of solving the model specification problem. Here, we present an approach that uses a neurosimulator, in this case NEURON, to describe and instantiate the network model in the simulator's native model language but then replaces the main integration loop with its own. Existing parallel network models are easily adopted to run in the presented framework. The presented approach is thus an extension to NEURON but uses a component-based architecture to allow for replaceable spike exchange components and pluggable components for monitoring, analysis, or control that can run in this framework alongside with the simulation. PMID:19430597

Theoretical models for coronary vascular biomechanics: Progress & challenges

PubMed Central

Waters, Sarah L.; Alastruey, Jordi; Beard, Daniel A.; Bovendeerd, Peter H.M.; Davies, Peter F.; Jayaraman, Girija; Jensen, Oliver E.; Lee, Jack; Parker, Kim H.; Popel, Aleksander S.; Secomb, Timothy W.; Siebes, Maria; Sherwin, Spencer J.; Shipley, Rebecca J.; Smith, Nicolas P.; van de Vosse, Frans N.

2013-01-01

A key aim of the cardiac Physiome Project is to develop theoretical models to simulate the functional behaviour of the heart under physiological and pathophysiological conditions. Heart function is critically dependent on the delivery of an adequate blood supply to the myocardium via the coronary vasculature. Key to this critical function of the coronary vasculature is system dynamics that emerge via the interactions of the numerous constituent components at a range of spatial and temporal scales. Here, we focus on several components for which theoretical approaches can be applied, including vascular structure and mechanics, blood flow and mass transport, flow regulation, angiogenesis and vascular remodelling, and vascular cellular mechanics. For each component, we summarise the current state of the art in model development, and discuss areas requiring further research. We highlight the major challenges associated with integrating the component models to develop a computational tool that can ultimately be used to simulate the responses of the coronary vascular system to changing demands and to diseases and therapies. PMID:21040741

Cytoscape: a software environment for integrated models of biomolecular interaction networks.

PubMed

Shannon, Paul; Markiel, Andrew; Ozier, Owen; Baliga, Nitin S; Wang, Jonathan T; Ramage, Daniel; Amin, Nada; Schwikowski, Benno; Ideker, Trey

2003-11-01

Cytoscape is an open source software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular states into a unified conceptual framework. Although applicable to any system of molecular components and interactions, Cytoscape is most powerful when used in conjunction with large databases of protein-protein, protein-DNA, and genetic interactions that are increasingly available for humans and model organisms. Cytoscape's software Core provides basic functionality to layout and query the network; to visually integrate the network with expression profiles, phenotypes, and other molecular states; and to link the network to databases of functional annotations. The Core is extensible through a straightforward plug-in architecture, allowing rapid development of additional computational analyses and features. Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.

Insight into the heterogeneous adsorption of humic acid fluorescent components on multi-walled carbon nanotubes by excitation-emission matrix and parallel factor analysis.

PubMed

Yang, Chenghu; Liu, Yangzhi; Cen, Qiulin; Zhu, Yaxian; Zhang, Yong

2018-02-01

The heterogeneous adsorption behavior of commercial humic acid (HA) on pristine and functionalized multi-walled carbon nanotubes (MWCNTs) was investigated by fluorescence excitation-emission matrix and parallel factor (EEM- PARAFAC) analysis. The kinetics, isotherms, thermodynamics and mechanisms of adsorption of HA fluorescent components onto MWCNTs were the focus of the present study. Three humic-like fluorescent components were distinguished, including one carboxylic-like fluorophore C1 (λ ex /λ em = (250, 310) nm/428nm), and two phenolic-like fluorophores, C2 (λ ex /λ em = (300, 460) nm/552nm) and C3 (λ ex /λ em = (270, 375) nm/520nm). The Lagergren pseudo-second-order model can be used to describe the adsorption kinetics of the HA fluorescent components. In addition, both the Freundlich and Langmuir models can be suitably employed to describe the adsorption of the HA fluorescent components onto MWCNTs with significantly high correlation coefficients (R 2 > 0.94, P< 0.05). The dissimilarity in the adsorption affinity (K d ) and nonlinear adsorption degree from the HA fluorescent components to MWCNTs was clearly observed. The adsorption mechanism suggested that the π-π electron donor-acceptor (EDA) interaction played an important role in the interaction between HA fluorescent components and the three MWCNTs. Furthermore, the values of the thermodynamic parameters, including the Gibbs free energy change (ΔG°), enthalpy change (ΔH°) and entropy change (ΔS°), showed that the adsorption of the HA fluorescent components on MWCNTs was spontaneous and exothermic. Copyright © 2017 Elsevier Inc. All rights reserved.

Drivers' communicative interactions: on-road observations and modelling for integration in future automation systems.

PubMed

Portouli, Evangelia; Nathanael, Dimitris; Marmaras, Nicolas

2014-01-01

Social interactions with other road users are an essential component of the driving activity and may prove critical in view of future automation systems; still up to now they have received only limited attention in the scientific literature. In this paper, it is argued that drivers base their anticipations about the traffic scene to a large extent on observations of social behaviour of other 'animate human-vehicles'. It is further argued that in cases of uncertainty, drivers seek to establish a mutual situational awareness through deliberate communicative interactions. A linguistic model is proposed for modelling these communicative interactions. Empirical evidence from on-road observations and analysis of concurrent running commentary by 25 experienced drivers support the proposed model. It is suggested that the integration of a social interactions layer based on illocutionary acts in future driving support and automation systems will improve their performance towards matching human driver's expectations. Practitioner Summary: Interactions between drivers on the road may play a significant role in traffic coordination. On-road observations and running commentaries are presented as empirical evidence to support a model of such interactions; incorporation of drivers' interactions in future driving support and automation systems may improve their performance towards matching driver's expectations.

On Nulling, Drifting, and Their Interactions in PSRs J1741-0840 and J1840-0840

NASA Astrophysics Data System (ADS)

Gajjar, V.; Yuan, J. P.; Yuen, R.; Wen, Z. G.; Liu, Z. Y.; Wang, N.

2017-12-01

We report detailed investigation of nulling and drifting behavior of two pulsars PSRs J1741-0840 and J1840-0840 observed from the Giant Meterwave Radio Telescope at 625 MHz. PSR J1741-0840 was found to show a nulling fraction (NF) of around 30% ± 5% while PSR J1840-0840 was shown to have an NF of around 50% ± 6%. We measured drifting behavior from different profile components in PSR J1840-0840 for the first time with the leading component showing drifting with 13.5 ± 0.7 periods while the weak trailing component showed drifting of around 18 ± 1 periods. Large nulling hampers accuracy of these quantities derived using standard Fourier techniques. A more accurate comparison was drawn from driftband slopes, measured after sub-pulse modeling. These measurements revealed interesting sporadic and irregular drifting behavior in both pulsars. We conclude that the previously reported different drifting periodicities in the trailing component of PSR J1741-0840 is likely due to the spread in these driftband slopes. We also find that both components of PSR J1840-0840 show similar driftband slopes within the uncertainties. Unique nulling-drifting interaction is identified in PSR J1840-0840 where, on most occasions, the pulsar tends to start nulling after what appears to be the end of a driftband. Similarly, when the pulsar switches back to an emission phase, on most occasions it starts at the beginning of a new driftband in both components. Such behaviors have not been detected in any other pulsars to our knowledge. We also found that PSR J1741-0840 seems to have no memory of its previous burst phase while PSR J1840-0840 clearly exhibits memory of its previous state even after longer nulls for both components. We discuss possible explanations for these intriguing nulling-drifting interactions seen in both pulsars based on various pulsar nulling models.

Testing of two source energy balance model under irrigated and dryland conditions using high resolution airborne imagery

USDA-ARS?s Scientific Manuscript database

Two Source Model (TSM) calculates the heat and water exchange and interaction between soil-atmosphere and vegetation-atmosphere separately. This is achieved through decomposition of radiometric surface temperature to soil and vegetation component temperatures either from multi-angular remotely sense...

Museum Accessibility: Combining Audience Research and Staff Training

ERIC Educational Resources Information Center

Levent, Nina; Reich, Christine

2013-01-01

This article discusses an audience-informed professional development model that combines audience research focus groups and staff training that includes interaction and direct feedback from visitors, in this case, visitors with low vision. There are two critical components to this model: one is that museums' programming decisions are informed by…

Extraction of CYP chemical interactions from biomedical literature using natural language processing methods.

PubMed

Jiao, Dazhi; Wild, David J

2009-02-01

This paper proposes a system that automatically extracts CYP protein and chemical interactions from journal article abstracts, using natural language processing (NLP) and text mining methods. In our system, we employ a maximum entropy based learning method, using results from syntactic, semantic, and lexical analysis of texts. We first present our system architecture and then discuss the data set for training our machine learning based models and the methods in building components in our system, such as part of speech (POS) tagging, Named Entity Recognition (NER), dependency parsing, and relation extraction. An evaluation of the system is conducted at the end, yielding very promising results: The POS, dependency parsing, and NER components in our system have achieved a very high level of accuracy as measured by precision, ranging from 85.9% to 98.5%, and the precision and the recall of the interaction extraction component are 76.0% and 82.6%, and for the overall system are 68.4% and 72.2%, respectively.

The secret to a successful relationship: lasting chemistry between ascidians and their symbiotic bacteria

PubMed Central

Schmidt, Eric W.

2014-01-01

Bioactive secondary metabolites are common components of marine animals. In many cases, symbiotic bacteria, and not the animals themselves, synthesize the compounds. Among marine animals, ascidians are good models for understanding these symbioses. Ascidians often contain potently bioactive secondary metabolites as their major extractable components. Strong evidence shows that ~8% of the known secondary metabolites from ascidians are made by symbiotic bacteria, and indirect evidence implicates bacteria in the synthesis of many more. Far from being “secondary” to the animals, secondary metabolites are essential components of the interaction between host animals and their symbiotic bacteria. These interactions have complex underlying biology, but the chemistry is clearly ascidian-species specific. The chemical interactions are ancient in at least some cases, and they are widespread among ascidians. Ascidians maintain secondary metabolic symbioses with bacteria that are phylogenetically diverse, indicating a convergent solution to obtaining secondary metabolites and reinforcing the importance of secondary metabolism in animal survival. PMID:25937788

Near infrared spectroscopy to estimate the temperature reached on burned soils: strategies to develop robust models.

NASA Astrophysics Data System (ADS)

Guerrero, César; Pedrosa, Elisabete T.; Pérez-Bejarano, Andrea; Keizer, Jan Jacob

2014-05-01

The temperature reached on soils is an important parameter needed to describe the wildfire effects. However, the methods for measure the temperature reached on burned soils have been poorly developed. Recently, the use of the near-infrared (NIR) spectroscopy has been pointed as a valuable tool for this purpose. The NIR spectrum of a soil sample contains information of the organic matter (quantity and quality), clay (quantity and quality), minerals (such as carbonates and iron oxides) and water contents. Some of these components are modified by the heat, and each temperature causes a group of changes, leaving a typical fingerprint on the NIR spectrum. This technique needs the use of a model (or calibration) where the changes in the NIR spectra are related with the temperature reached. For the development of the model, several aliquots are heated at known temperatures, and used as standards in the calibration set. This model offers the possibility to make estimations of the temperature reached on a burned sample from its NIR spectrum. However, the estimation of the temperature reached using NIR spectroscopy is due to changes in several components, and cannot be attributed to changes in a unique soil component. Thus, we can estimate the temperature reached by the interaction between temperature and the thermo-sensible soil components. In addition, we cannot expect the uniform distribution of these components, even at small scale. Consequently, the proportion of these soil components can vary spatially across the site. This variation will be present in the samples used to construct the model and also in the samples affected by the wildfire. Therefore, the strategies followed to develop robust models should be focused to manage this expected variation. In this work we compared the prediction accuracy of models constructed with different approaches. These approaches were designed to provide insights about how to distribute the efforts needed for the development of robust models, since this step is the bottle-neck of this technique. In the first approach, a plot-scale model was used to predict the temperature reached in samples collected in other plots from the same site. In a plot-scale model, all the heated aliquots come from a unique plot-scale sample. As expected, the results obtained with this approach were deceptive, because this approach was assuming that a plot-scale model would be enough to represent the whole variability of the site. The accuracy (measured as the root mean square error of prediction, thereinafter RMSEP) was 86ºC, and the bias was also high (>30ºC). In the second approach, the temperatures predicted through several plot-scale models were averaged. The accuracy was improved (RMSEP=65ºC) respect the first approach, because the variability from several plots was considered and biased predictions were partially counterbalanced. However, this approach implies more efforts, since several plot-scale models are needed. In the third approach, the predictions were obtained with site-scale models. These models were constructed with aliquots from several plots. In this case, the results were accurate, since the RMSEP was around 40ºC, the bias was very small (<1ºC) and the R2 was 0.92. As expected, this approach clearly outperformed the second approach, in spite of the fact that the same efforts were needed. In a plot-scale model, only one interaction between temperature and soil components was modelled. However, several different interactions between temperature and soil components were present in the calibration matrix of a site-scale model. Consequently, the site-scale models were able to model the temperature reached excluding the influence of the differences in soil composition, resulting in more robust models respect that variation. Summarizing, the results were highlighting the importance of an adequate strategy to develop robust and accurate models with moderate efforts, and how a wrong strategy can result in deceptive predictions.

Fungal-bacterial interactions and their relevance to oral health: linking the clinic and the bench

PubMed Central

Diaz, Patricia I.; Strausbaugh, Linda D.; Dongari-Bagtzoglou, Anna

2014-01-01

High throughput sequencing has accelerated knowledge on the oral microbiome. While the bacterial component of oral communities has been extensively characterized, the role of the fungal microbiota in the oral cavity is largely unknown. Interactions among fungi and bacteria are likely to influence oral health as exemplified by the synergistic relationship between Candida albicans and oral streptococci. In this perspective, we discuss the current state of the field of fungal-bacterial interactions in the context of the oral cavity. We highlight the need to conduct longitudinal clinical studies to simultaneously characterize the bacterial and fungal components of the human oral microbiome in health and during disease progression. Such studies need to be coupled with investigations using disease-relevant models to mechanistically test the associations observed in humans and eventually identify fungal-bacterial interactions that could serve as preventive or therapeutic targets for oral diseases. PMID:25120959

Fungal-bacterial interactions and their relevance to oral health: linking the clinic and the bench.

PubMed

Diaz, Patricia I; Strausbaugh, Linda D; Dongari-Bagtzoglou, Anna

2014-01-01

High throughput sequencing has accelerated knowledge on the oral microbiome. While the bacterial component of oral communities has been extensively characterized, the role of the fungal microbiota in the oral cavity is largely unknown. Interactions among fungi and bacteria are likely to influence oral health as exemplified by the synergistic relationship between Candida albicans and oral streptococci. In this perspective, we discuss the current state of the field of fungal-bacterial interactions in the context of the oral cavity. We highlight the need to conduct longitudinal clinical studies to simultaneously characterize the bacterial and fungal components of the human oral microbiome in health and during disease progression. Such studies need to be coupled with investigations using disease-relevant models to mechanistically test the associations observed in humans and eventually identify fungal-bacterial interactions that could serve as preventive or therapeutic targets for oral diseases.

MuTE: a MATLAB toolbox to compare established and novel estimators of the multivariate transfer entropy.

PubMed

Montalto, Alessandro; Faes, Luca; Marinazzo, Daniele

2014-01-01

A challenge for physiologists and neuroscientists is to map information transfer between components of the systems that they study at different scales, in order to derive important knowledge on structure and function from the analysis of the recorded dynamics. The components of physiological networks often interact in a nonlinear way and through mechanisms which are in general not completely known. It is then safer that the method of choice for analyzing these interactions does not rely on any model or assumption on the nature of the data and their interactions. Transfer entropy has emerged as a powerful tool to quantify directed dynamical interactions. In this paper we compare different approaches to evaluate transfer entropy, some of them already proposed, some novel, and present their implementation in a freeware MATLAB toolbox. Applications to simulated and real data are presented.

MuTE: A MATLAB Toolbox to Compare Established and Novel Estimators of the Multivariate Transfer Entropy

PubMed Central

Montalto, Alessandro; Faes, Luca; Marinazzo, Daniele

2014-01-01

A challenge for physiologists and neuroscientists is to map information transfer between components of the systems that they study at different scales, in order to derive important knowledge on structure and function from the analysis of the recorded dynamics. The components of physiological networks often interact in a nonlinear way and through mechanisms which are in general not completely known. It is then safer that the method of choice for analyzing these interactions does not rely on any model or assumption on the nature of the data and their interactions. Transfer entropy has emerged as a powerful tool to quantify directed dynamical interactions. In this paper we compare different approaches to evaluate transfer entropy, some of them already proposed, some novel, and present their implementation in a freeware MATLAB toolbox. Applications to simulated and real data are presented. PMID:25314003

Role of small-norm components in extended random-phase approximation

NASA Astrophysics Data System (ADS)

Tohyama, Mitsuru

2017-09-01

The role of the small-norm amplitudes in extended random-phase approximation (RPA) theories such as the particle-particle and hole-hole components of one-body amplitudes and the two-body amplitudes other than two-particle/two-hole components are investigated for the one-dimensional Hubbard model using an extended RPA derived from the time-dependent density matrix theory. It is found that these amplitudes cannot be neglected in strongly interacting regions where the effects of ground-state correlations are significant.

A hybridizable discontinuous Galerkin method for modeling fluid–structure interaction

DOE PAGES

Sheldon, Jason P.; Miller, Scott T.; Pitt, Jonathan S.

2016-08-31

This study presents a novel application of the hybridizable discontinuous Galerkin (HDG) finite element method to the multi-physics simulation of coupled fluid–structure interaction (FSI) problems. Recent applications of the HDG method have primarily been for single-physics problems including both solids and fluids, which are necessary building blocks for FSI modeling. Utilizing these established models, HDG formulations for linear elastostatics, a nonlinear elastodynamic model, and arbitrary Lagrangian–Eulerian Navier–Stokes are derived. The elasticity formulations are written in a Lagrangian reference frame, with the nonlinear formulation restricted to hyperelastic materials. With these individual solid and fluid formulations, the remaining challenge in FSI modelingmore » is coupling together their disparate mathematics on the fluid–solid interface. This coupling is presented, along with the resultant HDG FSI formulation. Verification of the component models, through the method of manufactured solutions, is performed and each model is shown to converge at the expected rate. The individual components, along with the complete FSI model, are then compared to the benchmark problems proposed by Turek and Hron [1]. The solutions from the HDG formulation presented in this work trend towards the benchmark as the spatial polynomial order and the temporal order of integration are increased.« less

Research on odor interaction between aldehyde compounds via a partial differential equation (PDE) model.

PubMed

Yan, Luchun; Liu, Jiemin; Qu, Chen; Gu, Xingye; Zhao, Xia

2015-01-28

In order to explore the odor interaction of binary odor mixtures, a series of odor intensity evaluation tests were performed using both individual components and binary mixtures of aldehydes. Based on the linear relation between the logarithm of odor activity value and odor intensity of individual substances, the relationship between concentrations of individual constituents and their joint odor intensity was investigated by employing a partial differential equation (PDE) model. The obtained results showed that the binary odor interaction was mainly influenced by the mixing ratio of two constituents, but not the concentration level of an odor sample. Besides, an extended PDE model was also proposed on the basis of the above experiments. Through a series of odor intensity matching tests for several different binary odor mixtures, the extended PDE model was proved effective at odor intensity prediction. Furthermore, odorants of the same chemical group and similar odor type exhibited similar characteristics in the binary odor interaction. The overall results suggested that the PDE model is a more interpretable way of demonstrating the odor interactions of binary odor mixtures.

A Model to Explain Plant Growth Promotion Traits: A Multivariate Analysis of 2,211 Bacterial Isolates

PubMed Central

da Costa, Pedro Beschoren; Granada, Camille E.; Ambrosini, Adriana; Moreira, Fernanda; de Souza, Rocheli; dos Passos, João Frederico M.; Arruda, Letícia; Passaglia, Luciane M. P.

2014-01-01

Plant growth-promoting bacteria can greatly assist sustainable farming by improving plant health and biomass while reducing fertilizer use. The plant-microorganism-environment interaction is an open and complex system, and despite the active research in the area, patterns in root ecology are elusive. Here, we simultaneously analyzed the plant growth-promoting bacteria datasets from seven independent studies that shared a methodology for bioprospection and phenotype screening. The soil richness of the isolate's origin was classified by a Principal Component Analysis. A Categorical Principal Component Analysis was used to classify the soil richness according to isolate's indolic compound production, siderophores production and phosphate solubilization abilities, and bacterial genera composition. Multiple patterns and relationships were found and verified with nonparametric hypothesis testing. Including niche colonization in the analysis, we proposed a model to explain the expression of bacterial plant growth-promoting traits according to the soil nutritional status. Our model shows that plants favor interaction with growth hormone producers under rich nutrient conditions but favor nutrient solubilizers under poor conditions. We also performed several comparisons among the different genera, highlighting interesting ecological interactions and limitations. Our model could be used to direct plant growth-promoting bacteria bioprospection and metagenomic sampling. PMID:25542031

Simulation of gamma-initiated showers

NASA Technical Reports Server (NTRS)

Stamenov, Y.; Vancov, K.; Vodenicharova, T.

1985-01-01

The main average characteristics of muon, electron and hadron components of extensive air showers were calculate using a standard model of nuclear interaction. The obtained results are in good agreement with Tien Shan experimental data.

Computer animation of modal and transient vibrations

NASA Technical Reports Server (NTRS)

Lipman, Robert R.

1987-01-01

An interactive computer graphics processor is described that is capable of generating input to animate modal and transient vibrations of finite element models on an interactive graphics system. The results from NASTRAN can be postprocessed such that a three dimensional wire-frame picture, in perspective, of the finite element mesh is drawn on the graphics display. Modal vibrations of any mode shape or transient motions over any range of steps can be animated. The finite element mesh can be color-coded by any component of displacement. Viewing parameters and the rate of vibration of the finite element model can be interactively updated while the structure is vibrating.

Metabolic networks in motion: 13C-based flux analysis

PubMed Central

Sauer, Uwe

2006-01-01

Many properties of complex networks cannot be understood from monitoring the components—not even when comprehensively monitoring all protein or metabolite concentrations—unless such information is connected and integrated through mathematical models. The reason is that static component concentrations, albeit extremely informative, do not contain functional information per se. The functional behavior of a network emerges only through the nonlinear gene, protein, and metabolite interactions across multiple metabolic and regulatory layers. I argue here that intracellular reaction rates are the functional end points of these interactions in metabolic networks, hence are highly relevant for systems biology. Methods for experimental determination of metabolic fluxes differ fundamentally from component concentration measurements; that is, intracellular reaction rates cannot be detected directly, but must be estimated through computer model-based interpretation of stable isotope patterns in products of metabolism. PMID:17102807

A Partial Least Square Approach for Modeling Gene-gene and Gene-environment Interactions When Multiple Markers Are Genotyped

PubMed Central

Wang, Tao; Ho, Gloria; Ye, Kenny; Strickler, Howard; Elston, Robert C.

2008-01-01

Genetic association studies achieve an unprecedented level of resolution in mapping disease genes by genotyping dense SNPs in a gene region. Meanwhile, these studies require new powerful statistical tools that can optimally handle a large amount of information provided by genotype data. A question that arises is how to model interactions between two genes. Simply modeling all possible interactions between the SNPs in two gene regions is not desirable because a greatly increased number of degrees of freedom can be involved in the test statistic. We introduce an approach to reduce the genotype dimension in modeling interactions. The genotype compression of this approach is built upon the information on both the trait and the cross-locus gametic disequilibrium between SNPs in two interacting genes, in such a way as to parsimoniously model the interactions without loss of useful information in the process of dimension reduction. As a result, it improves power to detect association in the presence of gene-gene interactions. This approach can be similarly applied for modeling gene-environment interactions. We compare this method with other approaches: the corresponding test without modeling any interaction, that based on a saturated interaction model, that based on principal component analysis, and that based on Tukey’s 1-df model. Our simulations suggest that this new approach has superior power to that of the other methods. In an application to endometrial cancer case-control data from the Women’s Health Initiative (WHI), this approach detected AKT1 and AKT2 as being significantly associated with endometrial cancer susceptibility by taking into account their interactions with BMI. PMID:18615621

A partial least-square approach for modeling gene-gene and gene-environment interactions when multiple markers are genotyped.

PubMed

Wang, Tao; Ho, Gloria; Ye, Kenny; Strickler, Howard; Elston, Robert C

2009-01-01

Genetic association studies achieve an unprecedented level of resolution in mapping disease genes by genotyping dense single nucleotype polymorphisms (SNPs) in a gene region. Meanwhile, these studies require new powerful statistical tools that can optimally handle a large amount of information provided by genotype data. A question that arises is how to model interactions between two genes. Simply modeling all possible interactions between the SNPs in two gene regions is not desirable because a greatly increased number of degrees of freedom can be involved in the test statistic. We introduce an approach to reduce the genotype dimension in modeling interactions. The genotype compression of this approach is built upon the information on both the trait and the cross-locus gametic disequilibrium between SNPs in two interacting genes, in such a way as to parsimoniously model the interactions without loss of useful information in the process of dimension reduction. As a result, it improves power to detect association in the presence of gene-gene interactions. This approach can be similarly applied for modeling gene-environment interactions. We compare this method with other approaches, the corresponding test without modeling any interaction, that based on a saturated interaction model, that based on principal component analysis, and that based on Tukey's one-degree-of-freedom model. Our simulations suggest that this new approach has superior power to that of the other methods. In an application to endometrial cancer case-control data from the Women's Health Initiative, this approach detected AKT1 and AKT2 as being significantly associated with endometrial cancer susceptibility by taking into account their interactions with body mass index.

A discrete decentralized variable structure robotic controller

NASA Technical Reports Server (NTRS)

Tumeh, Zuheir S.

1989-01-01

A decentralized trajectory controller for robotic manipulators is designed and tested using a multiprocessor architecture and a PUMA 560 robot arm. The controller is made up of a nominal model-based component and a correction component based on a variable structure suction control approach. The second control component is designed using bounds on the difference between the used and actual values of the model parameters. Since the continuous manipulator system is digitally controlled along a trajectory, a discretized equivalent model of the manipulator is used to derive the controller. The motivation for decentralized control is that the derived algorithms can be executed in parallel using a distributed, relatively inexpensive, architecture where each joint is assigned a microprocessor. Nonlinear interaction and coupling between joints is treated as a disturbance torque that is estimated and compensated for.

Psychological Empowerment Among Urban Youth: Measurement Model and Associations with Youth Outcomes

PubMed Central

Eisman, Andria B.; Zimmerman, Marc A.; Kruger, Daniel; Reischl, Thomas M.; Miller, Alison L.; Franzen, Susan P.; Morrel-Samuels, Susan

2016-01-01

Empowerment-based strategies have become widely used method to address health inequities and promote social change. Few researchers, however, have tested theoretical models of empowerment, including multidimensional, higher-order models. We test empirically a multidimensional, higher-order model of psychological empowerment (PE), guided by Zimmerman’s (1995) conceptual framework including three components of PE: intrapersonal, interactional and behavioral. We also investigate if PE is associated with positive and negative outcomes among youth. The sample included 367 middle school youth aged 11–16 (M = 12.71; SD = 0.91); 60% female, 32% (n =117) white youth, 46% (n = 170) African-American youth, and 22% (n = 80) identifying as mixed race, Asian-American, Latino, Native American or other ethnic/racial group; schools reported 61–75% free/reduced lunch students. Our results indicated that each of the latent factors for the three PE components demonstrate a good fit with the data. Our results also indicated that these components loaded on to a higher-order PE factor (X2=32.68, df: 22, p=0.07; RMSEA: 0.04, 95% CI: 0.00, 0.06; CFI: 0.99). We found that the second order PE factor was negatively associated with aggressive behavior and positively associated with prosocial engagement. Our results suggest that empowerment-focused programs would benefit from incorporating components addressing how youth think about themselves in relation to their social contexts (intrapersonal), understanding social and material resources needed to achieve specific goals (interactional) and actions taken to influence outcomes (behavioral). Our results also suggest that integrating the three components and promoting PE may help increase likelihood of positive behaviors (e.g., prosocial involvement); we did not find an association between PE and aggressive behavior. Implications and future directions for empowerment research are discussed. PMID:27709632

NuSTAR Detection of a Hard X-Ray Source in the Supernova Remnant-molecular Cloud Interaction Site of IC 443

NASA Astrophysics Data System (ADS)

Zhang, Shuo; Tang, Xiaping; Zhang, Xiao; Sun, Lei; Gotthelf, Eric V.; Zhang, Zhi-Yu; Li, Hui; Cheng, Allen; Pasham, Dheeraj; Baganoff, Frederick K.; Perez, Kerstin; Hailey, Charles J.; Mori, Kaya

2018-06-01

We report on a broadband study of a complex X-ray source (1SAX J0618.0+2227) associated with the interaction site of the supernova remnant (SNR) IC 443 and ambient molecular cloud (MC) using NuSTAR, XMM-Newton, and Chandra observations. Its X-ray spectrum is composed of both thermal and nonthermal components. The thermal component can be equally well represented by either a thin plasma model with kT = 0.19 keV or a blackbody model with kT = 0.11 keV. The nonthermal component can be fit with either a power law with Γ ∼ 1.7 or a cutoff power law with Γ ∼ 1.5 and a cutoff energy at E cut ∼ 18 keV. Using the newly obtained NuSTAR data set, we test three possible scenarios for isolated X-ray sources in the SNR–MC interaction site: (1) a pulsar wind nebula (PWN); (2) an SNR ejecta fragment; and (3) a shocked molecular clump. We conclude that this source is most likely composed of an SNR ejecta (or a PWN) and surrounding shocked molecular clumps. The nature of this hard X-ray source in the SNR–MC interaction site of IC 443 may shed light on unidentified X-ray sources with hard X-ray spectra in rich environments for star-forming regions, such as the Galactic center.

Description and evaluation of the Earth System Regional Climate Model (RegCM-ES)

NASA Astrophysics Data System (ADS)

Farneti, Riccardo; Sitz, Lina; Di Sante, Fabio; Fuentes-Franco, Ramon; Coppola, Erika; Mariotti, Laura; Reale, Marco; Sannino, Gianmaria; Barreiro, Marcelo; Nogherotto, Rita; Giuliani, Graziano; Graffino, Giorgio; Solidoro, Cosimo; Giorgi, Filippo

2017-04-01

The increasing availability of satellite remote sensing data, of high temporal frequency and spatial resolution, has provided a new and enhanced view of the global ocean and atmosphere, revealing strong air-sea coupling processes throughout the ocean basins. In order to obtain an accurate representation and better understanding of the climate system, its variability and change, the inclusion of all mechanisms of interaction among the different sub-components, at high temporal and spatial resolution, becomes ever more desirable. Recently, global coupled models have been able to progressively refine their horizontal resolution to attempt to resolve smaller-scale processes. However, regional coupled ocean-atmosphere models can achieve even finer resolutions and provide additional information on the mechanisms of air-sea interactions and feedbacks. Here we describe a new, state-of-the-art, Earth System Regional Climate Model (RegCM-ES). RegCM-ES presently includes the coupling between atmosphere, ocean, land surface and sea-ice components, as well as an hydrological and ocean biogeochemistry model. The regional coupled model has been implemented and tested over some of the COordinated Regional climate Downscaling Experiment (CORDEX) domains. RegCM-ES has shown improvements in the representation of precipitation and SST fields over the tested domains, as well as realistic representations of coupled air-sea processes and interactions. The RegCM-ES model, which can be easily implemented over any regional domain of interest, is open source making it suitable for usage by the large scientific community.

A formulation to analyze system-of-systems problems: A case study of airport metroplex operations

NASA Astrophysics Data System (ADS)

Ayyalasomayajula, Sricharan Kishore

A system-of-systems (SoS) can be described as a collection of multiple, heterogeneous, distributed, independent components interacting to achieve a range of objectives. A generic formulation was developed to model component interactions in an SoS to understand their influence on overall SoS performance. The formulation employs a lexicon to aggregate components into hierarchical interaction networks and understand how their topological properties affect the performance of the aggregations. Overall SoS performance is evaluated by monitoring the changes in stakeholder profitability due to changes in component interactions. The formulation was applied to a case study in air transportation focusing on operations at airport metroplexes. Metroplexes are geographical regions with two or more airports in close proximity to one another. The case study explored how metroplex airports interact with one another, what dependencies drive these interactions, and how these dependencies affect metroplex throughput and capacity. Metrics were developed to quantify runway dependencies at a metroplex and were correlated with its throughput and capacity. Operations at the New York/New Jersey metroplex (NYNJ) airports were simulated to explore the feasibility of operating very large aircraft (VLA), such as the Airbus A380, as a delay-mitigation strategy at these airports. The proposed formulation was employed to analyze the impact of this strategy on different stakeholders in the national air transportation system (ATS), such as airlines and airports. The analysis results and their implications were used to compare the pros and cons of operating VLAs at NYNJ from the perspectives of airline profitability, and flight delays at NYNJ and across the ATS.

Construction of a Cyber Attack Model for Nuclear Power Plants

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

Varuttamaseni, Athi; Bari, Robert A.; Youngblood, Robert

The consideration of how one compromised digital equipment can impact neighboring equipment is critical to understanding the progression of cyber attacks. The degree of influence that one component may have on another depends on a variety of factors, including the sharing of resources such as network bandwidth or processing power, the level of trust between components, and the inclusion of segmentation devices such as firewalls. The interactions among components via mechanisms that are unique to the digital world are not usually considered in traditional PRA. This means potential sequences of events that may occur during an attack may be missedmore » if one were to only look at conventional accident sequences. This paper presents a method where, starting from the initial attack vector, the progression of a cyber attack can be modeled. The propagation of the attack is modeled by considering certain attributes of the digital components in the system. These attributes determine the potential vulnerability of a component to a class of attack and the capability gained by the attackers once they are in control of the equipment. The use of attributes allows similar components (components with the same set of attributes) to be modeled in the same way, thereby reducing the computing resources required for analysis of large systems.« less

OCSEGen: Open Components and Systems Environment Generator

NASA Technical Reports Server (NTRS)

Tkachuk, Oksana

2014-01-01

To analyze a large system, one often needs to break it into smaller components.To analyze a component or unit under analysis, one needs to model its context of execution, called environment, which represents the components with which the unit interacts. Environment generation is a challenging problem, because the environment needs to be general enough to uncover unit errors, yet precise enough to make the analysis tractable. In this paper, we present a tool for automated environment generation for open components and systems. The tool, called OCSEGen, is implemented on top of the Soot framework. We present the tool's current support and discuss its possible future extensions.

An Analysis of a Comprehensive Evaluation Model for Guided Group Interaction Techniques with Juvenile Delinquents. Final Report.

ERIC Educational Resources Information Center

Silverman, Mitchell

Reported are the first phase activities of a longitudinal project designed to evaluate the effectiveness of Guided Group Interaction (GGI) technique as a meaningful approach in the field of corrections. The main findings relate to the establishment of reliability for the main components of the Revised Behavior Scores System developed to assess the…

CICE, The Los Alamos Sea Ice Model

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

Hunke, Elizabeth; Lipscomb, William; Jones, Philip

The Los Alamos sea ice model (CICE) is the result of an effort to develop a computationally efficient sea ice component for a fully coupled atmosphere–land–ocean–ice global climate model. It was originally designed to be compatible with the Parallel Ocean Program (POP), an ocean circulation model developed at Los Alamos National Laboratory for use on massively parallel computers. CICE has several interacting components: a vertical thermodynamic model that computes local growth rates of snow and ice due to vertical conductive, radiative and turbulent fluxes, along with snowfall; an elastic-viscous-plastic model of ice dynamics, which predicts the velocity field of themore » ice pack based on a model of the material strength of the ice; an incremental remapping transport model that describes horizontal advection of the areal concentration, ice and snow volume and other state variables; and a ridging parameterization that transfers ice among thickness categories based on energetic balances and rates of strain. It also includes a biogeochemical model that describes evolution of the ice ecosystem. The CICE sea ice model is used for climate research as one component of complex global earth system models that include atmosphere, land, ocean and biogeochemistry components. It is also used for operational sea ice forecasting in the polar regions and in numerical weather prediction models.« less

Anselm's Discovery of the Gross-Neveu Model in 1958

NASA Astrophysics Data System (ADS)

Shifman, M.

2013-06-01

The Gross-Neveu model comprises quantum field theory of N Dirac fermions interacting via four-fermion interaction in one spatial and one time dimension. It was introduced in 1974 (shortly after quantum chromodynamics was discovered) by David Gross and André Neveu [1] as a toy model which mimics two crucial features of quantum chromodynamics: asymptotic freedom and spontaneous breaking of a chiral symmetry. The model is based on N Dirac (i.e. complex two-component) fermions, ψ1, ψ2, ..., ψN. The Lagrangian of the Gross-Neveau model is [ {L} = bar{psi}ipartial_{mu}gamma^{mu}psi + frac{g^{2}}{2}(sumlimits_{k = 1}^{N}bar{psi}_{k}psi^{k})^{2}.

[Tapentadol: with two mechanisms of action in one molecule effective against nociceptive and neuropathic pain. Preclinical overview].

PubMed

Tzschentke, T M; Christoph, T; Schröder, W; Englberger, W; De Vry, J; Jahnel, U; Kögel, B Y

2011-02-01

Tapentadol (3-[(1R, 2R)-3-(dimethylamino)-1-ethyl-2-methylpropyl] phenol) is a centrally acting analgesic of a new substance class for the treatment of severe nociceptive and neuropathic pain. Tapentadol combines μ-opioid receptor (MOR) agonism and noradrenaline reuptake inhibition (NRI) in one molecule. Because of the combined mechanisms of action tapentadol offers a broad therapeutic spectrum for nociceptive as well as neuropathic pain. In different animal models its high efficacy was shown in acute nociceptive, acute and chronic inflammatory as well as in chronic neuropathic pain. Using several preclinical approaches it was shown that the noradrenergic component of tapentadol interacts with the opioid component and that both synergistically contribute to the analgesic effect of the substance. In comparison to known drugs with only one of the two modes of action, tapentadol, despite its high potency, has an improved tolerability profile in the relevant animal models, particularly with regard to gastrointestinal and central side effects. Tapentadol acts directly without metabolic activation and without formation of analgesically relevant metabolites. In different interaction studies a low potential for interactions was shown, thus clinically relevant drug-drug interactions are unlikely. Overall, tapentadol provides a safe pharmacodynamic-pharmacokinetic profile.

Bimanual motor coordination controlled by cooperative interactions in intrinsic and extrinsic coordinates.

PubMed

Sakurada, Takeshi; Ito, Koji; Gomi, Hiroaki

2016-01-01

Although strong motor coordination in intrinsic muscle coordinates has frequently been reported for bimanual movements, coordination in extrinsic visual coordinates is also crucial in various bimanual tasks. To explore the bimanual coordination mechanisms in terms of the frame of reference, here we characterized implicit bilateral interactions in visuomotor tasks. Visual perturbations (finger-cursor gain change) were applied while participants performed a rhythmic tracking task with both index fingers under an in-phase or anti-phase relationship in extrinsic coordinates. When they corrected the right finger's amplitude, the left finger's amplitude unintentionally also changed [motor interference (MI)], despite the instruction to keep its amplitude constant. Notably, we observed two specificities: one was large MI and low relative-phase variability (PV) under the intrinsic in-phase condition, and the other was large MI and high PV under the extrinsic in-phase condition. Additionally, using a multiple-interaction model, we successfully decomposed MI into intrinsic components caused by motor correction and extrinsic components caused by visual-cursor mismatch of the right finger's movements. This analysis revealed that the central nervous system facilitates MI by combining intrinsic and extrinsic components in the condition with in-phases in both intrinsic and extrinsic coordinates, and that under-additivity of the effects is explained by the brain's preference for the intrinsic interaction over extrinsic interaction. In contrast, the PV was significantly correlated with the intrinsic component, suggesting that the intrinsic interaction dominantly contributed to bimanual movement stabilization. The inconsistent features of MI and PV suggest that the central nervous system regulates multiple levels of bilateral interactions for various bimanual tasks. © 2015 The Authors. European Journal of Neuroscience published by Federation of European Neuroscience Societies and John Wiley & Sons Ltd.

Role of electrostatic interaction on surfactant induced protein unfolding

NASA Astrophysics Data System (ADS)

Sumit, Kumar, Sugam; Aswal, V. K.

2013-02-01

Small Angle Neutron Scattering has been used to examine the effect of electrostatic interaction on surfactant induced protein unfolding. Measurements are carried out from 1 wt% Bovine Serum Albumin (BSA) protein with 1 wt% Sodium Dodecyl Sulphate (SDS) surfactant at pH 7 in presence of varying concentration of NaCl. It is found that both the components (protein and surfactant micelle which are likely charged) exist individually without any interaction in absence of salt, whereas their interaction and protein unfolding is enhanced with the increase in salt concentration. The structure of protein-surfactant interaction is characterized by fractal bead-necklace model.

Five challenges for spatial epidemic models

PubMed Central

Riley, Steven; Eames, Ken; Isham, Valerie; Mollison, Denis; Trapman, Pieter

2015-01-01

Infectious disease incidence data are increasingly available at the level of the individual and include high-resolution spatial components. Therefore, we are now better able to challenge models that explicitly represent space. Here, we consider five topics within spatial disease dynamics: the construction of network models; characterising threshold behaviour; modelling long-distance interactions; the appropriate scale for interventions; and the representation of population heterogeneity. PMID:25843387

Digital Avionics Information System (DAIS): Life Cycle Cost Impact Modeling System Reliability, Maintainability, and Cost Model (RMCM)--Description. Users Guide. Final Report.

ERIC Educational Resources Information Center

Goclowski, John C.; And Others

The Reliability, Maintainability, and Cost Model (RMCM) described in this report is an interactive mathematical model with a built-in sensitivity analysis capability. It is a major component of the Life Cycle Cost Impact Model (LCCIM), which was developed as part of the DAIS advanced development program to be used to assess the potential impacts…

Neptune's inner magnetosphere and aurora: Energetic particle constraints

NASA Technical Reports Server (NTRS)

Mauk, B. H.; Krimigis, S. M.; Acuna, M. H.

1994-01-01

A dramatic and peculiar dropout of greater than 500-keV ions (but not electrons) was observed within Neptune's inner magnetosphere near 2 R(sub N) as the Voyager 2 spacecraft approached the planet. Unlike a number of other energetic particle features this feature could not be accounted for by known material bodies in the context of the most utilized magnetic field models (neither the offset tilted dipole models nor the spehrical harmonic model 'O8'). However, the configuration of Neptune's inner magnetosphere is highly uncertain. By applying a novel technique, utilizing energetic particle measurements, to constrain the magnetic field configuration of the inner regions, we show that appeals to unobserved materials within Neptune's system are unnecessary, and that the ion dropout feature was, in all likelihood, the result of ion interactions with maximum L excursions of the ring 1989N1R. The constraints also favor the se of the M2 magnetic field model (Selesnick, 1992) over the previous models. An electron feature was probably absent because the electron interactions with the ring occurred substantially before the ion interactions (about 2 hours for the electrons versus a few minutes for the ions). Pitch-angle scattering apparently eliminated the electron signature. Minimum scattering rates determined based on this premise yield enough electron precipitation power to explain the brightest component of Neptune's aurora. We propose that this bright component is analogous to the Earth's diffuse aurora.

The effect of macromolecular crowding on the electrostatic component of barnase-barstar binding: a computational, implicit solvent-based study.

PubMed

Qi, Helena W; Nakka, Priyanka; Chen, Connie; Radhakrishnan, Mala L

2014-01-01

Macromolecular crowding within the cell can impact both protein folding and binding. Earlier models of cellular crowding focused on the excluded volume, entropic effect of crowding agents, which generally favors compact protein states. Recently, other effects of crowding have been explored, including enthalpically-related crowder-protein interactions and changes in solvation properties. In this work, we explore the effects of macromolecular crowding on the electrostatic desolvation and solvent-screened interaction components of protein-protein binding. Our simple model enables us to focus exclusively on the electrostatic effects of water depletion on protein binding due to crowding, providing us with the ability to systematically analyze and quantify these potentially intuitive effects. We use the barnase-barstar complex as a model system and randomly placed, uncharged spheres within implicit solvent to model crowding in an aqueous environment. On average, we find that the desolvation free energy penalties incurred by partners upon binding are lowered in a crowded environment and solvent-screened interactions are amplified. At a constant crowder density (fraction of total available volume occupied by crowders), this effect generally increases as the radius of model crowders decreases, but the strength and nature of this trend can depend on the water probe radius used to generate the molecular surface in the continuum model. In general, there is huge variation in desolvation penalties as a function of the random crowder positions. Results with explicit model crowders can be qualitatively similar to those using a lowered "effective" solvent dielectric to account for crowding, although the "best" effective dielectric constant will likely depend on multiple system properties. Taken together, this work systematically demonstrates, quantifies, and analyzes qualitative intuition-based insights into the effects of water depletion due to crowding on the electrostatic component of protein binding, and it provides an initial framework for future analyses.

The Effect of Macromolecular Crowding on the Electrostatic Component of Barnase–Barstar Binding: A Computational, Implicit Solvent-Based Study

PubMed Central

Qi, Helena W.; Nakka, Priyanka; Chen, Connie; Radhakrishnan, Mala L.

2014-01-01

Macromolecular crowding within the cell can impact both protein folding and binding. Earlier models of cellular crowding focused on the excluded volume, entropic effect of crowding agents, which generally favors compact protein states. Recently, other effects of crowding have been explored, including enthalpically-related crowder–protein interactions and changes in solvation properties. In this work, we explore the effects of macromolecular crowding on the electrostatic desolvation and solvent-screened interaction components of protein–protein binding. Our simple model enables us to focus exclusively on the electrostatic effects of water depletion on protein binding due to crowding, providing us with the ability to systematically analyze and quantify these potentially intuitive effects. We use the barnase–barstar complex as a model system and randomly placed, uncharged spheres within implicit solvent to model crowding in an aqueous environment. On average, we find that the desolvation free energy penalties incurred by partners upon binding are lowered in a crowded environment and solvent-screened interactions are amplified. At a constant crowder density (fraction of total available volume occupied by crowders), this effect generally increases as the radius of model crowders decreases, but the strength and nature of this trend can depend on the water probe radius used to generate the molecular surface in the continuum model. In general, there is huge variation in desolvation penalties as a function of the random crowder positions. Results with explicit model crowders can be qualitatively similar to those using a lowered “effective” solvent dielectric to account for crowding, although the “best” effective dielectric constant will likely depend on multiple system properties. Taken together, this work systematically demonstrates, quantifies, and analyzes qualitative intuition-based insights into the effects of water depletion due to crowding on the electrostatic component of protein binding, and it provides an initial framework for future analyses. PMID:24915485

Modeling of the Dorsal Gradient across Species Reveals Interaction between Embryo Morphology and Toll Signaling Pathway during Evolution

PubMed Central

Koslen, Hannah R.; Chiel, Hillel J.; Mizutani, Claudia Mieko

2014-01-01

Morphogenetic gradients are essential to allocate cell fates in embryos of varying sizes within and across closely related species. We previously showed that the maternal NF-κB/Dorsal (Dl) gradient has acquired different shapes in Drosophila species, which result in unequally scaled germ layers along the dorso-ventral axis and the repositioning of the neuroectodermal borders. Here we combined experimentation and mathematical modeling to investigate which factors might have contributed to the fast evolutionary changes of this gradient. To this end, we modified a previously developed model that employs differential equations of the main biochemical interactions of the Toll (Tl) signaling pathway, which regulates Dl nuclear transport. The original model simulations fit well the D. melanogaster wild type, but not mutant conditions. To broaden the applicability of this model and probe evolutionary changes in gradient distributions, we adjusted a set of 19 independent parameters to reproduce three quantified experimental conditions (i.e. Dl levels lowered, nuclear size and density increased or decreased). We next searched for the most relevant parameters that reproduce the species-specific Dl gradients. We show that adjusting parameters relative to morphological traits (i.e. embryo diameter, nuclear size and density) alone is not sufficient to reproduce the species Dl gradients. Since components of the Tl pathway simulated by the model are fast-evolving, we next asked which parameters related to Tl would most effectively reproduce these gradients and identified a particular subset. A sensitivity analysis reveals the existence of nonlinear interactions between the two fast-evolving traits tested above, namely the embryonic morphological changes and Tl pathway components. Our modeling further suggests that distinct Dl gradient shapes observed in closely related melanogaster sub-group lineages may be caused by similar sequence modifications in Tl pathway components, which are in agreement with their phylogenetic relationships. PMID:25165818

On the dynamics of a shock-bubble interaction

NASA Technical Reports Server (NTRS)

Quirk, James J.; Karni, Smadar

1994-01-01

We present a detailed numerical study of the interaction of a weak shock wave with an isolated cylindrical gas inhomogenity. Such interactions have been studied experimentally in an attempt to elucidate the mechanisms whereby shock waves propagating through random media enhance mixing. Our study concentrates on the early phases of the interaction process which are dominated by repeated refractions of acoustic fronts at the bubble interface. Specifically, we have reproduced two of the experiments performed by Haas and Sturtevant : M(sub s) = 1.22 planar shock wave, moving through air, impinges on a cylindrical bubble which contains either helium or Refrigerant 22. These flows are modelled using the two-dimensional, compressible Euler equations for a two component fluid (air-helium or air-Refrigerant 22). Although simulations of shock wave phenomena are now fairly commonplace, they are mostly restricted to single component flows. Unfortunately, multi-component extensions of successful single component schemes often suffer from spurious oscillations which are generated at material interfaces. Here we avoid such problems by employing a novel, nonconservative shock-capturing scheme. In addition, we have utilized a sophisticated adaptive mesh refinement algorithm which enables extremely high resolution simulations to be performed relatively cheaply. Thus we have been able to reproduce numerically all the intricate mechanisms that were observed experimentally (e.g., transitions from regular to irregular refraction, cusp formation and shock wave focusing, multi-shock and Mach shock structures, jet formation, etc.), and we can now present an updated description for the dynamics of a shock-bubble interaction.

Estimation of Soil Moisture with L-band Multi-polarization Radar

NASA Technical Reports Server (NTRS)

Shi, J.; Chen, K. S.; Kim, Chung-Li Y.; Van Zyl, J. J.; Njoku, E.; Sun, G.; O'Neill, P.; Jackson, T.; Entekhabi, D.

2004-01-01

Through analyses of the model simulated data-base, we developed a technique to estimate surface soil moisture under HYDROS radar sensor (L-band multi-polarizations and 40deg incidence) configuration. This technique includes two steps. First, it decomposes the total backscattering signals into two components - the surface scattering components (the bare surface backscattering signals attenuated by the overlaying vegetation layer) and the sum of the direct volume scattering components and surface-volume interaction components at different polarizations. From the model simulated data-base, our decomposition technique works quit well in estimation of the surface scattering components with RMSEs of 0.12,0.25, and 0.55 dB for VV, HH, and VH polarizations, respectively. Then, we use the decomposed surface backscattering signals to estimate the soil moisture and the combined surface roughness and vegetation attenuation correction factors with all three polarizations.

A Calculus for Boxes and Traits in a Java-Like Setting

NASA Astrophysics Data System (ADS)

Bettini, Lorenzo; Damiani, Ferruccio; de Luca, Marco; Geilmann, Kathrin; Schäfer, Jan

The box model is a component model for the object-oriented paradigm, that defines components (the boxes) with clear encapsulation boundaries. Having well-defined boundaries is crucial in component-based software development, because it enables to argue about the interference and interaction between a component and its context. In general, boxes contain several objects and inner boxes, of which some are local to the box and cannot be accessed from other boxes and some can be accessible by other boxes. A trait is a set of methods divorced from any class hierarchy. Traits can be composed together to form classes or other traits. We present a calculus for boxes and traits. Traits are units of fine-grained reuse, whereas boxes can be seen as units of coarse-grained reuse. The calculus is equipped with an ownership type system and allows us to combine coarse- and fine-grained reuse of code by maintaining encapsulation of components.

THE EARTH SYSTEM PREDICTION SUITE: Toward a Coordinated U.S. Modeling Capability

PubMed Central

Theurich, Gerhard; DeLuca, C.; Campbell, T.; Liu, F.; Saint, K.; Vertenstein, M.; Chen, J.; Oehmke, R.; Doyle, J.; Whitcomb, T.; Wallcraft, A.; Iredell, M.; Black, T.; da Silva, AM; Clune, T.; Ferraro, R.; Li, P.; Kelley, M.; Aleinov, I.; Balaji, V.; Zadeh, N.; Jacob, R.; Kirtman, B.; Giraldo, F.; McCarren, D.; Sandgathe, S.; Peckham, S.; Dunlap, R.

2017-01-01

The Earth System Prediction Suite (ESPS) is a collection of flagship U.S. weather and climate models and model components that are being instrumented to conform to interoperability conventions, documented to follow metadata standards, and made available either under open source terms or to credentialed users. The ESPS represents a culmination of efforts to create a common Earth system model architecture, and the advent of increasingly coordinated model development activities in the U.S. ESPS component interfaces are based on the Earth System Modeling Framework (ESMF), community-developed software for building and coupling models, and the National Unified Operational Prediction Capability (NUOPC) Layer, a set of ESMF-based component templates and interoperability conventions. This shared infrastructure simplifies the process of model coupling by guaranteeing that components conform to a set of technical and semantic behaviors. The ESPS encourages distributed, multi-agency development of coupled modeling systems, controlled experimentation and testing, and exploration of novel model configurations, such as those motivated by research involving managed and interactive ensembles. ESPS codes include the Navy Global Environmental Model (NavGEM), HYbrid Coordinate Ocean Model (HYCOM), and Coupled Ocean Atmosphere Mesoscale Prediction System (COAMPS®); the NOAA Environmental Modeling System (NEMS) and the Modular Ocean Model (MOM); the Community Earth System Model (CESM); and the NASA ModelE climate model and GEOS-5 atmospheric general circulation model. PMID:29568125

THE EARTH SYSTEM PREDICTION SUITE: Toward a Coordinated U.S. Modeling Capability.

PubMed

Theurich, Gerhard; DeLuca, C; Campbell, T; Liu, F; Saint, K; Vertenstein, M; Chen, J; Oehmke, R; Doyle, J; Whitcomb, T; Wallcraft, A; Iredell, M; Black, T; da Silva, A M; Clune, T; Ferraro, R; Li, P; Kelley, M; Aleinov, I; Balaji, V; Zadeh, N; Jacob, R; Kirtman, B; Giraldo, F; McCarren, D; Sandgathe, S; Peckham, S; Dunlap, R

2016-07-01

The Earth System Prediction Suite (ESPS) is a collection of flagship U.S. weather and climate models and model components that are being instrumented to conform to interoperability conventions, documented to follow metadata standards, and made available either under open source terms or to credentialed users. The ESPS represents a culmination of efforts to create a common Earth system model architecture, and the advent of increasingly coordinated model development activities in the U.S. ESPS component interfaces are based on the Earth System Modeling Framework (ESMF), community-developed software for building and coupling models, and the National Unified Operational Prediction Capability (NUOPC) Layer, a set of ESMF-based component templates and interoperability conventions. This shared infrastructure simplifies the process of model coupling by guaranteeing that components conform to a set of technical and semantic behaviors. The ESPS encourages distributed, multi-agency development of coupled modeling systems, controlled experimentation and testing, and exploration of novel model configurations, such as those motivated by research involving managed and interactive ensembles. ESPS codes include the Navy Global Environmental Model (NavGEM), HYbrid Coordinate Ocean Model (HYCOM), and Coupled Ocean Atmosphere Mesoscale Prediction System (COAMPS ® ); the NOAA Environmental Modeling System (NEMS) and the Modular Ocean Model (MOM); the Community Earth System Model (CESM); and the NASA ModelE climate model and GEOS-5 atmospheric general circulation model.

The Earth System Prediction Suite: Toward a Coordinated U.S. Modeling Capability

NASA Technical Reports Server (NTRS)

Theurich, Gerhard; DeLuca, C.; Campbell, T.; Liu, F.; Saint, K.; Vertenstein, M.; Chen, J.; Oehmke, R.; Doyle, J.; Whitcomb, T.;

Statefinder analysis of the superfluid Chaplygin gas model

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

Popov, V.A., E-mail: vladipopov@mail.ru

2011-10-01

The statefinder indices are employed to test the superfluid Chaplygin gas (SCG) model describing the dark sector of the universe. The model involves Bose-Einstein condensate (BEC) as dark energy (DE) and an excited state above it as dark matter (DM). The condensate is assumed to have a negative pressure and is embodied as an exotic fluid with the Chaplygin equation of state. Excitations forms the normal component of superfluid. The statefinder diagrams show the discrimination between the SCG scenario and other models with the Chaplygin gas and indicates a pronounced effect of the DM equation of state and an indirectmore » interaction between their two components on statefinder trajectories and a current statefinder location.« less

Statefinder analysis of the superfluid Chaplygin gas model

NASA Astrophysics Data System (ADS)

Popov, V. A.

2011-10-01

The statefinder indices are employed to test the superfluid Chaplygin gas (SCG) model describing the dark sector of the universe. The model involves Bose-Einstein condensate (BEC) as dark energy (DE) and an excited state above it as dark matter (DM). The condensate is assumed to have a negative pressure and is embodied as an exotic fluid with the Chaplygin equation of state. Excitations forms the normal component of superfluid. The statefinder diagrams show the discrimination between the SCG scenario and other models with the Chaplygin gas and indicates a pronounced effect of the DM equation of state and an indirect interaction between their two components on statefinder trajectories and a current statefinder location.

Refining metabolic models and accounting for regulatory effects.

PubMed

Kim, Joonhoon; Reed, Jennifer L

2014-10-01

Advances in genome-scale metabolic modeling allow us to investigate and engineer metabolism at a systems level. Metabolic network reconstructions have been made for many organisms and computational approaches have been developed to convert these reconstructions into predictive models. However, due to incomplete knowledge these reconstructions often have missing or extraneous components and interactions, which can be identified by reconciling model predictions with experimental data. Recent studies have provided methods to further improve metabolic model predictions by incorporating transcriptional regulatory interactions and high-throughput omics data to yield context-specific metabolic models. Here we discuss recent approaches for resolving model-data discrepancies and building context-specific metabolic models. Once developed highly accurate metabolic models can be used in a variety of biotechnology applications. Copyright © 2014 Elsevier Ltd. All rights reserved.

Characterization of MRP RNA–protein interactions within the perinucleolar compartment

PubMed Central

Pollock, Callie; Daily, Kelly; Nguyen, Van Trung; Wang, Chen; Lewandowska, Marzena Anna; Bensaude, Olivier; Huang, Sui

2011-01-01

The perinucleolar compartment (PNC) forms in cancer cells and is highly enriched with a subset of polymerase III RNAs and RNA-binding proteins. Here we report that PNC components mitochondrial RNA–processing (MRP) RNA, pyrimidine tract–binding protein (PTB), and CUG-binding protein (CUGBP) interact in vivo, as demonstrated by coimmunoprecipitation and RNA pull-down experiments. Glycerol gradient analyses show that this complex is large and sediments at a different fraction from known MRP RNA–containing complexes, the MRP ribonucleoprotein ribozyme and human telomerase reverse transcriptase. Tethering PNC components to a LacO locus recruits other PNC components, further confirming the in vivo interactions. These interactions are present both in PNC-containing and -lacking cells. High-resolution localization analyses demonstrate that MRP RNA, CUGBP, and PTB colocalize at the PNC as a reticulated network, intertwining with newly synthesized RNA. Furthermore, green fluorescent protein (GFP)–PTB and GFP-CUGBP show a slower rate of fluorescence recovery after photobleaching at the PNC than in the nucleoplasm, illustrating the different molecular interaction of the complexes associated with the PNC. These findings support a working model in which the MRP RNA–protein complex becomes nucleated at the PNC in cancer cells and may play a role in gene expression regulation at the DNA locus that associates with the PNC. PMID:21233287

Characterization of MRP RNA-protein interactions within the perinucleolar compartment.

PubMed

Pollock, Callie; Daily, Kelly; Nguyen, Van Trung; Wang, Chen; Lewandowska, Marzena Anna; Bensaude, Olivier; Huang, Sui

2011-03-15

The perinucleolar compartment (PNC) forms in cancer cells and is highly enriched with a subset of polymerase III RNAs and RNA-binding proteins. Here we report that PNC components mitochondrial RNA-processing (MRP) RNA, pyrimidine tract-binding protein (PTB), and CUG-binding protein (CUGBP) interact in vivo, as demonstrated by coimmunoprecipitation and RNA pull-down experiments. Glycerol gradient analyses show that this complex is large and sediments at a different fraction from known MRP RNA-containing complexes, the MRP ribonucleoprotein ribozyme and human telomerase reverse transcriptase. Tethering PNC components to a LacO locus recruits other PNC components, further confirming the in vivo interactions. These interactions are present both in PNC-containing and -lacking cells. High-resolution localization analyses demonstrate that MRP RNA, CUGBP, and PTB colocalize at the PNC as a reticulated network, intertwining with newly synthesized RNA. Furthermore, green fluorescent protein (GFP)-PTB and GFP-CUGBP show a slower rate of fluorescence recovery after photobleaching at the PNC than in the nucleoplasm, illustrating the different molecular interaction of the complexes associated with the PNC. These findings support a working model in which the MRP RNA-protein complex becomes nucleated at the PNC in cancer cells and may play a role in gene expression regulation at the DNA locus that associates with the PNC.

Can biophysical properties of submersed macrophytes be determined by remote sensing?

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

Malthus, T.J.; Ciraolo, G.; La Loggia, G.

1997-06-01

This paper details the development of a computationally efficient Monte Carlo simulation program to model photon transport through submersed plant canopies, with emphasis on Seagrass communities. The model incorporates three components: the transmission of photons through a water column of varying depth and turbidity; the interaction of photons within a submersed plant canopy of varying biomass; and interactions with the bottom substrate. The three components of the model are discussed. Simulations were performed based on measured parameters for Posidonia oceanica and compared to measured subsurface reflectance spectra made over comparable seagrass communities in Sicilian coastal waters. It is shown thatmore » the output is realistic. Further simulations are undertaken to investigate the effect of depth and turbidity of the overlying water column. Both sets of results indicate the rapid loss of canopy signal as depth increases and water column phytoplankton concentrations increase. The implications for the development of algorithms for the estimation of submersed canopy biophysical parameters are briefly discussed.« less

Toroidal halos in a nontopological soliton model of dark matter

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

Mielke, Eckehard W.; Perez, Jose A. Velez

2007-02-15

Soliton type solutions of an axionlike scalar model with self-interaction are analyzed further as a toy model of dark matter halos. For a 'nonlinear superposition' of round and flattened configurations we found ringlike substructures in the density profile similarly as has been inferred for our Galaxy from the observed excess of the diffuse component of cosmic gamma rays.

An integrated model of soil, hydrology, and vegetation for carbon dynamics in wetland ecosystems

Treesearch

Yu Zhang; Changsheng Li; Carl C. Trettin; Harbin Li; Ge Sun

2002-01-01

Wetland ecosystems are an important component in global carbon (C) cycles and may exert a large influence on global clinlate change. Predictions of C dynamics require us to consider interactions among many critical factors of soil, hydrology, and vegetation. However, few such integrated C models exist for wetland ecosystems. In this paper, we report a simulation model...

A Three Component Model to Estimate Sensible Heat Flux Over Sparse Shrubs in Nevada

USGS Publications Warehouse

Chehbouni, A.; Nichols, W.D.; Njoku, E.G.; Qi, J.; Kerr, Y.H.; Cabot, F.

1997-01-01

It is now recognized that accurate partitioning of available energy into sensible and latent heat flux is crucial to understanding surface-atmosphere interactions. This issue is more complicated in arid and semi-arid regions where the relative contribution to surface fluxes from the soil and vegetation may vary significantly throughout the day and throughout the season. The objective of this paper is to present a three-component model to estimate sensible heat flux over heterogeneous surfaces. The surface was represented with two adjacent compartments. The first compartment is made up of two components, shrubs and shaded soil; the second compartment consists of bare, unshaded soil. Data collected at two different sites in Nevada during the summers of 1991 and 1992 were used to evaluate model performance. The results show that the present model is sufficiently general to yield satisfactory results for both sites.

Insights from Modeling the Integrated Climate, Biogeochemical Cycles, Human Activities and Their Interactions in the ACME Earth System Model

NASA Astrophysics Data System (ADS)

Leung, L. R.; Thornton, P. E.; Riley, W. J.; Calvin, K. V.

2017-12-01

Towards the goal of understanding the contributions from natural and managed systems to current and future greenhouse gas fluxes and carbon-climate and carbon-CO2 feedbacks, efforts have been underway to improve representations of the terrestrial, river, and human components of the ACME earth system model. Broadly, our efforts include implementation and comparison of approaches to represent the nutrient cycles and nutrient limitations on ecosystem production, extending the river transport model to represent sediment and riverine biogeochemistry, and coupling of human systems such as irrigation, reservoir operations, and energy and land use with the ACME land and river components. Numerical experiments have been designed to understand how terrestrial carbon, nitrogen, and phosphorus cycles regulate climate system feedbacks and the sensitivity of the feedbacks to different model treatments, examine key processes governing sediment and biogeochemistry in the rivers and their role in the carbon cycle, and exploring the impacts of human systems in perturbing the hydrological and carbon cycles and their interactions. This presentation will briefly introduce the ACME modeling approaches and discuss preliminary results and insights from numerical experiments that lay the foundation for improving understanding of the integrated climate-biogeochemistry-human system.

Latent feature decompositions for integrative analysis of multi-platform genomic data

PubMed Central

Gregory, Karl B.; Momin, Amin A.; Coombes, Kevin R.; Baladandayuthapani, Veerabhadran

2015-01-01

Increased availability of multi-platform genomics data on matched samples has sparked research efforts to discover how diverse molecular features interact both within and between platforms. In addition, simultaneous measurements of genetic and epigenetic characteristics illuminate the roles their complex relationships play in disease progression and outcomes. However, integrative methods for diverse genomics data are faced with the challenges of ultra-high dimensionality and the existence of complex interactions both within and between platforms. We propose a novel modeling framework for integrative analysis based on decompositions of the large number of platform-specific features into a smaller number of latent features. Subsequently we build a predictive model for clinical outcomes accounting for both within- and between-platform interactions based on Bayesian model averaging procedures. Principal components, partial least squares and non-negative matrix factorization as well as sparse counterparts of each are used to define the latent features, and the performance of these decompositions is compared both on real and simulated data. The latent feature interactions are shown to preserve interactions between the original features and not only aid prediction but also allow explicit selection of outcome-related features. The methods are motivated by and applied to, a glioblastoma multiforme dataset from The Cancer Genome Atlas to predict patient survival times integrating gene expression, microRNA, copy number and methylation data. For the glioblastoma data, we find a high concordance between our selected prognostic genes and genes with known associations with glioblastoma. In addition, our model discovers several relevant cross-platform interactions such as copy number variation associated gene dosing and epigenetic regulation through promoter methylation. On simulated data, we show that our proposed method successfully incorporates interactions within and between genomic platforms to aid accurate prediction and variable selection. Our methods perform best when principal components are used to define the latent features. PMID:26146492

In-situ molecular-level elucidation of organofluorine binding sites in a whole peat soil.

PubMed

Longstaffe, James G; Courtier-Murias, Denis; Soong, Ronald; Simpson, Myrna J; Maas, Werner E; Fey, Michael; Hutchins, Howard; Krishnamurthy, Sridevi; Struppe, Jochem; Alaee, Mehran; Kumar, Rajeev; Monette, Martine; Stronks, Henry J; Simpson, André J

2012-10-02

The chemical nature of xenobiotic binding sites in soils is of vital importance to environmental biogeochemistry. Interactions between xenobiotics and the naturally occurring organic constituents of soils are strongly correlated to environmental persistence, bioaccessibility, and ecotoxicity. Nevertheless, because of the complex structural and chemical heterogeneity of soils, studies of these interactions are most commonly performed indirectly, using correlative methods, fractionation, or chemical modification. Here we identify the organic components of an unmodified peat soil where some organofluorine xenobiotic compounds interact using direct molecular-level methods. Using (19)F→(1)H cross-polarization magic angle spinning (CP-MAS) nuclear magnetic resonance (NMR) spectroscopy, the (19)F nuclei of organofluorine compounds are used to induce observable transverse magnetization in the (1)H nuclei of organic components of the soil with which they interact after sorption. The observed (19)F→(1)H CP-MAS spectra and dynamics are compared to those produced using model soil organic compounds, lignin and albumin. It is found that lignin-like components can account for the interactions observed in this soil for heptafluoronaphthol (HFNap) while protein structures can account for the interactions observed for perfluorooctanoic acid (PFOA). This study employs novel comprehensive multi-phase (CMP) NMR technology that permits the application of solution-, gel-, and solid-state NMR experiments on intact soil samples in their swollen state.

Agent-based models of cellular systems.

PubMed

Cannata, Nicola; Corradini, Flavio; Merelli, Emanuela; Tesei, Luca

2013-01-01

Software agents are particularly suitable for engineering models and simulations of cellular systems. In a very natural and intuitive manner, individual software components are therein delegated to reproduce "in silico" the behavior of individual components of alive systems at a given level of resolution. Individuals' actions and interactions among individuals allow complex collective behavior to emerge. In this chapter we first introduce the readers to software agents and multi-agent systems, reviewing the evolution of agent-based modeling of biomolecular systems in the last decade. We then describe the main tools, platforms, and methodologies available for programming societies of agents, possibly profiting also of toolkits that do not require advanced programming skills.

Monitoring Wind Turbine Loading Using Power Converter Signals

NASA Astrophysics Data System (ADS)

Rieg, C. A.; Smith, C. J.; Crabtree, C. J.

2016-09-01

The ability to detect faults and predict loads on a wind turbine drivetrain's mechanical components cost-effectively is critical to making the cost of wind energy competitive. In order to investigate whether this is possible using the readily available power converter current signals, an existing permanent magnet synchronous generator based wind energy conversion system computer model was modified to include a grid-side converter (GSC) for an improved converter model and a gearbox. The GSC maintains a constant DC link voltage via vector control. The gearbox was modelled as a 3-mass model to allow faults to be included. Gusts and gearbox faults were introduced to investigate the ability of the machine side converter (MSC) current (I q) to detect and quantify loads on the mechanical components. In this model, gearbox faults were not detectable in the I q signal due to shaft stiffness and damping interaction. However, a model that predicts the load change on mechanical wind turbine components using I q was developed and verified using synthetic and real wind data.

A Molecular Dynamic Modeling of Hemoglobin-Hemoglobin Interactions

NASA Astrophysics Data System (ADS)

Wu, Tao; Yang, Ye; Sheldon Wang, X.; Cohen, Barry; Ge, Hongya

2010-05-01

In this paper, we present a study of hemoglobin-hemoglobin interaction with model reduction methods. We begin with a simple spring-mass system with given parameters (mass and stiffness). With this known system, we compare the mode superposition method with Singular Value Decomposition (SVD) based Principal Component Analysis (PCA). Through PCA we are able to recover the principal direction of this system, namely the model direction. This model direction will be matched with the eigenvector derived from mode superposition analysis. The same technique will be implemented in a much more complicated hemoglobin-hemoglobin molecule interaction model, in which thousands of atoms in hemoglobin molecules are coupled with tens of thousands of T3 water molecule models. In this model, complex inter-atomic and inter-molecular potentials are replaced by nonlinear springs. We employ the same method to get the most significant modes and their frequencies of this complex dynamical system. More complex physical phenomena can then be further studied by these coarse grained models.

Effects of changes along the risk chain on flood risk

NASA Astrophysics Data System (ADS)

Duha Metin, Ayse; Apel, Heiko; Viet Dung, Nguyen; Guse, Björn; Kreibich, Heidi; Schröter, Kai; Vorogushyn, Sergiy; Merz, Bruno

2017-04-01

Interactions of hydrological and socio-economic factors shape flood disaster risk. For this reason, assessment of flood risk ideally takes into account the whole flood risk chain from atmospheric processes, through the catchment and river system processes to the damage mechanisms in the affected areas. Since very different processes at various scales are interacting along the flood risk, the impact of the single components is rather unclear. However for flood risk management, it is required to know the controlling factor of flood damages. The present study, using the flood-prone Mulde catchment in Germany, discusses the sensitivity of flood risk to disturbances along the risk chain: How do disturbances propagate through the risk chain? How do different disturbances combine or conflict and affect flood risk? In this sensitivity analysis, the five components of the flood risk change are included. These are climate, catchment, river system, exposure and vulnerability. A model framework representing the complete risk chain is combined with observational data to understand how the sensitivities evolve along the risk chain by considering three plausible change scenarios for each of five components. The flood risk is calculated by using the Regional Flood Model (RFM) which is based on a continuous simulation approach, including rainfall-runoff, 1D river network, 2D hinterland inundation and damage estimation models. The sensitivity analysis covers more than 240 scenarios with different combinations of the five components. It is investigated how changes in different components affect risk indicators, such as the risk curve and expected annual damage (EAD). In conclusion, it seems that changes in exposure and vulnerability seem to outweigh changes in hazard.

Optimization of Borehole Thermal Energy Storage System Design Using Comprehensive Coupled Simulation Models

NASA Astrophysics Data System (ADS)

Welsch, Bastian; Rühaak, Wolfram; Schulte, Daniel O.; Formhals, Julian; Bär, Kristian; Sass, Ingo

2017-04-01

Large-scale borehole thermal energy storage (BTES) is a promising technology in the development of sustainable, renewable and low-emission district heating concepts. Such systems consist of several components and assemblies like the borehole heat exchangers (BHE), other heat sources (e.g. solarthermics, combined heat and power plants, peak load boilers, heat pumps), distribution networks and heating installations. The complexity of these systems necessitates numerical simulations in the design and planning phase. Generally, the subsurface components are simulated separately from the above ground components of the district heating system. However, as fluid and heat are exchanged, the subsystems interact with each other and thereby mutually affect their performances. For a proper design of the overall system, it is therefore imperative to take into account the interdependencies of the subsystems. Based on a TCP/IP communication we have developed an interface for the coupling of a simulation package for heating installations with a finite element software for the modeling of the heat flow in the subsurface and the underground installations. This allows for a co-simulation of all system components, whereby the interaction of the different subsystems is considered. Furthermore, the concept allows for a mathematical optimization of the components and the operational parameters. Consequently, a finer adjustment of the system can be ensured and a more precise prognosis of the system's performance can be realized.

Integrated modeling of land-use change: the role of coupling, interactions and feedbacks between the human and Earth systems

NASA Astrophysics Data System (ADS)

Monier, E.; Kicklighter, D. W.; Ejaz, Q.; Winchester, N.; Paltsev, S.; Reilly, J. M.

2016-12-01

Land-use change integrates a large number of components of the human and Earth systems, including climate, energy, water, and land. These complex coupling elements, interactions and feedbacks take place on a variety of space and time scales, thus increasing the complexity of land-use change modeling frameworks. In this study, we aim to identify which coupling elements, interactions and feedbacks are important for modeling land-use change, both at the global and regional level. First, we review the existing land-use change modeling framework used to develop land-use change projections for the Representative Concentration Pathways (RCP) scenarios. In such framework, land-use change is simulated by Integrated Assessment Models (IAMs) and mainly influenced by economic, energy, demographic and policy drivers. IAMs focus on representing the demand for agriculture and forestry goods (crops for food and bioenergy, forest products for construction and bioenergy), the interactions with other sectors of the economy and trade between various regions of the world. Then, we investigate how important various coupling elements and feedbacks with the Earth system are for projections of land-use change at the global and regional level. We focus on the following: i) the climate impacts on land productivity and greenhouse gas emissions, which requires climate change information and coupling to a terrestrial ecosystem model/crop model; ii) the climate and economic impacts on irrigation availability, which requires coupling the LUC modeling framework to a water resources management model and disaggregating rainfed and irrigated croplands; iii) the feedback of land-use change on the global and regional climate system through land-use change emissions and changes in the surface albedo and hydrology, which requires coupling to an Earth system model. Finally, we conclude our study by highlighting the current lack of clarity in how various components of the human and Earth systems are coupled in IAMs , and the need for a lexicon that is agreed upon by the IAM community.

No direct by maternal effects interaction detected for pre-weaning growth in Romane sheep using a reaction norm model.

PubMed

David, Ingrid; Bouvier, Frédéric; Ricard, Edmond; Ruesche, Julien; Weisbecker, Jean-Louis

2013-09-30

The pre-weaning growth of lambs, an important component of meat production, depends on maternal and direct effects. These effects cannot be observed directly and models used to study pre-weaning growth assume that they are additive. However, it is reasonable to suggest that the influence of direct effects on growth may differ depending on the value of maternal effects i.e. an interaction may exist between the two components. To test this hypothesis, an experiment was carried out in Romane sheep in order to obtain observations of maternal phenotypic effects (milk yield and milk quality) and pre-weaning growth of the lambs. The experiment consisted of mating ewes that had markedly different maternal genetic effects with rams that contributed very different genetic effects in four replicates of a 3 × 2 factorial plan. Milk yield was measured using the lamb suckling weight differential technique and milk composition (fat and protein contents) was determined by infrared spectroscopy at 15, 21 and 35 days after lambing. Lambs were weighed at birth and then at 15, 21 and 35 days. An interaction between genotype (of the lamb) and environment (milk yield and quality) for average daily gain was tested using a restricted likelihood ratio test, comparing a linear reaction norm model (interaction model) to a classical additive model (no interaction model). A total of 1284 weights of 442 lambs born from 166 different ewes were analysed. On average, the ewes produced 2.3 ± 0.8 L milk per day. The average protein and fat contents were 50 ± 4 g/L and 60 ± 18 g/L, respectively. The mean 0-35 day average daily gain was 207 ± 46 g/d. Results of the restricted likelihood ratio tests did not highlight any significant interactions between the genotype of the lambs and milk production of the ewe. Our results support the hypothesis of additivity of maternal and direct effects on growth that is currently applied in genetic evaluation models.

Social Network Extraction and Analysis Based on Multimodal Dyadic Interaction

PubMed Central

Escalera, Sergio; Baró, Xavier; Vitrià, Jordi; Radeva, Petia; Raducanu, Bogdan

2012-01-01

Social interactions are a very important component in people’s lives. Social network analysis has become a common technique used to model and quantify the properties of social interactions. In this paper, we propose an integrated framework to explore the characteristics of a social network extracted from multimodal dyadic interactions. For our study, we used a set of videos belonging to New York Times’ Blogging Heads opinion blog. The Social Network is represented as an oriented graph, whose directed links are determined by the Influence Model. The links’ weights are a measure of the “influence” a person has over the other. The states of the Influence Model encode automatically extracted audio/visual features from our videos using state-of-the art algorithms. Our results are reported in terms of accuracy of audio/visual data fusion for speaker segmentation and centrality measures used to characterize the extracted social network. PMID:22438733

Plant microRNA-Target Interaction Identification Model Based on the Integration of Prediction Tools and Support Vector Machine

PubMed Central

Meng, Jun; Shi, Lin; Luan, Yushi

2014-01-01

Background Confident identification of microRNA-target interactions is significant for studying the function of microRNA (miRNA). Although some computational miRNA target prediction methods have been proposed for plants, results of various methods tend to be inconsistent and usually lead to more false positive. To address these issues, we developed an integrated model for identifying plant miRNA–target interactions. Results Three online miRNA target prediction toolkits and machine learning algorithms were integrated to identify and analyze Arabidopsis thaliana miRNA-target interactions. Principle component analysis (PCA) feature extraction and self-training technology were introduced to improve the performance. Results showed that the proposed model outperformed the previously existing methods. The results were validated by using degradome sequencing supported Arabidopsis thaliana miRNA-target interactions. The proposed model constructed on Arabidopsis thaliana was run over Oryza sativa and Vitis vinifera to demonstrate that our model is effective for other plant species. Conclusions The integrated model of online predictors and local PCA-SVM classifier gained credible and high quality miRNA-target interactions. The supervised learning algorithm of PCA-SVM classifier was employed in plant miRNA target identification for the first time. Its performance can be substantially improved if more experimentally proved training samples are provided. PMID:25051153

Integrating Spatial Components into FIA Models of Forest Resources: Some Technical Aspects

Treesearch

Pat Terletzky; Tracey Frescino

2005-01-01

We examined two software packages to determine their feasibility of implementing spatially explicit, forest resource models that integrate Forest Inventory and Analysis data (FIA). ARCINFO and Interactive Data Language (IDL) were examined for their input requirements, speed of processing, storage requirements, and flexibility of implementing. Implementations of two...

Integrative approaches for modeling regulation and function of the respiratory system.

PubMed

Ben-Tal, Alona; Tawhai, Merryn H

2013-01-01

Mathematical models have been central to understanding the interaction between neural control and breathing. Models of the entire respiratory system-which comprises the lungs and the neural circuitry that controls their ventilation-have been derived using simplifying assumptions to compartmentalize each component of the system and to define the interactions between components. These full system models often rely-through necessity-on empirically derived relationships or parameters, in addition to physiological values. In parallel with the development of whole respiratory system models are mathematical models that focus on furthering a detailed understanding of the neural control network, or of the several functions that contribute to gas exchange within the lung. These models are biophysically based, and rely on physiological parameters. They include single-unit models for a breathing lung or neural circuit, through to spatially distributed models of ventilation and perfusion, or multicircuit models for neural control. The challenge is to bring together these more recent advances in models of neural control with models of lung function, into a full simulation for the respiratory system that builds upon the more detailed models but remains computationally tractable. This requires first understanding the mathematical models that have been developed for the respiratory system at different levels, and which could be used to study how physiological levels of O2 and CO2 in the blood are maintained. Copyright © 2013 Wiley Periodicals, Inc.

Survey of perceived influence of the conceptual design model of interactive television advertising towards impulse purchase tendency

NASA Astrophysics Data System (ADS)

Sarif, Siti Mahfuzah; Omar, Azizah Che; Shiratuddin, Norshuhada

2016-08-01

With the proliferation of technology assisted shopping, there is growing evidence that impulse buying is an emerging phenomenon, which has been the focus of this study. Literatures indicate that studies related to impulse purchase for interactive television (iTV) advertising are highly scarce. It was found that most of the existing impulse purchase elements are mainly focusing on traditional retail store, website advertising, and traditional TV advertising, but not on iTV advertising. Due to that, through a systematic process, a design model for developing iTV advertising with influence towards impulse purchase tendency was developed and tested in this study. The design model is named as iTVAdIP and comprises of three main components; technology, impulse purchase components, and development process. This paper describes the survey, which measures the influence of iTVAdIP design model towards impulse purchase tendency. 37 potential advertising designers were involved in the survey. The results indicate that the iTVAdIP is practical and workable in developing iTV advertisement that could influence consumer to buy the advertised product.

Army-NASA aircrew/aircraft integration program (A3I) software detailed design document, phase 3

NASA Technical Reports Server (NTRS)

Banda, Carolyn; Chiu, Alex; Helms, Gretchen; Hsieh, Tehming; Lui, Andrew; Murray, Jerry; Shankar, Renuka

1990-01-01

The capabilities and design approach of the MIDAS (Man-machine Integration Design and Analysis System) computer-aided engineering (CAE) workstation under development by the Army-NASA Aircrew/Aircraft Integration Program is detailed. This workstation uses graphic, symbolic, and numeric prototyping tools and human performance models as part of an integrated design/analysis environment for crewstation human engineering. Developed incrementally, the requirements and design for Phase 3 (Dec. 1987 to Jun. 1989) are described. Software tools/models developed or significantly modified during this phase included: an interactive 3-D graphic cockpit design editor; multiple-perspective graphic views to observe simulation scenarios; symbolic methods to model the mission decomposition, equipment functions, pilot tasking and loading, as well as control the simulation; a 3-D dynamic anthropometric model; an intermachine communications package; and a training assessment component. These components were successfully used during Phase 3 to demonstrate the complex interactions and human engineering findings involved with a proposed cockpit communications design change in a simulated AH-64A Apache helicopter/mission that maps to empirical data from a similar study and AH-1 Cobra flight test.

The Software Architecture of Global Climate Models

NASA Astrophysics Data System (ADS)

Alexander, K. A.; Easterbrook, S. M.

2011-12-01

It has become common to compare and contrast the output of multiple global climate models (GCMs), such as in the Climate Model Intercomparison Project Phase 5 (CMIP5). However, intercomparisons of the software architecture of GCMs are almost nonexistent. In this qualitative study of seven GCMs from Canada, the United States, and Europe, we attempt to fill this gap in research. We describe the various representations of the climate system as computer programs, and account for architectural differences between models. Most GCMs now practice component-based software engineering, where Earth system components (such as the atmosphere or land surface) are present as highly encapsulated sub-models. This architecture facilitates a mix-and-match approach to climate modelling that allows for convenient sharing of model components between institutions, but it also leads to difficulty when choosing where to draw the lines between systems that are not encapsulated in the real world, such as sea ice. We also examine different styles of couplers in GCMs, which manage interaction and data flow between components. Finally, we pay particular attention to the varying levels of complexity in GCMs, both between and within models. Many GCMs have some components that are significantly more complex than others, a phenomenon which can be explained by the respective institution's research goals as well as the origin of the model components. In conclusion, although some features of software architecture have been adopted by every GCM we examined, other features show a wide range of different design choices and strategies. These architectural differences may provide new insights into variability and spread between models.

Metamodels for Transdisciplinary Analysis of Wildlife Population Dynamics

PubMed Central

Lacy, Robert C.; Miller, Philip S.; Nyhus, Philip J.; Pollak, J. P.; Raboy, Becky E.; Zeigler, Sara L.

2013-01-01

Wildlife population models have been criticized for their narrow disciplinary perspective when analyzing complexity in coupled biological – physical – human systems. We describe a “metamodel” approach to species risk assessment when diverse threats act at different spatiotemporal scales, interact in non-linear ways, and are addressed by distinct disciplines. A metamodel links discrete, individual models that depict components of a complex system, governing the flow of information among models and the sequence of simulated events. Each model simulates processes specific to its disciplinary realm while being informed of changes in other metamodel components by accessing common descriptors of the system, populations, and individuals. Interactions among models are revealed as emergent properties of the system. We introduce a new metamodel platform, both to further explain key elements of the metamodel approach and as an example that we hope will facilitate the development of other platforms for implementing metamodels in population biology, species risk assessments, and conservation planning. We present two examples – one exploring the interactions of dispersal in metapopulations and the spread of infectious disease, the other examining predator-prey dynamics – to illustrate how metamodels can reveal complex processes and unexpected patterns when population dynamics are linked to additional extrinsic factors. Metamodels provide a flexible, extensible method for expanding population viability analyses beyond models of isolated population demographics into more complete representations of the external and intrinsic threats that must be understood and managed for species conservation. PMID:24349567

Effects of air-sea interaction on extended-range prediction of geopotential height at 500 hPa over the northern extratropical region

NASA Astrophysics Data System (ADS)

Wang, Xujia; Zheng, Zhihai; Feng, Guolin

2018-04-01

The contribution of air-sea interaction on the extended-range prediction of geopotential height at 500 hPa in the northern extratropical region has been analyzed with a coupled model form Beijing Climate Center and its atmospheric components. Under the assumption of the perfect model, the extended-range prediction skill was evaluated by anomaly correlation coefficient (ACC), root mean square error (RMSE), and signal-to-noise ratio (SNR). The coupled model has a better prediction skill than its atmospheric model, especially, the air-sea interaction in July made a greater contribution for the improvement of prediction skill than other months. The prediction skill of the extratropical region in the coupled model reaches 16-18 days in all months, while the atmospheric model reaches 10-11 days in January, April, and July and only 7-8 days in October, indicating that the air-sea interaction can extend the prediction skill of the atmospheric model by about 1 week. The errors of both the coupled model and the atmospheric model reach saturation in about 20 days, suggesting that the predictable range is less than 3 weeks.

Augmenting Microarray Data with Literature-Based Knowledge to Enhance Gene Regulatory Network Inference

PubMed Central

Kilicoglu, Halil; Shin, Dongwook; Rindflesch, Thomas C.

2014-01-01

Gene regulatory networks are a crucial aspect of systems biology in describing molecular mechanisms of the cell. Various computational models rely on random gene selection to infer such networks from microarray data. While incorporation of prior knowledge into data analysis has been deemed important, in practice, it has generally been limited to referencing genes in probe sets and using curated knowledge bases. We investigate the impact of augmenting microarray data with semantic relations automatically extracted from the literature, with the view that relations encoding gene/protein interactions eliminate the need for random selection of components in non-exhaustive approaches, producing a more accurate model of cellular behavior. A genetic algorithm is then used to optimize the strength of interactions using microarray data and an artificial neural network fitness function. The result is a directed and weighted network providing the individual contribution of each gene to its target. For testing, we used invasive ductile carcinoma of the breast to query the literature and a microarray set containing gene expression changes in these cells over several time points. Our model demonstrates significantly better fitness than the state-of-the-art model, which relies on an initial random selection of genes. Comparison to the component pathways of the KEGG Pathways in Cancer map reveals that the resulting networks contain both known and novel relationships. The p53 pathway results were manually validated in the literature. 60% of non-KEGG relationships were supported (74% for highly weighted interactions). The method was then applied to yeast data and our model again outperformed the comparison model. Our results demonstrate the advantage of combining gene interactions extracted from the literature in the form of semantic relations with microarray analysis in generating contribution-weighted gene regulatory networks. This methodology can make a significant contribution to understanding the complex interactions involved in cellular behavior and molecular physiology. PMID:24921649

Augmenting microarray data with literature-based knowledge to enhance gene regulatory network inference.

PubMed

Chen, Guocai; Cairelli, Michael J; Kilicoglu, Halil; Shin, Dongwook; Rindflesch, Thomas C

2014-06-01

Gene regulatory networks are a crucial aspect of systems biology in describing molecular mechanisms of the cell. Various computational models rely on random gene selection to infer such networks from microarray data. While incorporation of prior knowledge into data analysis has been deemed important, in practice, it has generally been limited to referencing genes in probe sets and using curated knowledge bases. We investigate the impact of augmenting microarray data with semantic relations automatically extracted from the literature, with the view that relations encoding gene/protein interactions eliminate the need for random selection of components in non-exhaustive approaches, producing a more accurate model of cellular behavior. A genetic algorithm is then used to optimize the strength of interactions using microarray data and an artificial neural network fitness function. The result is a directed and weighted network providing the individual contribution of each gene to its target. For testing, we used invasive ductile carcinoma of the breast to query the literature and a microarray set containing gene expression changes in these cells over several time points. Our model demonstrates significantly better fitness than the state-of-the-art model, which relies on an initial random selection of genes. Comparison to the component pathways of the KEGG Pathways in Cancer map reveals that the resulting networks contain both known and novel relationships. The p53 pathway results were manually validated in the literature. 60% of non-KEGG relationships were supported (74% for highly weighted interactions). The method was then applied to yeast data and our model again outperformed the comparison model. Our results demonstrate the advantage of combining gene interactions extracted from the literature in the form of semantic relations with microarray analysis in generating contribution-weighted gene regulatory networks. This methodology can make a significant contribution to understanding the complex interactions involved in cellular behavior and molecular physiology.

MORE: mixed optimization for reverse engineering--an application to modeling biological networks response via sparse systems of nonlinear differential equations.

PubMed

Sambo, Francesco; de Oca, Marco A Montes; Di Camillo, Barbara; Toffolo, Gianna; Stützle, Thomas

2012-01-01

Reverse engineering is the problem of inferring the structure of a network of interactions between biological variables from a set of observations. In this paper, we propose an optimization algorithm, called MORE, for the reverse engineering of biological networks from time series data. The model inferred by MORE is a sparse system of nonlinear differential equations, complex enough to realistically describe the dynamics of a biological system. MORE tackles separately the discrete component of the problem, the determination of the biological network topology, and the continuous component of the problem, the strength of the interactions. This approach allows us both to enforce system sparsity, by globally constraining the number of edges, and to integrate a priori information about the structure of the underlying interaction network. Experimental results on simulated and real-world networks show that the mixed discrete/continuous optimization approach of MORE significantly outperforms standard continuous optimization and that MORE is competitive with the state of the art in terms of accuracy of the inferred networks.

Analysis and Modeling of the Arctic Oscillation Using a Simple Barotropic Model with Baroclinic Eddy Forcing.

NASA Astrophysics Data System (ADS)

Tanaka, H. L.

2003-06-01

In this study, a numerical simulation of the Arctic Oscillation (AO) is conducted using a simple barotropic model that considers the barotropic-baroclinic interactions as the external forcing. The model is referred to as a barotropic S model since the external forcing is obtained statistically from the long-term historical data, solving an inverse problem. The barotropic S model has been integrated for 51 years under a perpetual January condition and the dominant empirical orthogonal function (EOF) modes in the model have been analyzed. The results are compared with the EOF analysis of the barotropic component of the real atmosphere based on the daily NCEP-NCAR reanalysis for 50 yr from 1950 to 1999.According to the result, the first EOF of the model atmosphere appears to be the AO similar to the observation. The annular structure of the AO and the two centers of action at Pacific and Atlantic are simulated nicely by the barotropic S model. Therefore, the atmospheric low-frequency variabilities have been captured satisfactorily even by the simple barotropic model.The EOF analysis is further conducted to the external forcing of the barotropic S model. The structure of the dominant forcing shows the characteristics of synoptic-scale disturbances of zonal wavenumber 6 along the Pacific storm track. The forcing is induced by the barotropic-baroclinic interactions associated with baroclinic instability.The result suggests that the AO can be understood as the natural variability of the barotropic component of the atmosphere induced by the inherent barotropic dynamics, which is forced by the barotropic-baroclinic interactions. The fluctuating upscale energy cascade from planetary waves and synoptic disturbances to the zonal motion plays the key role for the excitation of the AO.

Point-to-point migration functions and gravity model renormalization: approaches to aggregation in spatial interaction modeling.

PubMed

Slater, P B

1985-08-01

Two distinct approaches to assessing the effect of geographic scale on spatial interactions are modeled. In the first, the question of whether a distance deterrence function, which explains interactions for one system of zones, can also succeed on a more aggregate scale, is examined. Only the two-parameter function for which it is found that distances between macrozones are weighted averaged of distances between component zones is satisfactory in this regard. Estimation of continuous (point-to-point) functions--in the form of quadrivariate cubic polynomials--for US interstate migration streams, is then undertaken. Upon numerical integration, these higher order surfaces yield predictions of interzonal and intrazonal movements at any scale of interest. Test of spatial stationarity, isotropy, and symmetry of interstate migration are conducted in this framework.

Biomolecular electrostatics and solvation: a computational perspective

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

Ren, Pengyu; Chun, Jaehun; Thomas, Dennis G.

2012-11-01

An understanding of molecular interactions is essential for insight into biological systems at the molecular scale. Among the various components of molecular interactions, electrostatics are of special importance because of their long-range nature and their influence on polar or charged molecules, including water, aqueous ions, proteins, nucleic acids, carbohydrates, and membrane lipids. In particular, robust models of electrostatic interactions are essential for understanding the solvation properties of biomolecules and the effects of solvation upon biomolecular folding, binding, enzyme catalysis and dynamics. Electrostatics, therefore, are of central importance to understanding biomolecular structure and modeling interactions within and among biological molecules. Thismore » review discusses the solvation of biomolecules with a computational biophysics view towards describing the phenomenon. While our main focus lies on the computational aspect of the models, we summarize the common characteristics of biomolecular solvation (e.g., solvent structure, polarization, ion binding, and nonpolar behavior) in order to provide reasonable backgrounds to understand the solvation models.« less

Monodisperse self-assembly in a model with protein-like interactions

NASA Astrophysics Data System (ADS)

Wilber, Alex W.; Doye, Jonathan P. K.; Louis, Ard A.; Lewis, Anna C. F.

2009-11-01

We study the self-assembly behavior of patchy particles with "proteinlike" interactions that can be considered as a minimal model for the assembly of viral capsids and other shell-like protein complexes. We thoroughly explore the thermodynamics and dynamics of self-assembly as a function of the parameters of the model and find robust assembly of all target structures considered. Optimal assembly occurs in the region of parameter space where a free energy barrier regulates the rate of nucleation, thus preventing the premature exhaustion of the supply of monomers that can lead to the formation of incomplete shells. The interactions also need to be specific enough to prevent the assembly of malformed shells, but while maintaining kinetic accessibility. Free energy landscapes computed for our model have a funnel-like topography guiding the system to form the target structure and show that the torsional component of the interparticle interactions prevents the formation of disordered aggregates that would otherwise act as kinetic traps.

Biomolecular electrostatics and solvation: a computational perspective

PubMed Central

Ren, Pengyu; Chun, Jaehun; Thomas, Dennis G.; Schnieders, Michael J.; Marucho, Marcelo; Zhang, Jiajing; Baker, Nathan A.

2012-01-01

An understanding of molecular interactions is essential for insight into biological systems at the molecular scale. Among the various components of molecular interactions, electrostatics are of special importance because of their long-range nature and their influence on polar or charged molecules, including water, aqueous ions, proteins, nucleic acids, carbohydrates, and membrane lipids. In particular, robust models of electrostatic interactions are essential for understanding the solvation properties of biomolecules and the effects of solvation upon biomolecular folding, binding, enzyme catalysis, and dynamics. Electrostatics, therefore, are of central importance to understanding biomolecular structure and modeling interactions within and among biological molecules. This review discusses the solvation of biomolecules with a computational biophysics view towards describing the phenomenon. While our main focus lies on the computational aspect of the models, we provide an overview of the basic elements of biomolecular solvation (e.g., solvent structure, polarization, ion binding, and nonpolar behavior) in order to provide a background to understand the different types of solvation models. PMID:23217364

Biomolecular electrostatics and solvation: a computational perspective.

PubMed

Ren, Pengyu; Chun, Jaehun; Thomas, Dennis G; Schnieders, Michael J; Marucho, Marcelo; Zhang, Jiajing; Baker, Nathan A

2012-11-01

An understanding of molecular interactions is essential for insight into biological systems at the molecular scale. Among the various components of molecular interactions, electrostatics are of special importance because of their long-range nature and their influence on polar or charged molecules, including water, aqueous ions, proteins, nucleic acids, carbohydrates, and membrane lipids. In particular, robust models of electrostatic interactions are essential for understanding the solvation properties of biomolecules and the effects of solvation upon biomolecular folding, binding, enzyme catalysis, and dynamics. Electrostatics, therefore, are of central importance to understanding biomolecular structure and modeling interactions within and among biological molecules. This review discusses the solvation of biomolecules with a computational biophysics view toward describing the phenomenon. While our main focus lies on the computational aspect of the models, we provide an overview of the basic elements of biomolecular solvation (e.g. solvent structure, polarization, ion binding, and non-polar behavior) in order to provide a background to understand the different types of solvation models.

The KASCADE-Grande energy spectrum of cosmic rays and the role of hadronic interaction models

NASA Astrophysics Data System (ADS)

Apel, W. D.; Arteaga-Velázquez, J. C.; Bekk, K.; Bertaina, M.; Blümer, J.; Bozdog, H.; Brancus, I. M.; Cantoni, E.; Chiavassa, A.; Cossavella, F.; Daumiller, K.; de Souza, V.; Di Pierro, F.; Doll, P.; Engel, R.; Engler, J.; Finger, M.; Fuchs, B.; Fuhrmann, D.; Gils, H. J.; Glasstetter, R.; Grupen, C.; Haungs, A.; Heck, D.; Hörandel, J. R.; Huber, D.; Huege, T.; Kampert, K.-H.; Kang, D.; Klages, H. O.; Link, K.; Łuczak, P.; Ludwig, M.; Mathes, H. J.; Mayer, H. J.; Melissas, M.; Milke, J.; Mitrica, B.; Morello, C.; Oehlschläger, J.; Ostapchenko, S.; Palmieri, N.; Petcu, M.; Pierog, T.; Rebel, H.; Roth, M.; Schieler, H.; Schoo, S.; Schröder, F. G.; Sima, O.; Toma, G.; Trinchero, G. C.; Ulrich, H.; Weindl, A.; Wochele, J.; Wommer, M.; Zabierowski, J.

2014-05-01

Previous results obtained by KASCADE-Grande using the QGSjetII-02 hadronic interaction model have shown that the energy spectrum of cosmic rays between 1016 eV and 1018 eV exhibits a significant hardening at approximately 2×1016 eV and a slight but statistically significant steepening close to 1017 eV. Moreover, the analysis with QGSjetII-02 suggests that the break observed around 1017 eV is caused by the heavy component of primary cosmic rays. In this paper, we report on the results of similar analyses performed using the SIBYLL 2.1 and EPOS 1.99 hadronic interaction models to interpret the data. The present results confirm qualitatively the previous findings. However, the intensity of the all-particle spectrum, the positions of the hardening and steepening of the spectrum, as well as the relative abundance of the heavy and light mass groups depend on the hadronic interaction model used to interpret the data.

InterPred: A pipeline to identify and model protein-protein interactions.

PubMed

Mirabello, Claudio; Wallner, Björn

2017-06-01

Protein-protein interactions (PPI) are crucial for protein function. There exist many techniques to identify PPIs experimentally, but to determine the interactions in molecular detail is still difficult and very time-consuming. The fact that the number of PPIs is vastly larger than the number of individual proteins makes it practically impossible to characterize all interactions experimentally. Computational approaches that can bridge this gap and predict PPIs and model the interactions in molecular detail are greatly needed. Here we present InterPred, a fully automated pipeline that predicts and model PPIs from sequence using structural modeling combined with massive structural comparisons and molecular docking. A key component of the method is the use of a novel random forest classifier that integrate several structural features to distinguish correct from incorrect protein-protein interaction models. We show that InterPred represents a major improvement in protein-protein interaction detection with a performance comparable or better than experimental high-throughput techniques. We also show that our full-atom protein-protein complex modeling pipeline performs better than state of the art protein docking methods on a standard benchmark set. In addition, InterPred was also one of the top predictors in the latest CAPRI37 experiment. InterPred source code can be downloaded from http://wallnerlab.org/InterPred Proteins 2017; 85:1159-1170. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

ISAC - A tool for aeroservoelastic modeling and analysis. [Interaction of Structures, Aerodynamics, and Control

NASA Technical Reports Server (NTRS)

Adams, William M., Jr.; Hoadley, Sherwood T.

1993-01-01

This paper discusses the capabilities of the Interaction of Structures, Aerodynamics, and Controls (ISAC) system of program modules. The major modeling, analysis, and data management components of ISAC are identified. Equations of motion are displayed for a Laplace-domain representation of the unsteady aerodynamic forces. Options for approximating a frequency-domain representation of unsteady aerodynamic forces with rational functions of the Laplace variable are shown. Linear time invariant state-space equations of motion that result are discussed. Model generation and analyses of stability and dynamic response characteristics are shown for an aeroelastic vehicle which illustrate some of the capabilities of ISAC as a modeling and analysis tool for aeroelastic applications.

Development of structural model of adaptive training complex in ergatic systems for professional use

NASA Astrophysics Data System (ADS)

Obukhov, A. D.; Dedov, D. L.; Arkhipov, A. E.

2018-03-01

The article considers the structural model of the adaptive training complex (ATC), which reflects the interrelations between the hardware, software and mathematical model of ATC and describes the processes in this subject area. The description of the main components of software and hardware complex, their interaction and functioning within the common system are given. Also the article scrutinizers a brief description of mathematical models of personnel activity, a technical system and influences, the interactions of which formalize the regularities of ATC functioning. The studies of main objects of training complexes and connections between them will make it possible to realize practical implementation of ATC in ergatic systems for professional use.

Electric field-induced reorganization of two-component supported bilayer membranes

PubMed Central

Groves, Jay T.; Boxer, Steven G.; McConnell, Harden M.

1997-01-01

Application of electric fields tangent to the plane of a confined patch of fluid bilayer membrane can create lateral concentration gradients of the lipids. A thermodynamic model of this steady-state behavior is developed for binary systems and tested with experiments in supported lipid bilayers. The model uses Flory’s approximation for the entropy of mixing and allows for effects arising when the components have different molecular areas. In the special case of equal area molecules the concentration gradient reduces to a Fermi–Dirac distribution. The theory is extended to include effects from charged molecules in the membrane. Calculations show that surface charge on the supporting substrate substantially screens electrostatic interactions within the membrane. It also is shown that concentration profiles can be affected by other intermolecular interactions such as clustering. Qualitative agreement with this prediction is provided by comparing phosphatidylserine- and cardiolipin-containing membranes. PMID:9391034

Model-based error diffusion for high fidelity lenticular screening.

PubMed

Lau, Daniel; Smith, Trebor

2006-04-17

Digital halftoning is the process of converting a continuous-tone image into an arrangement of black and white dots for binary display devices such as digital ink-jet and electrophotographic printers. As printers are achieving print resolutions exceeding 1,200 dots per inch, it is becoming increasingly important for halftoning algorithms to consider the variations and interactions in the size and shape of printed dots between neighboring pixels. In the case of lenticular screening where statistically independent images are spatially multiplexed together, ignoring these variations and interactions, such as dot overlap, will result in poor lenticular image quality. To this end, we describe our use of model-based error-diffusion for the lenticular screening problem where statistical independence between component images is achieved by restricting the diffusion of error to only those pixels of the same component image where, in order to avoid instabilities, the proposed approach involves a novel error-clipping procedure.

Electric field-induced reorganization of two-component supported bilayer membranes.

PubMed

Groves, J T; Boxer, S G; McConnell, H M

1997-12-09

Application of electric fields tangent to the plane of a confined patch of fluid bilayer membrane can create lateral concentration gradients of the lipids. A thermodynamic model of this steady-state behavior is developed for binary systems and tested with experiments in supported lipid bilayers. The model uses Flory's approximation for the entropy of mixing and allows for effects arising when the components have different molecular areas. In the special case of equal area molecules the concentration gradient reduces to a Fermi-Dirac distribution. The theory is extended to include effects from charged molecules in the membrane. Calculations show that surface charge on the supporting substrate substantially screens electrostatic interactions within the membrane. It also is shown that concentration profiles can be affected by other intermolecular interactions such as clustering. Qualitative agreement with this prediction is provided by comparing phosphatidylserine- and cardiolipin-containing membranes.

Designers' models of the human-computer interface

NASA Technical Reports Server (NTRS)

Gillan, Douglas J.; Breedin, Sarah D.

1993-01-01

Understanding design models of the human-computer interface (HCI) may produce two types of benefits. First, interface development often requires input from two different types of experts: human factors specialists and software developers. Given the differences in their backgrounds and roles, human factors specialists and software developers may have different cognitive models of the HCI. Yet, they have to communicate about the interface as part of the design process. If they have different models, their interactions are likely to involve a certain amount of miscommunication. Second, the design process in general is likely to be guided by designers' cognitive models of the HCI, as well as by their knowledge of the user, tasks, and system. Designers do not start with a blank slate; rather they begin with a general model of the object they are designing. The author's approach to a design model of the HCI was to have three groups make judgments of categorical similarity about the components of an interface: human factors specialists with HCI design experience, software developers with HCI design experience, and a baseline group of computer users with no experience in HCI design. The components of the user interface included both display components such as windows, text, and graphics, and user interaction concepts, such as command language, editing, and help. The judgments of the three groups were analyzed using hierarchical cluster analysis and Pathfinder. These methods indicated, respectively, how the groups categorized the concepts, and network representations of the concepts for each group. The Pathfinder analysis provides greater information about local, pairwise relations among concepts, whereas the cluster analysis shows global, categorical relations to a greater extent.

Probabilistic modeling of discourse-aware sentence processing.

PubMed

Dubey, Amit; Keller, Frank; Sturt, Patrick

2013-07-01

Probabilistic models of sentence comprehension are increasingly relevant to questions concerning human language processing. However, such models are often limited to syntactic factors. This restriction is unrealistic in light of experimental results suggesting interactions between syntax and other forms of linguistic information in human sentence processing. To address this limitation, this article introduces two sentence processing models that augment a syntactic component with information about discourse co-reference. The novel combination of probabilistic syntactic components with co-reference classifiers permits them to more closely mimic human behavior than existing models. The first model uses a deep model of linguistics, based in part on probabilistic logic, allowing it to make qualitative predictions on experimental data; the second model uses shallow processing to make quantitative predictions on a broad-coverage reading-time corpus. Copyright © 2013 Cognitive Science Society, Inc.

Estimation of the binding modes with important human cytochrome P450 enzymes, drug interaction potential, pharmacokinetics, and hepatotoxicity of ginger components using molecular docking, computational, and pharmacokinetic modeling studies.

PubMed

Qiu, Jia-Xuan; Zhou, Zhi-Wei; He, Zhi-Xu; Zhang, Xueji; Zhou, Shu-Feng; Zhu, Shengrong

2015-01-01

Ginger is one of the most commonly used herbal medicines for the treatment of numerous ailments and improvement of body functions. It may be used in combination with prescribed drugs. The coadministration of ginger with therapeutic drugs raises a concern of potential deleterious drug interactions via the modulation of the expression and/or activity of drug-metabolizing enzymes and drug transporters, resulting in unfavorable therapeutic outcomes. This study aimed to determine the molecular interactions between 12 main active ginger components (6-gingerol, 8-gingerol, 10-gingerol, 6-shogaol, 8-shogaol, 10-shogaol, ar-curcumene, β-bisabolene, β-sesquiphelandrene, 6-gingerdione, (-)-zingiberene, and methyl-6-isogingerol) and human cytochrome P450 (CYP) 1A2, 2C9, 2C19, 2D6, and 3A4 and to predict the absorption, distribution, metabolism, excretion, and toxicity (ADMET) of the 12 ginger components using computational approaches and comprehensive literature search. Docking studies showed that ginger components interacted with a panel of amino acids in the active sites of CYP1A2, 2C9, 2C19, 2D6, and 3A4 mainly through hydrogen bond formation, to a lesser extent, via π-π stacking. The pharmacokinetic simulation studies showed that the [I]/[Ki ] value for CYP2C9, 2C19, and 3A4 ranged from 0.0002 to 19.6 and the R value ranged from 1.0002 to 20.6 and that ginger might exhibit a high risk of drug interaction via inhibition of the activity of human CYP2C9 and CYP3A4, but a low risk of drug interaction toward CYP2C19-mediated drug metabolism. Furthermore, it has been evaluated that the 12 ginger components possessed a favorable ADMET profiles with regard to the solubility, absorption, permeability across the blood-brain barrier, interactions with CYP2D6, hepatotoxicity, and plasma protein binding. The validation results showed that there was no remarkable effect of ginger on the metabolism of warfarin in humans, whereas concurrent use of ginger and nifedipine exhibited a synergistic effect on platelet aggregation in humans. Moreover, ginger components showed a rapid half-life and no to low toxicity in humans. Taken together, this study shows that ginger components may regulate the activity and expression of various human CYPs, probably resulting in alterations in drug clearance and response. More studies are warranted to identify and confirm potential ginger-drug interactions and explore possible interactions of ginger with human CYPs and other functionally important proteins, to reduce and avoid side effects induced by unfavorable ginger-drug interactions.

Estimation of the binding modes with important human cytochrome P450 enzymes, drug interaction potential, pharmacokinetics, and hepatotoxicity of ginger components using molecular docking, computational, and pharmacokinetic modeling studies

PubMed Central

Qiu, Jia-Xuan; Zhou, Zhi-Wei; He, Zhi-Xu; Zhang, Xueji; Zhou, Shu-Feng; Zhu, Shengrong

2015-01-01

Ginger is one of the most commonly used herbal medicines for the treatment of numerous ailments and improvement of body functions. It may be used in combination with prescribed drugs. The coadministration of ginger with therapeutic drugs raises a concern of potential deleterious drug interactions via the modulation of the expression and/or activity of drug-metabolizing enzymes and drug transporters, resulting in unfavorable therapeutic outcomes. This study aimed to determine the molecular interactions between 12 main active ginger components (6-gingerol, 8-gingerol, 10-gingerol, 6-shogaol, 8-shogaol, 10-shogaol, ar-curcumene, β-bisabolene, β-sesquiphelandrene, 6-gingerdione, (−)-zingiberene, and methyl-6-isogingerol) and human cytochrome P450 (CYP) 1A2, 2C9, 2C19, 2D6, and 3A4 and to predict the absorption, distribution, metabolism, excretion, and toxicity (ADMET) of the 12 ginger components using computational approaches and comprehensive literature search. Docking studies showed that ginger components interacted with a panel of amino acids in the active sites of CYP1A2, 2C9, 2C19, 2D6, and 3A4 mainly through hydrogen bond formation, to a lesser extent, via π–π stacking. The pharmacokinetic simulation studies showed that the [I]/[Ki] value for CYP2C9, 2C19, and 3A4 ranged from 0.0002 to 19.6 and the R value ranged from 1.0002 to 20.6 and that ginger might exhibit a high risk of drug interaction via inhibition of the activity of human CYP2C9 and CYP3A4, but a low risk of drug interaction toward CYP2C19-mediated drug metabolism. Furthermore, it has been evaluated that the 12 ginger components possessed a favorable ADMET profiles with regard to the solubility, absorption, permeability across the blood–brain barrier, interactions with CYP2D6, hepatotoxicity, and plasma protein binding. The validation results showed that there was no remarkable effect of ginger on the metabolism of warfarin in humans, whereas concurrent use of ginger and nifedipine exhibited a synergistic effect on platelet aggregation in humans. Moreover, ginger components showed a rapid half-life and no to low toxicity in humans. Taken together, this study shows that ginger components may regulate the activity and expression of various human CYPs, probably resulting in alterations in drug clearance and response. More studies are warranted to identify and confirm potential ginger–drug interactions and explore possible interactions of ginger with human CYPs and other functionally important proteins, to reduce and avoid side effects induced by unfavorable ginger–drug interactions. PMID:25733806

Detailed Post-Soft Impact Progressive Damage Assessment for Hybrid Structure Jet Engines

NASA Technical Reports Server (NTRS)

Siddens, Aaron; Bayandor, Javid; Celestina, Mark L.

2014-01-01

Currently, certification of engine designs for resistance to bird strike is reliant on physical tests. Predictive modeling of engine structural damage has mostly been limited to evaluation of individual forward section components, such as fan blades within a fixed frame of reference, to direct impact with a bird. Such models must be extended to include interactions among engine components under operating conditions to evaluate the full extent of engine damage. This paper presents the results of a study aim to develop a methodology for evaluating bird strike damage in advanced propulsion systems incorporating hybrid composite/metal structures. The initial degradation and failure of individual fan blades struck by a bird were investigated. Subsequent damage to other fan blades and engine components due to resultant violent fan assembly vibrations and fragmentation was further evaluated. Various modeling parameters for the bird and engine components were investigated to determine guidelines for accurately capturing initial damage and progressive failure of engine components. Then, a novel hybrid structure modeling approach was investigated and incorporated into the crashworthiness methodology. Such a tool is invaluable to the process of design, development, and certification of future advanced propulsion systems.

Nonlinear mode interaction in equal-leg angle struts susceptible to cellular buckling.

PubMed

Bai, L; Wang, F; Wadee, M A; Yang, J

2017-11-01

A variational model that describes the interactive buckling of a thin-walled equal-leg angle strut under pure axial compression is presented. A formulation combining the Rayleigh-Ritz method and continuous displacement functions is used to derive a system of differential and integral equilibrium equations for the structural component. Solving the equations using numerical continuation reveals progressive cellular buckling (or snaking) arising from the nonlinear interaction between the weak-axis flexural buckling mode and the strong-axis flexural-torsional buckling mode for the first time-the resulting behaviour being highly unstable. Physical experiments conducted on 10 cold-formed steel specimens are presented and the results show good agreement with the variational model.

Virulence control in group A Streptococcus by a two-component gene regulatory system: global expression profiling and in vivo infection modeling.

PubMed

Graham, Morag R; Smoot, Laura M; Migliaccio, Cristi A Lux; Virtaneva, Kimmo; Sturdevant, Daniel E; Porcella, Stephen F; Federle, Michael J; Adams, Gerald J; Scott, June R; Musser, James M

2002-10-15

Two-component gene regulatory systems composed of a membrane-bound sensor and cytoplasmic response regulator are important mechanisms used by bacteria to sense and respond to environmental stimuli. Group A Streptococcus, the causative agent of mild infections and life-threatening invasive diseases, produces many virulence factors that promote survival in humans. A two-component regulatory system, designated covRS (cov, control of virulence; csrRS), negatively controls expression of five proven or putative virulence factors (capsule, cysteine protease, streptokinase, streptolysin S, and streptodornase). Inactivation of covRS results in enhanced virulence in mouse models of invasive disease. Using DNA microarrays and quantitative RT-PCR, we found that CovR influences transcription of 15% (n = 271) of all chromosomal genes, including many that encode surface and secreted proteins mediating host-pathogen interactions. CovR also plays a central role in gene regulatory networks by influencing expression of genes encoding transcriptional regulators, including other two-component systems. Differential transcription of genes influenced by covR also was identified in mouse soft-tissue infection. This analysis provides a genome-scale overview of a virulence gene network in an important human pathogen and adds insight into the molecular mechanisms used by group A Streptococcus to interact with the host, promote survival, and cause disease.

Nonassociative Plasticity Alters Competitive Interactions Among Mixture Components In Early Olfactory Processing

PubMed Central

Locatelli, Fernando F; Fernandez, Patricia C; Villareal, Francis; Muezzinoglu, Kerem; Huerta, Ramon; Galizia, C. Giovanni; Smith, Brian H.

2012-01-01

Experience related plasticity is an essential component of networks involved in early olfactory processing. However, the mechanisms and functions of plasticity in these neural networks are not well understood. We studied nonassociative plasticity by evaluating responses to two pure odors (A and X) and their binary mixture using calcium imaging of odor elicited activity in output neurons of the honey bee antennal lobe. Unreinforced exposure to A or X produced no change in the neural response elicited by the pure odors. However, exposure to one odor (e.g. A) caused the response to the mixture to become more similar to the other component (X). We also show in behavioral analyses that unreinforced exposure to A caused the mixture to become perceptually more similar to X. These results suggest that nonassociative plasticity modifies neural networks in such a way that it affects local competitive interactions among mixture components. We used a computational model to evaluate the most likely targets for modification. Hebbian modification of synapses from inhibitory local interneurons to projection neurons most reliably produces the observed shift in response to the mixture. These results are consistent with a model in which the antennal lobe acts to filter olfactory information according to its relevance for performing a particular task. PMID:23167675

Identification of Key Interactions in the Initial Self-Assembly of Amylin in a Membrane Environment.

PubMed

Christensen, Mikkel; Skeby, Katrine K; Schiøtt, Birgit

2017-09-12

Islet amyloid polypeptide, also known as amylin, forms aggregates that reduce the amount of insulin-producing cells in patients with type II diabetes mellitus. Much remains unknown about the process of aggregation and cytotoxicity, but it is known that certain cell membrane components can alter the rate of aggregation. Using atomistic molecular dynamics simulations combined with the highly mobile membrane mimetic model incorporating enhanced sampling of lipid diffusion, we investigate interaction of amylin peptides with the membrane components as well as the self-assembly of amylin. Consistent with experimental evidence, we find that an initial membrane-bound α-helical state folds into stable β-sheet structures upon self-assembly. Our results suggest the following mechanism for the initial phase of amylin self-assembly. The peptides move around on the membrane with the positively charged N-terminus interacting with the negatively charged lipid headgroups. When the peptides start to interact, they partly unfold and break some of the contacts with the membrane. The initial interactions between the peptides are dominated by aromatic and hydrophobic interactions. Oligomers are formed showing both intra- and interpeptide β-sheets, initially with interactions mainly in the C-terminal domain of the peptides. Decreasing the pH to 5.5 is known to inhibit amyloid formation. At low pH, His18 is protonated, adding a fourth positive charge at the peptide. With His18 protonated, no oligomerization is observed in the simulations. The additional charge gives a strong midpoint anchoring of the peptides to negatively charged membrane components, and the peptides experience additional interpeptide repulsion, thereby preventing interactions.

Models of borderline personality disorder: recent advances and new perspectives.

PubMed

D'Agostino, Alessandra; Rossi Monti, Mario; Starcevic, Vladan

2018-01-01

The purpose of this article is to review the most relevant conceptual models of borderline personality disorder (BPD), with a focus on recent developments in this area. Several conceptual models have been proposed with the aim of better understanding BPD: the borderline personality organization, emotion dysregulation, reflective (mentalization) dysfunction, interpersonal hypersensitivity and hyperbolic temperament models. These models have all been supported to some extent and their common components include disorganized attachment and traumatic early experiences, emotion dysregulation, interpersonal sensitivity and difficulties with social cognition. An attempt to integrate some components of the conceptual models of BPD has resulted in an emerging new perspective, the interpersonal dysphoria model, which emphasizes dysphoria as an overarching phenomenon that connects the dispositional and situational aspects of BPD. Various conceptual models have expanded our understanding of BPD, but it appears that further development entails theoretical integration. More research is needed to better understand interactions between various components of BPD, including the situational factors that activate symptoms of BPD. This will help develop therapeutic approaches that are more tailored to the heterogeneous psychopathology of BPD.

A modeling approach to account for toxicokinetic interactions in the calculation of biological hazard index for chemical mixtures.

PubMed

Haddad, S; Tardif, R; Viau, C; Krishnan, K

1999-09-05

Biological hazard index (BHI) is defined as biological level tolerable for exposure to mixture, and is calculated by an equation similar to the conventional hazard index. The BHI calculation, at the present time, is advocated for use in situations where toxicokinetic interactions do not occur among mixture constituents. The objective of this study was to develop an approach for calculating interactions-based BHI for chemical mixtures. The approach consisted of simulating the concentration of exposure indicator in the biological matrix of choice (e.g. venous blood) for each component of the mixture to which workers are exposed and then comparing these to the established BEI values, for calculating the BHI. The simulation of biomarker concentrations was performed using a physiologically-based toxicokinetic (PBTK) model which accounted for the mechanism of interactions among all mixture components (e.g. competitive inhibition). The usefulness of the present approach is illustrated by calculating BHI for varying ambient concentrations of a mixture of three chemicals (toluene (5-40 ppm), m-xylene (10-50 ppm), and ethylbenzene (10-50 ppm)). The results show that the interactions-based BHI can be greater or smaller than that calculated on the basis of additivity principle, particularly at high exposure concentrations. At lower exposure concentrations (e.g. 20 ppm each of toluene, m-xylene and ethylbenzene), the BHI values obtained using the conventional methodology are similar to the interactions-based methodology, confirming that the consequences of competitive inhibition are negligible at lower concentrations. The advantage of the PBTK model-based methodology developed in this study relates to the fact that, the concentrations of individual chemicals in mixtures that will not result in a significant increase in the BHI (i.e. > 1) can be determined by iterative simulation.

Climatology and natural variability of the global hydrologic cycle in the GLA atmospheric general circulation model

NASA Technical Reports Server (NTRS)

Lau, K.-M.; Mehta, V. M.; Sud, Y. C.; Walker, G. K.

1994-01-01

Time average climatology and low-frequency variabilities of the global hydrologic cycle (GHC) in the Goddard Laboratory for Atmospheres (GLA) general circulation model (GCM) were investigated in the present work. A 730-day experiment was conducted with the GLA GCM forced by insolation, sea surface temperature, and ice-snow undergoing climatological annual cycles. Ifluences of interactive soil moisture on time average climatology and natural variability of the GHC were also investigated by conducting 365-day experiments with and without interactive soil moisture. Insolation, sea surface temperature, and ice-snow were fixed at their July levels in the latter two experiments. Results show that the model's time average hydrologic cycle variables for July in all three experiments agree reasonably well with observations. Except in the case of precipitable water, the zonal average climates of the annual cycle experiment and the two perpetual July experiments are alike, i.e., their differences are within limits of the natural variability of the model's climate. Statistics of various components of the GHC, i.e., water vapor, evaporation, and precipitation, are significantly affected by the presence of interactive soil moisture. A long-term trend is found in the principal empirical modes of variability of ground wetness, evaporation, and sensible heat. Dominant modes of variability of these quantities over land are physically consistent with one another and with land surface energy balance requirements. The dominant mode of precipitation variability is found to be closely related to organized convection over the tropical western Pacific Ocean. The precipitation variability has timescales in the range of 2 to 3 months and can be identified with the stationary component of the Madden-Julian Oscillation. The precipitation mode is not sensitive to the presence of interactive soil moisture but is closely linked to both the rotational and divergent components of atmospheric moisture transport. The present results indicate that globally coherent natural variability of the GHC in the GLA GCM has two basic timescales in the absence of annual cycles of external forcings: a long-term trend associated with atmosphere-soil moisture interaction which affects the model atmosphere mostly over midlatitude continental regions and a large-scale 2- to 3-month variability associated with atmospheric moist processes over the western Pacific Ocean.

Genotype by environment (climate) interaction improves genomic prediction for production traits in US Holstein cattle.

PubMed

Tiezzi, F; de Los Campos, G; Parker Gaddis, K L; Maltecca, C

2017-03-01

Genotype by environment interaction (G × E) in dairy cattle productive traits has been shown to exist, but current genetic evaluation methods do not take this component into account. As several environmental descriptors (e.g., climate, farming system) are known to vary within the United States, not accounting for the G × E could lead to reranking of bulls and loss in genetic gain. Using test-day records on milk yield, somatic cell score, fat, and protein percentage from all over the United States, we computed within herd-year-season daughter yield deviations for 1,087 Holstein bulls and regressed them on genetic and environmental information to estimate variance components and to assess prediction accuracy. Genomic information was obtained from a 50k SNP marker panel. Environmental effect inputs included herd (160 levels), geographical region (7 levels), geographical location (2 variables), climate information (7 variables), and management conditions of the herds (16 total variables divided in 4 subgroups). For each set of environmental descriptors, environmental, genomic, and G × E components were sequentially fitted. Variance components estimates confirmed the presence of G × E on milk yield, with its effect being larger than main genetic effect and the environmental effect for some models. Conversely, G × E was moderate for somatic cell score and small for milk composition. Genotype by environment interaction, when included, partially eroded the genomic effect (as compared with the models where G × E was not included), suggesting that the genomic variance could at least in part be attributed to G × E not appropriately accounted for. Model predictive ability was assessed using 3 cross-validation schemes (new bulls, incomplete progeny test, and new environmental conditions), and performance was compared with a reference model including only the main genomic effect. In each scenario, at least 1 of the models including G × E was able to perform better than the reference model, although it was not possible to find the overall best-performing model that included the same set of environmental descriptors. In general, the methodology used is promising in accounting for G × E in genomic predictions, but challenges exist in identifying a unique set of covariates capable of describing the entire variety of environments. Copyright © 2017 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Use of AMMI and linear regression models to analyze genotype-environment interaction in durum wheat.

PubMed

Nachit, M M; Nachit, G; Ketata, H; Gauch, H G; Zobel, R W

1992-03-01

The joint durum wheat (Triticum turgidum L var 'durum') breeding program of the International Maize and Wheat Improvement Center (CIMMYT) and the International Center for Agricultural Research in the Dry Areas (ICARDA) for the Mediterranean region employs extensive multilocation testing. Multilocation testing produces significant genotype-environment (GE) interaction that reduces the accuracy for estimating yield and selecting appropriate germ plasm. The sum of squares (SS) of GE interaction was partitioned by linear regression techniques into joint, genotypic, and environmental regressions, and by Additive Main effects and the Multiplicative Interactions (AMMI) model into five significant Interaction Principal Component Axes (IPCA). The AMMI model was more effective in partitioning the interaction SS than the linear regression technique. The SS contained in the AMMI model was 6 times higher than the SS for all three regressions. Postdictive assessment recommended the use of the first five IPCA axes, while predictive assessment AMMI1 (main effects plus IPCA1). After elimination of random variation, AMMI1 estimates for genotypic yields within sites were more precise than unadjusted means. This increased precision was equivalent to increasing the number of replications by a factor of 3.7.

Modeling Costal Zone Responses to Sea-Level Rise Using MoCCS: A Model of Complex Coastal System

NASA Astrophysics Data System (ADS)

Dai, H.; Niedoroda, A. W.; Ye, M.; Saha, B.; Donoghue, J. F.; Kish, S.

2011-12-01

Large-scale coastal systems consisting of several morphological components (e.g. beach, surf zone, dune, inlet, shoreface, and estuary) can be expected to exhibit complex and interacting responses to changes in the rate of sea level rise and storm climate. We have developed a numerical model of complex coastal systems (MoCCS), derived from earlier morphdynamic models, to represent the large-scale time-averaged physical processes that shape each component and govern the component interactions. These control the ongoing evolution of the barrier islands, beach and dune erosion, shoal formation and sand withdrawal at tidal inlets, depth changes in the bay, and changes in storm flooding. The model has been used to study the response of an idealized coastal system with physical characteristics and storm climatology similar to Santa Rosa Island on the Florida Panhandle coast. Five SLR scenarios have been used, covering the range of recently published projections for the next century. Each scenario has been input with a constant and then a time-varying storm climate. The results indicate that substantial increases in the rate of beach erosion are largely due to increased sand transfer to inlet shoals with increased rates of sea level rise. The barrier island undergoes cycles of dune destruction and regrowth, leading to sand deposition. This largely maintains island freeboard but is progressively less effective in offsetting bayside inundation and marsh habitat loss at accelerated sea level rise rates.

Analytic models of ducted turbomachinery tone noise sources. Volume 1: Analysis

NASA Technical Reports Server (NTRS)

Clark, T. L.; Ganz, U. W.; Graf, G. A.; Westall, J. S.

1974-01-01

The analytic models developed for computing the periodic sound pressure of subsonic fans and compressors in an infinite, hardwall annular duct with uniform flow are described. The basic sound-generating mechanism is the scattering into sound waves of velocity disturbances appearing to the rotor or stator blades as a series of harmonic gusts. The models include component interactions and rotor alone.

Interstellar matter in early-type galaxies. II - The relationship between gaseous components and galaxy types

NASA Technical Reports Server (NTRS)

Bregman, Joel N.; Hogg, David E.; Roberts, Morton S.

1992-01-01

Interstellar components of early-type galaxies are established by galactic type and luminosity in order to search for relationships between the different interstellar components and to test the predictions of theoretical models. Some of the data include observations of neutral hydrogen, carbon monoxide, and radio continuum emission. An alternative distance model which yields LX varies as LB sup 2.45, a relation which is in conflict with simple cooling flow models, is discussed. The dispersion of the X-ray luminosity about this regression line is unlikely to result from stripping. The striking lack of clear correlations between hot and cold interstellar components, taken together with their morphologies, suggests that the cold gas is a disk phenomenon while the hot gas is a bulge phenomenon, with little interaction between the two. The progression of galaxy type from E to Sa is not only a sequence of decreasing stellar bulge-to-disk ratio, but also of hot-to-cold-gas ratio.

Computer-aided operations engineering with integrated models of systems and operations

NASA Technical Reports Server (NTRS)

Malin, Jane T.; Ryan, Dan; Fleming, Land

1994-01-01

CONFIG 3 is a prototype software tool that supports integrated conceptual design evaluation from early in the product life cycle, by supporting isolated or integrated modeling, simulation, and analysis of the function, structure, behavior, failures and operation of system designs. Integration and reuse of models is supported in an object-oriented environment providing capabilities for graph analysis and discrete event simulation. Integration is supported among diverse modeling approaches (component view, configuration or flow path view, and procedure view) and diverse simulation and analysis approaches. Support is provided for integrated engineering in diverse design domains, including mechanical and electro-mechanical systems, distributed computer systems, and chemical processing and transport systems. CONFIG supports abstracted qualitative and symbolic modeling, for early conceptual design. System models are component structure models with operating modes, with embedded time-related behavior models. CONFIG supports failure modeling and modeling of state or configuration changes that result in dynamic changes in dependencies among components. Operations and procedure models are activity structure models that interact with system models. CONFIG is designed to support evaluation of system operability, diagnosability and fault tolerance, and analysis of the development of system effects of problems over time, including faults, failures, and procedural or environmental difficulties.

On Complex Networks Representation and Computation of Hydrologycal Quantities

NASA Astrophysics Data System (ADS)

Serafin, F.; Bancheri, M.; David, O.; Rigon, R.

2017-12-01

Water is our blue gold. Despite results of discovery-based science keep warning public opinion about the looming worldwide water crisis, water is still treated as a not worth taking resource. Could a different multi-scale perspective affect environmental decision-making more deeply? Can also a further pairing to a new graphical representation of processes interaction sway decision-making more effectively and public opinion consequently?This abstract introduces a complex networks driven way to represent catchments eco-hydrology and related flexible informatics to manage it. The representation is built upon mathematical category. A category is an algebraic structure that comprises "objects" linked by "arrows". It is an evolution of Petri Nets said Time Continuous Petri Nets (TCPN). It aims to display (water) budgets processes and catchment interactions using explicative and self-contained symbolism. The result improves readability of physical processes compared to current descriptions. The IT perspective hinges on the Object Modeling System (OMS) v3. The latter is a non-invasive flexible environmental modeling framework designed to support component-based model development. The implementation of a Directed Acyclic Graph (DAG) data structure, named Net3, has recently enhanced its flexibility. Net3 represents interacting systems as complex networks: vertices match up with any sort of time evolving quantity; edges correspond to their data (fluxes) interchange. It currently hosts JGrass-NewAge components, and those implementing travel time analysis of fluxes. Further bio-physical or management oriented components can be easily added.This talk introduces both graphical representation and related informatics exercising actual applications and examples.

Modeling effectiveness of management practices for flood mitigation using GIS spatial analysis functions in Upper Cilliwung watershed

NASA Astrophysics Data System (ADS)

Darma Tarigan, Suria

2016-01-01

Flooding is caused by excessive rainfall flowing downstream as cumulative surface runoff. Flooding event is a result of complex interaction of natural system components such as rainfall events, land use, soil, topography and channel characteristics. Modeling flooding event as a result of interaction of those components is a central theme in watershed management. The model is usually used to test performance of various management practices in flood mitigation. There are various types of management practices for flood mitigation including vegetative and structural management practices. Existing hydrological model such as SWAT and HEC-HMS models have limitation to accommodate discrete management practices such as infiltration well, small farm reservoir, silt pits in its analysis due to the lumped structure of these models. Aim of this research is to use raster spatial analysis functions of Geo-Information System (RGIS-HM) to model flooding event in Ciliwung watershed and to simulate impact of discrete management practices on surface runoff reduction. The model was validated using flooding data event of Ciliwung watershed on 29 January 2004. The hourly hydrograph data and rainfall data were available during period of model validation. The model validation provided good result with Nash-Suthcliff efficiency of 0.8. We also compared the RGIS-HM with Netlogo Hydrological Model (NL-HM). The RGIS-HM has similar capability with NL-HM in simulating discrete management practices in watershed scale.

Proposal for Holistic Assessment of Urban System Resilience to Natural Disasters

NASA Astrophysics Data System (ADS)

Koren, David; Kilar, Vojko; Rus, Katarina

2017-10-01

Urban system is a complex mix of interdependent components and dynamic interactions between them that enable it to function effectively. Resilience of urban system indicates the ability of a system to resist, absorb, accommodate to and recover from the effects of a hazard in a timely and efficient manner. In the relevant literature, most studies consider individual components separately. On the other hand, the purpose of this paper is to assess the urban system as a whole, considering all relevant components and their interactions. The goal is a study of possibilities for holistic evaluation of urban system resilience to natural disasters. Findings from the preliminary study are presented: (i) the definition of urban system and categorization of its components, (ii) a set of attributes of individual components with impact on disaster resilience of the entire system and (iii) review of different methods and approaches for resilience assessment. Based on literature review and extensive preliminary studies a new conceptual framework for urban resilience assessment is proposed. In the presented paper, a conceptual model of urban system by abstraction of its components as nodes (buildings), patches - specific nodes with spatial properties (open space), links (infrastructures) and base layer (community) is created. In the suggested model, each component is defined by its own quantitative attributes, which have been identified to have an important impact on the urban system resilience to natural disasters. System is presented as a mathematical graph model. Natural disaster is considered an external factor that affects the existing system and leads to some system distortion. In further analyses, mathematical simulation of various natural disasters scenarios is going to be carried out, followed by comparison of the system functionality before and after the accident. Various properties of the system (accessibility, transition, complexity etc.) are going to be analysed with graph theory. The final result is going to be an identification of critical points and system bottlenecks as basis for further actions of risk mitigation.

The Earth System Prediction Suite: Toward a Coordinated U.S. Modeling Capability

DOE PAGES

Theurich, Gerhard; DeLuca, C.; Campbell, T.; ...

2016-08-22

The Earth System Prediction Suite (ESPS) is a collection of flagship U.S. weather and climate models and model components that are being instrumented to conform to interoperability conventions, documented to follow metadata standards, and made available either under open-source terms or to credentialed users. Furthermore, the ESPS represents a culmination of efforts to create a common Earth system model architecture, and the advent of increasingly coordinated model development activities in the United States. ESPS component interfaces are based on the Earth System Modeling Framework (ESMF), community-developed software for building and coupling models, and the National Unified Operational Prediction Capability (NUOPC)more » Layer, a set of ESMF-based component templates and interoperability conventions. Our shared infrastructure simplifies the process of model coupling by guaranteeing that components conform to a set of technical and semantic behaviors. The ESPS encourages distributed, multiagency development of coupled modeling systems; controlled experimentation and testing; and exploration of novel model configurations, such as those motivated by research involving managed and interactive ensembles. ESPS codes include the Navy Global Environmental Model (NAVGEM), the Hybrid Coordinate Ocean Model (HYCOM), and the Coupled Ocean–Atmosphere Mesoscale Prediction System (COAMPS); the NOAA Environmental Modeling System (NEMS) and the Modular Ocean Model (MOM); the Community Earth System Model (CESM); and the NASA ModelE climate model and the Goddard Earth Observing System Model, version 5 (GEOS-5), atmospheric general circulation model.« less

The Earth System Prediction Suite: Toward a Coordinated U.S. Modeling Capability

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

Theurich, Gerhard; DeLuca, C.; Campbell, T.

The Earth System Prediction Suite (ESPS) is a collection of flagship U.S. weather and climate models and model components that are being instrumented to conform to interoperability conventions, documented to follow metadata standards, and made available either under open-source terms or to credentialed users. Furthermore, the ESPS represents a culmination of efforts to create a common Earth system model architecture, and the advent of increasingly coordinated model development activities in the United States. ESPS component interfaces are based on the Earth System Modeling Framework (ESMF), community-developed software for building and coupling models, and the National Unified Operational Prediction Capability (NUOPC)more » Layer, a set of ESMF-based component templates and interoperability conventions. Our shared infrastructure simplifies the process of model coupling by guaranteeing that components conform to a set of technical and semantic behaviors. The ESPS encourages distributed, multiagency development of coupled modeling systems; controlled experimentation and testing; and exploration of novel model configurations, such as those motivated by research involving managed and interactive ensembles. ESPS codes include the Navy Global Environmental Model (NAVGEM), the Hybrid Coordinate Ocean Model (HYCOM), and the Coupled Ocean–Atmosphere Mesoscale Prediction System (COAMPS); the NOAA Environmental Modeling System (NEMS) and the Modular Ocean Model (MOM); the Community Earth System Model (CESM); and the NASA ModelE climate model and the Goddard Earth Observing System Model, version 5 (GEOS-5), atmospheric general circulation model.« less

Dark-matter particles without weak-scale masses or weak interactions.

PubMed

Feng, Jonathan L; Kumar, Jason

2008-12-05

We propose that dark matter is composed of particles that naturally have the correct thermal relic density, but have neither weak-scale masses nor weak interactions. These models emerge naturally from gauge-mediated supersymmetry breaking, where they elegantly solve the dark-matter problem. The framework accommodates single or multiple component dark matter, dark-matter masses from 10 MeV to 10 TeV, and interaction strengths from gravitational to strong. These candidates enhance many direct and indirect signals relative to weakly interacting massive particles and have qualitatively new implications for dark-matter searches and cosmological implications for colliders.

Multi-component dark matter through a radiative Higgs portal

DOE PAGES

DiFranzo, Anthony; Univ. of California, Irvine, CA; Rutgers Univ., Piscataway, NJ; ...

2017-01-18

Here, we study a multi-component dark matter model where interactions with the Standard Model are primarily via the Higgs boson. The model contains vector-like fermions charged undermore » $$SU(2)_W \\times U(1)_Y$$ and under the dark gauge group, $$U(1)^\\prime$$. This results in two dark matter candidates. A spin-1 and a spin-1/2 candidate, which have loop and tree-level couplings to the Higgs, respectively. We explore the resulting effect on the dark matter relic abundance, while also evaluating constraints on the Higgs invisible width and from direct detection experiments. Generally, we find that this model is highly constrained when the fermionic candidate is the predominant fraction of the dark matter relic abundance.« less

Calculation of atmospheric neutrino flux using the interaction model calibrated with atmospheric muon data

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

Honda, M.; Kajita, T.; Kasahara, K.

2007-02-15

Using the 'modified DPMJET-III' model explained in the previous paper [T. Sanuki et al., preceding Article, Phys. Rev. D 75, 043005 (2007).], we calculate the atmospheric neutrino flux. The calculation scheme is almost the same as HKKM04 [M. Honda, T. Kajita, K. Kasahara, and S. Midorikawa, Phys. Rev. D 70, 043008 (2004).], but the usage of the 'virtual detector' is improved to reduce the error due to it. Then we study the uncertainty of the calculated atmospheric neutrino flux summarizing the uncertainties of individual components of the simulation. The uncertainty of K-production in the interaction model is estimated using othermore » interaction models: FLUKA'97 and FRITIOF 7.02, and modifying them so that they also reproduce the atmospheric muon flux data correctly. The uncertainties of the flux ratio and zenith angle dependence of the atmospheric neutrino flux are also studied.« less

Toward lattice fractional vector calculus

NASA Astrophysics Data System (ADS)

Tarasov, Vasily E.

2014-09-01

An analog of fractional vector calculus for physical lattice models is suggested. We use an approach based on the models of three-dimensional lattices with long-range inter-particle interactions. The lattice analogs of fractional partial derivatives are represented by kernels of lattice long-range interactions, where the Fourier series transformations of these kernels have a power-law form with respect to wave vector components. In the continuum limit, these lattice partial derivatives give derivatives of non-integer order with respect to coordinates. In the three-dimensional description of the non-local continuum, the fractional differential operators have the form of fractional partial derivatives of the Riesz type. As examples of the applications of the suggested lattice fractional vector calculus, we give lattice models with long-range interactions for the fractional Maxwell equations of non-local continuous media and for the fractional generalization of the Mindlin and Aifantis continuum models of gradient elasticity.

The GISS global climate-middle atmosphere model. II - Model variability due to interactions between planetary waves, the mean circulation and gravity wave drag

NASA Technical Reports Server (NTRS)

Rind, D.; Suozzo, R.; Balachandran, N. K.

1988-01-01

The variability which arises in the GISS Global Climate-Middle Atmosphere Model on two time scales is reviewed: interannual standard deviations, derived from the five-year control run, and intraseasonal variability as exemplified by statospheric warnings. The model's extratropical variability for both mean fields and eddy statistics appears reasonable when compared with observations, while the tropical wind variability near the stratopause may be excessive possibly, due to inertial oscillations. Both wave 1 and wave 2 warmings develop, with connections to tropospheric forcing. Variability on both time scales results from a complex set of interactions among planetary waves, the mean circulation, and gravity wave drag. Specific examples of these interactions are presented, which imply that variability in gravity wave forcing and drag may be an important component of the variability of the middle atmosphere.

A numeric investigation of co-flowing liquid streams using the Lattice Boltzmann Method

NASA Astrophysics Data System (ADS)

Somogyi, Andy; Tagg, Randall

2007-11-01

We present a numerical investigation of co-flowing immiscible liquid streams using the Lattice Boltzmann Method (LBM) for multi component, dissimilar viscosity, immiscible fluid flow. When a liquid is injected into another immiscible liquid, the flow will eventually transition from jetting to dripping due to interfacial tension. Our implementation of LBM models the interfacial tension through a variety of techniques. Parallelization is also straightforward for both single and multi component models as only near local interaction is required. We compare the results of our numerical investigation using LBM to several recent physical experiments.

A phase field approach for multicellular aggregate fusion in biofabrication.

PubMed

Yang, Xiaofeng; Sun, Yi; Wang, Qi

2013-07-01

We present a modeling and computational approach to study fusion of multicellular aggregates during tissue and organ fabrication, which forms the foundation for the scaffold-less biofabrication of tissues and organs known as bioprinting. It is known as the phase field method, where multicellular aggregates are modeled as mixtures of multiphase complex fluids whose phase mixing or separation is governed by interphase force interactions, mimicking the cell-cell interaction in the multicellular aggregates, and intermediate range interaction mediated by the surrounding hydrogel. The material transport in the mixture is dictated by hydrodynamics as well as forces due to the interphase interactions. In a multicellular aggregate system with fixed number of cells and fixed amount of the hydrogel medium, the effect of cell differentiation, proliferation, and death are neglected in the current model, which can be readily included in the model, and the interaction between different components is dictated by the interaction energy between cell and cell as well as between cell and medium particles, respectively. The modeling approach is applicable to transient simulations of fusion of cellular aggregate systems at the time and length scale appropriate to biofabrication. Numerical experiments are presented to demonstrate fusion and cell sorting during tissue and organ maturation processes in biofabrication.

Mechanics of a two-fiber model with one nested fiber network, as applied to the collagen-fibrin system.

PubMed

Nedrelow, David S; Bankwala, Danesh; Hyypio, Jeffrey D; Lai, Victor K; Barocas, Victor H

2018-05-01

The mechanical behavior of collagen-fibrin (col-fib) co-gels is both scientifically interesting and clinically relevant. Collagen-fibrin networks are a staple of tissue engineering research, but the mechanical consequences of changes in co-gel composition have remained difficult to predict or even explain. We previously observed fundamental differences in failure behavior between collagen-rich and fibrin-rich co-gels, suggesting an essential change in how the two components interact as the co-gel's composition changes. In this work, we explored the hypothesis that the co-gel behavior is due to a lack of percolation by the dilute component. We generated a series of computational models based on interpenetrating fiber networks. In these models, the major network component percolated the model space but the minor component did not, instead occupying a small island embedded within the larger network. Each component was assigned properties based on a fit of single-component gel data. Island size was varied to match the relative concentrations of the two components. The model predicted that networks rich in collagen, the stiffer component, would roughly match pure-collagen gel behavior with little additional stress due to the fibrin, as seen experimentally. For fibrin-rich gels, however, the model predicted a smooth increase in the overall network strength with added collagen, as seen experimentally but not consistent with an additive parallel model. We thus conclude that incomplete percolation by the low-concentration component of a co-gel is a major determinant of its macroscopic properties, especially if the low-concentration component is the stiffer component. Models for the behavior of fibrous networks have useful applications in many different fields, including polymer science, textiles, and tissue engineering. In addition to being important structural components in soft tissues and blood clots, these protein networks can serve as scaffolds for bioartificial tissues. Thus, their mechanical behavior, especially in co-gels, is both interesting from a materials science standpoint and significant with regard to tissue engineering. Copyright © 2018 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Changing the Rules: Making Space for Interactive Learning in the Galleries of the Detroit Institute of Arts

ERIC Educational Resources Information Center

Czajkowski, Jennifer Wild

2011-01-01

Three years after the Detroit Institute of Arts opened with all new, "visitor-centered" galleries, the museum's executive director of learning and interpretation shares the processes, successes, and lessons learned at an institution that embraced an array of hands-on learning models. The models are discussed as components of a…

Design Environment for Multifidelity and Multidisciplinary Components

NASA Technical Reports Server (NTRS)

Platt, Michael

2014-01-01

One of the greatest challenges when developing propulsion systems is predicting the interacting effects between the fluid loads, thermal loads, and structural deflection. The interactions between technical disciplines often are not fully analyzed, and the analysis in one discipline often uses a simplified representation of other disciplines as an input or boundary condition. For example, the fluid forces in an engine generate static and dynamic rotor deflection, but the forces themselves are dependent on the rotor position and its orbit. It is important to consider the interaction between the physical phenomena where the outcome of each analysis is heavily dependent on the inputs (e.g., changes in flow due to deflection, changes in deflection due to fluid forces). A rigid design process also lacks the flexibility to employ multiple levels of fidelity in the analysis of each of the components. This project developed and validated an innovative design environment that has the flexibility to simultaneously analyze multiple disciplines and multiple components with multiple levels of model fidelity. Using NASA's open-source multidisciplinary design analysis and optimization (OpenMDAO) framework, this multifaceted system will provide substantially superior capabilities to current design tools.

North Atlantic Ocean OSSE system development: Nature Run evaluation and application to hurricane interaction with the Gulf Stream

NASA Astrophysics Data System (ADS)

Kourafalou, Vassiliki H.; Androulidakis, Yannis S.; Halliwell, George R.; Kang, HeeSook; Mehari, Michael M.; Le Hénaff, Matthieu; Atlas, Robert; Lumpkin, Rick

2016-11-01

A high resolution, free-running model has been developed for the hurricane region of the North Atlantic Ocean. The model is evaluated with a variety of observations to ensure that it adequately represents both the ocean climatology and variability over this region, with a focus on processes relevant to hurricane-ocean interactions. As such, it can be used as the "Nature Run" (NR) model within the framework of Observing System Simulation Experiments (OSSEs), designed specifically to improve the ocean component of coupled ocean-atmosphere hurricane forecast models. The OSSE methodology provides quantitative assessment of the impact of specific observations on the skill of forecast models and enables the comprehensive design of future observational platforms and the optimization of existing ones. Ocean OSSEs require a state-of-the-art, high-resolution free-running model simulation that represents the true ocean (the NR). This study concentrates on the development and data based evaluation of the NR model component, which leads to a reliable model simulation that has a dual purpose: (a) to provide the basis for future hurricane related OSSEs; (b) to explore process oriented studies of hurricane-ocean interactions. A specific example is presented, where the impact of Hurricane Bill (2009) on the eastward extension and transport of the Gulf Stream is analyzed. The hurricane induced cold wake is shown in both NR simulation and observations. Interaction of storm-forced currents with the Gulf Stream produced a temporary large reduction in eastward transport downstream from Cape Hatteras and had a marked influence on frontal displacement in the upper ocean. The kinetic energy due to ageostrophic currents showed a significant increase as the storm passed, and then decreased to pre-storm levels within 8 days after the hurricane advanced further north. This is a unique result of direct hurricane impact on a western boundary current, with possible implications on the ocean feedback on hurricane evolution.

Microstructure-sensitive Crystal Viscoplasticity for Ni-base Superalloys Targeting Long-term Creep-Fatigue Interaction Modeling

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

Neu, Richard W.

The aim of this project is to develop a microstructure-sensitive crystal viscoplasticity (CVP) model for single-crystal Ni-base superalloys to model the behavior of the material and components in the hot gas path sections of industrial gas turbines (IGT). Microstructure degradation associated with aging critical to predicting long-term creep-fatigue interactions will be embedded into the model through the γ' precipitate morphology evolution by coupling the coarsening drivers and kinetics into the constitutive equations of the CVP model. Model parameters will be determined using new experimental protocols that involve systematically artificially aging the alloy under different stress conditions to determine the relationshipmore » between the size and morphology g' precipitates on the creep and thermomechanical fatigue response.« less

Microstructure-sensitive Crystal Viscoelasticity for Ni-base Superalloys Targeting Long-term Creep-Fatigue Interaction Modeling

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

Neu, Richard W

The aim of this project is to develop a microstructure-sensitive crystal viscoplasticity (CVP) model for single-crystal Ni-base superalloys to model the behavior of the material and components in the hot gas path sections of industrial gas turbines (IGT). Microstructure degradation associated with aging critical to predicting long-term creep-fatigue interactions will be embedded into the model through the γ' precipitate morphology evolution by coupling the coarsening drivers and kinetics into the constitutive equations of the CVP model. Model parameters will be determined using new experimental protocols that involve systematically artificially aging the alloy under different stress conditions to determine the relationshipmore » between the size and morphology g' precipitates on the creep and thermomechanical fatigue response.« less

Using a LIDAR Vegetation Model to Predict UHF SAR Attenuation in Coniferous Forests

PubMed Central

Swanson, Alan; Huang, Shengli; Crabtree, Robert

2009-01-01

Attenuation of radar signals by vegetation can be a problem for target detection and GPS reception, and is an important parameter in models describing vegetation backscatter. Here we first present a model describing the 3D distribution of stem and foliage structure based on small footprint scanning LIDAR data. Secondly we present a model that uses ray-tracing methodology to record detailed interactions between simulated radar beams and vegetation components. These interactions are combined over the SAR aperture and used to predict two-way attenuation of the SAR signal. Accuracy of the model is demonstrated using UHF SAR observations of large trihedral corner reflectors in coniferous forest stands. Our study showed that the model explains between 66% and 81% of the variability in observed attenuation. PMID:22573972

Methodologies for validating ray-based forward model using finite element method in ultrasonic array data simulation

NASA Astrophysics Data System (ADS)

Zhang, Jie; Nixon, Andrew; Barber, Tom; Budyn, Nicolas; Bevan, Rhodri; Croxford, Anthony; Wilcox, Paul

2018-04-01

In this paper, a methodology of using finite element (FE) model to validate a ray-based model in the simulation of full matrix capture (FMC) ultrasonic array data set is proposed. The overall aim is to separate signal contributions from different interactions in FE results for easier comparing each individual component in the ray-based model results. This is achieved by combining the results from multiple FE models of the system of interest that include progressively more geometrical features while preserving the same mesh structure. It is shown that the proposed techniques allow the interactions from a large number of different ray-paths to be isolated in FE results and compared directly to the results from a ray-based forward model.

Six-color intravital two-photon imaging of brain tumors and their dynamic microenvironment.

PubMed

Ricard, Clément; Debarbieux, Franck Christian

2014-01-01

The majority of intravital studies on brain tumor in living animal so far rely on dual color imaging. We describe here a multiphoton imaging protocol to dynamically characterize the interactions between six cellular components in a living mouse. We applied this methodology to a clinically relevant glioblastoma multiforme (GBM) model designed in reporter mice with targeted cell populations labeled by fluorescent proteins of different colors. This model permitted us to make non-invasive longitudinal and multi-scale observations of cell-to-cell interactions. We provide examples of such 5D (x,y,z,t,color) images acquired on a daily basis from volumes of interest, covering most of the mouse parietal cortex at subcellular resolution. Spectral deconvolution allowed us to accurately separate each cell population as well as some components of the extracellular matrix. The technique represents a powerful tool for investigating how tumor progression is influenced by the interactions of tumor cells with host cells and the extracellular matrix micro-environment. It will be especially valuable for evaluating neuro-oncological drug efficacy and target specificity. The imaging protocol provided here can be easily translated to other mouse models of neuropathologies, and should also be of fundamental interest for investigations in other areas of systems biology.

Constraints and consequences of reducing small scale structure via large dark matter-neutrino interactions

DOE PAGES

Bertoni, Bridget; Ipek, Seyda; McKeen, David; ...

2015-04-30

Here, cold dark matter explains a wide range of data on cosmological scales. However, there has been a steady accumulation of evidence for discrepancies between simulations and observations at scales smaller than galaxy clusters. One promising way to affect structure formation on small scales is a relatively strong coupling of dark matter to neutrinos. We construct an experimentally viable, simple, renormalizable model with new interactions between neutrinos and dark matter and provide the first discussion of how these new dark matter-neutrino interactions affect neutrino phenomenology. We show that addressing the small scale structure problems requires asymmetric dark matter with amore » mass that is tens of MeV. Generating a sufficiently large dark matter-neutrino coupling requires a new heavy neutrino with a mass around 100 MeV. The heavy neutrino is mostly sterile but has a substantial τ neutrino component, while the three nearly massless neutrinos are partly sterile. This model can be tested by future astrophysical, particle physics, and neutrino oscillation data. Promising signatures of this model include alterations to the neutrino energy spectrum and flavor content observed from a future nearby supernova, anomalous matter effects in neutrino oscillations, and a component of the τ neutrino with mass around 100 MeV.« less

A classical model for closed-loop diagrams of binary liquid mixtures

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

Schnitzler, J.v.; Prausnitz, J.M.

1994-03-01

A classical lattice model for closed-loop temperature-composition phase diagrams has been developed. It considers the effect of specific interactions, such as hydrogen bonding, between dissimilar components. This van Laar-type model includes a Flory-Huggins term for the excess entropy of mixing. It is applied to several liquid-liquid equilibria of nonelectrolytes, where the molecules of the two components differ in size. The model is able to represent the observed data semi-quantitatively, but in most cases it is not flexible enough to predict all parts of the closed loop quantitatively. The ability of the model to represent different binary systems is discussed. Finally,more » attention is given to a correction term, concerning the effect of concentration fluctuations near the upper critical solution temperature.« less

Five challenges for spatial epidemic models.

PubMed

Riley, Steven; Eames, Ken; Isham, Valerie; Mollison, Denis; Trapman, Pieter

2015-03-01

Infectious disease incidence data are increasingly available at the level of the individual and include high-resolution spatial components. Therefore, we are now better able to challenge models that explicitly represent space. Here, we consider five topics within spatial disease dynamics: the construction of network models; characterising threshold behaviour; modelling long-distance interactions; the appropriate scale for interventions; and the representation of population heterogeneity. Copyright © 2014 The Authors. Published by Elsevier B.V. All rights reserved.

Gene–Physical Activity Interactions: Overview of Human Studies

PubMed Central

Rankinen, Tuomo; Bouchard, Claude

2009-01-01

Physical activity level is an important component of the total daily energy expenditure and as such contributes to body weight regulation. A body of data indicates that the level of physical activity plays a role in the risk of excessive weight gain, in weight loss programs, and particularly in the prevention of weight regain. Most studies dealing with potential gene–physical activity interaction effects use an exercise and fitness or performance paradigm as opposed to an obesity-driven model. From these studies, it is clear that there are considerable individual differences in the response to an exercise regimen and that there is a substantial familial aggregation component to the observed heterogeneity. Few studies have focused on the role of specific genes in accounting for the highly prevalent gene–exercise interaction effects. Results for specific genes have been inconsistent with few exceptions. Progress is likely to come when studies will be designed to truly address gene–exercise or physical activity interaction issues and with sample sizes that will provide adequate statistical power. PMID:19037212

Neural evidence for moral intuition and the temporal dynamics of interactions between emotional processes and moral cognition.

PubMed

Gui, Dan-Yang; Gan, Tian; Liu, Chao

2016-01-01

Behavioral and neurological studies have revealed that emotions influence moral cognition. Although moral stimuli are emotionally charged, the time course of interactions between emotions and moral judgments remains unknown. In the present study, we investigated the temporal dynamics of the interaction between emotional processes and moral cognition. The results revealed that when making moral judgments, the time course of the event-related potential (ERP) waveform was significantly different between high emotional arousal and low emotional arousal contexts. Different stages of processing were distinguished, showing distinctive interactions between emotional processes and moral reasoning. The precise time course of moral intuition and moral reasoning sheds new light on theoretical models of moral psychology. Specifically, the N1 component (interpreted as representing moral intuition) did not appear to be influenced by emotional arousal. However, the N2 component and late positive potential were strongly affected by emotional arousal; the slow wave was influenced by both emotional arousal and morality, suggesting distinct moral processing at different emotional arousal levels.

Dark Coulomb binding of heavy neutrinos of fourth family

NASA Astrophysics Data System (ADS)

Belotsky, K. M.; Esipova, E. A.; Khlopov, M. Yu.; Laletin, M. N.

2015-11-01

Direct dark matter searches put severe constraints on the weakly interacting massive particles (WIMPs). These constraints cause serious troubles for the model of stable neutrino of fourth generation with mass around 50GeV. Though the calculations of primordial abundance of these particles make them in the charge symmetric case a sparse subdominant component of the modern dark matter, their presence in the universe would exceed the current upper limits by several orders of the magnitude. However, if quarks and leptons of fourth generation possess their own Coulomb-like y-interaction, recombination of pairs of heavy neutrinos and antineutrinos and their annihilation in the “neutrinium” atoms can play important role in their cosmological evolution, reducing their modern abundance far below the experimental upper limits. The model of stable fourth generation assumes that the dominant part of dark matter is explained by excessive Ū antiquarks, forming (ŪŪŪ)-- charged clusters, bound with primordial helium in nuclear-interacting O-helium (OHe) dark atoms. The y charge conservation implies generation of the same excess of fourth generation neutrinos, potentially dangerous WIMP component of this scenario. We show that due to y-interaction recombination of fourth neutrinos with OHe hides these WIMPs from direct WIMP searches, leaving the negligible fraction of free neutrinos, what makes their existence compatible with the experimental constraints.

Accurate and efficient modeling of the detector response in small animal multi-head PET systems.

PubMed

Cecchetti, Matteo; Moehrs, Sascha; Belcari, Nicola; Del Guerra, Alberto

2013-10-07

In fully three-dimensional PET imaging, iterative image reconstruction techniques usually outperform analytical algorithms in terms of image quality provided that an appropriate system model is used. In this study we concentrate on the calculation of an accurate system model for the YAP-(S)PET II small animal scanner, with the aim to obtain fully resolution- and contrast-recovered images at low levels of image roughness. For this purpose we calculate the system model by decomposing it into a product of five matrices: (1) a detector response component obtained via Monte Carlo simulations, (2) a geometric component which describes the scanner geometry and which is calculated via a multi-ray method, (3) a detector normalization component derived from the acquisition of a planar source, (4) a photon attenuation component calculated from x-ray computed tomography data, and finally, (5) a positron range component is formally included. This system model factorization allows the optimization of each component in terms of computation time, storage requirements and accuracy. The main contribution of this work is a new, efficient way to calculate the detector response component for rotating, planar detectors, that consists of a GEANT4 based simulation of a subset of lines of flight (LOFs) for a single detector head whereas the missing LOFs are obtained by using intrinsic detector symmetries. Additionally, we introduce and analyze a probability threshold for matrix elements of the detector component to optimize the trade-off between the matrix size in terms of non-zero elements and the resulting quality of the reconstructed images. In order to evaluate our proposed system model we reconstructed various images of objects, acquired according to the NEMA NU 4-2008 standard, and we compared them to the images reconstructed with two other system models: a model that does not include any detector response component and a model that approximates analytically the depth of interaction as detector response component. The comparisons confirm previous research results, showing that the usage of an accurate system model with a realistic detector response leads to reconstructed images with better resolution and contrast recovery at low levels of image roughness.

Accurate and efficient modeling of the detector response in small animal multi-head PET systems

NASA Astrophysics Data System (ADS)

Cecchetti, Matteo; Moehrs, Sascha; Belcari, Nicola; Del Guerra, Alberto

2013-10-01

In fully three-dimensional PET imaging, iterative image reconstruction techniques usually outperform analytical algorithms in terms of image quality provided that an appropriate system model is used. In this study we concentrate on the calculation of an accurate system model for the YAP-(S)PET II small animal scanner, with the aim to obtain fully resolution- and contrast-recovered images at low levels of image roughness. For this purpose we calculate the system model by decomposing it into a product of five matrices: (1) a detector response component obtained via Monte Carlo simulations, (2) a geometric component which describes the scanner geometry and which is calculated via a multi-ray method, (3) a detector normalization component derived from the acquisition of a planar source, (4) a photon attenuation component calculated from x-ray computed tomography data, and finally, (5) a positron range component is formally included. This system model factorization allows the optimization of each component in terms of computation time, storage requirements and accuracy. The main contribution of this work is a new, efficient way to calculate the detector response component for rotating, planar detectors, that consists of a GEANT4 based simulation of a subset of lines of flight (LOFs) for a single detector head whereas the missing LOFs are obtained by using intrinsic detector symmetries. Additionally, we introduce and analyze a probability threshold for matrix elements of the detector component to optimize the trade-off between the matrix size in terms of non-zero elements and the resulting quality of the reconstructed images. In order to evaluate our proposed system model we reconstructed various images of objects, acquired according to the NEMA NU 4-2008 standard, and we compared them to the images reconstructed with two other system models: a model that does not include any detector response component and a model that approximates analytically the depth of interaction as detector response component. The comparisons confirm previous research results, showing that the usage of an accurate system model with a realistic detector response leads to reconstructed images with better resolution and contrast recovery at low levels of image roughness.

Ecological monitoring in a discrete-time prey-predator model.

PubMed

Gámez, M; López, I; Rodríguez, C; Varga, Z; Garay, J

2017-09-21

The paper is aimed at the methodological development of ecological monitoring in discrete-time dynamic models. In earlier papers, in the framework of continuous-time models, we have shown how a systems-theoretical methodology can be applied to the monitoring of the state process of a system of interacting populations, also estimating certain abiotic environmental changes such as pollution, climatic or seasonal changes. In practice, however, there may be good reasons to use discrete-time models. (For instance, there may be discrete cycles in the development of the populations, or observations can be made only at discrete time steps.) Therefore the present paper is devoted to the development of the monitoring methodology in the framework of discrete-time models of population ecology. By monitoring we mean that, observing only certain component(s) of the system, we reconstruct the whole state process. This may be necessary, e.g., when in a complex ecosystem the observation of the densities of certain species is impossible, or too expensive. For the first presentation of the offered methodology, we have chosen a discrete-time version of the classical Lotka-Volterra prey-predator model. This is a minimal but not trivial system where the methodology can still be presented. We also show how this methodology can be applied to estimate the effect of an abiotic environmental change, using a component of the population system as an environmental indicator. Although this approach is illustrated in a simplest possible case, it can be easily extended to larger ecosystems with several interacting populations and different types of abiotic environmental effects. Copyright © 2017 Elsevier Ltd. All rights reserved.

Facilitative and competitive interaction components among New England salt marsh plants

USDA-ARS?s Scientific Manuscript database

Intra- and interspecific interactions can be broken down into facilitative and competitive components. The net interaction between two organisms is simply the sum of these counteracting elements. Disentangling the positive and negative components of species interactions is a critical step in advanc...

Partially acoustic dark matter, interacting dark radiation, and large scale structure

NASA Astrophysics Data System (ADS)

Chacko, Zackaria; Cui, Yanou; Hong, Sungwoo; Okui, Takemichi; Tsai, Yuhsinz

2016-12-01

The standard paradigm of collisionless cold dark matter is in tension with measurements on large scales. In particular, the best fit values of the Hubble rate H 0 and the matter density perturbation σ 8 inferred from the cosmic microwave background seem inconsistent with the results from direct measurements. We show that both problems can be solved in a framework in which dark matter consists of two distinct components, a dominant component and a subdominant component. The primary component is cold and collisionless. The secondary component is also cold, but interacts strongly with dark radiation, which itself forms a tightly coupled fluid. The growth of density perturbations in the subdominant component is inhibited by dark acoustic oscillations due to its coupling to the dark radiation, solving the σ 8 problem, while the presence of tightly coupled dark radiation ameliorates the H 0 problem. The subdominant component of dark matter and dark radiation continue to remain in thermal equilibrium until late times, inhibiting the formation of a dark disk. We present an example of a simple model that naturally realizes this scenario in which both constituents of dark matter are thermal WIMPs. Our scenario can be tested by future stage-IV experiments designed to probe the CMB and large scale structure.

Characterization of the interaction between subunits of the botulinum toxin complex produced by serotype D through tryptic susceptibility of the isolated components and complex forms.

PubMed

Suzuki, Tomonori; Watanabe, Toshihiro; Mutoh, Shingo; Hasegawa, Kimiko; Kouguchi, Hirokazu; Sagane, Yoshimasa; Fujinaga, Yukako; Oguma, Keiji; Ohyama, Tohru

2005-05-01

The 650 kDa large toxin complex (L-TC) produced by Clostridium botulinum serotype D strain 4947 (D-4947) has a subunit structure composed of unnicked components, i.e. neurotoxin (NT), non-toxic non-haemagglutinin (NTNHA) and three haemagglutinin subcomponents (HA-70, HA-33 and HA-17). In this study, subunit interactions were investigated through the susceptibilities of the toxin components to limited trypsin proteolysis. Additionally, complex forms were reconstituted in vitro by various combinations of individual components. Trypsin treatment of intact D-4947 L-TC led to the formation of mature L-TC with nicks at specific sites of each component, which is usually observed in other strains of serotype D. NT, NTNHA and HA-17 were cleaved at their specific sites in either the single or complex forms, but HA-33 showed no sign of proteolysis. Unlike the other components, HA-70 was digested into random fragments as a single form, but it was cleaved into two fragments in the complex form. Based on the relative position of exposed or hidden regions of the individual components in the complex derived from their tryptic susceptibilities, an assembly model is proposed for the arrangement of individual subunits in the botulinum L-TC.

Partially acoustic dark matter, interacting dark radiation, and large scale structure

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

Chacko, Zackaria; Cui, Yanou; Hong, Sungwoo

The standard paradigm of collisionless cold dark matter is in tension with measurements on large scales. In particular, the best fit values of the Hubble rate H 0 and the matter density perturbation σ 8 inferred from the cosmic microwave background seem inconsistent with the results from direct measurements. We show that both problems can be solved in a framework in which dark matter consists of two distinct components, a dominant component and a subdominant component. The primary component is cold and collisionless. The secondary component is also cold, but interacts strongly with dark radiation, which itself forms a tightlymore » coupled fluid. The growth of density perturbations in the subdominant component is inhibited by dark acoustic oscillations due to its coupling to the dark radiation, solving the σ 8 problem, while the presence of tightly coupled dark radiation ameliorates the H 0 problem. The subdominant component of dark matter and dark radiation continue to remain in thermal equilibrium until late times, inhibiting the formation of a dark disk. We present an example of a simple model that naturally realizes this scenario in which both constituents of dark matter are thermal WIMPs. Our scenario can be tested by future stage-IV experiments designed to probe the CMB and large scale structure.« less

Partially acoustic dark matter, interacting dark radiation, and large scale structure

DOE PAGES

Chacko, Zackaria; Cui, Yanou; Hong, Sungwoo; ...

2016-12-21

The standard paradigm of collisionless cold dark matter is in tension with measurements on large scales. In particular, the best fit values of the Hubble rate H 0 and the matter density perturbation σ 8 inferred from the cosmic microwave background seem inconsistent with the results from direct measurements. We show that both problems can be solved in a framework in which dark matter consists of two distinct components, a dominant component and a subdominant component. The primary component is cold and collisionless. The secondary component is also cold, but interacts strongly with dark radiation, which itself forms a tightlymore » coupled fluid. The growth of density perturbations in the subdominant component is inhibited by dark acoustic oscillations due to its coupling to the dark radiation, solving the σ 8 problem, while the presence of tightly coupled dark radiation ameliorates the H 0 problem. The subdominant component of dark matter and dark radiation continue to remain in thermal equilibrium until late times, inhibiting the formation of a dark disk. We present an example of a simple model that naturally realizes this scenario in which both constituents of dark matter are thermal WIMPs. Our scenario can be tested by future stage-IV experiments designed to probe the CMB and large scale structure.« less

Micromotors with Step-Motor Characteristics by Controlled Magnetic Interactions among Assembled Components

PubMed Central

2015-01-01

In this study, we investigated the control of the rotation dynamics of an innovative type of rotary micromotors with desired performances by tuning the magnetic interactions among the assembled micro/nanoscale components. The micromotors are made of metallic nanowires as rotors, patterned magnetic nanodisks as bearings and actuated by external electric fields. The magnetic forces for anchoring the rotors on the bearings play an essential role in the rotation dynamics of the micromotors. By varying the moment, orientation, and dimension of the magnetic components, distinct rotation behaviors can be observed, including repeatable wobbling and rolling in addition to rotation. We understood the rotation behaviors by analytical modeling, designed and realized micromotors with step-motor characteristics. The outcome of this research could inspire the development of high-performance nanomachines assembled from synthetic nanoentities, relevant to nanorobotics, microfluidics, and biomedical research. PMID:25536023

A possible four-phase coexistence in a single-component system

NASA Astrophysics Data System (ADS)

Akahane, Kenji; Russo, John; Tanaka, Hajime

2016-08-01

For different phases to coexist in equilibrium at constant temperature T and pressure P, the condition of equal chemical potential μ must be satisfied. This condition dictates that, for a single-component system, the maximum number of phases that can coexist is three. Historically this is known as the Gibbs phase rule, and is one of the oldest and venerable rules of thermodynamics. Here we make use of the fact that, by varying model parameters, the Gibbs phase rule can be generalized so that four phases can coexist even in single-component systems. To systematically search for the quadruple point, we use a monoatomic system interacting with a Stillinger-Weber potential with variable tetrahedrality. Our study indicates that the quadruple point provides flexibility in controlling multiple equilibrium phases and may be realized in systems with tunable interactions, which are nowadays feasible in several soft matter systems such as patchy colloids.

Design of Instrument Control Software for Solar Vector Magnetograph at Udaipur Solar Observatory

NASA Astrophysics Data System (ADS)

Gosain, Sanjay; Venkatakrishnan, P.; Venugopalan, K.

2004-04-01

A magnetograph is an instrument which makes measurement of solar magnetic field by measuring Zeeman induced polarization in solar spectral lines. In a typical filter based magnetograph there are three main modules namely, polarimeter, narrow-band spectrometer (filter), and imager(CCD camera). For a successful operation of magnetograph it is essential that these modules work in synchronization with each other. Here, we describe the design of instrument control system implemented for the Solar Vector Magnetograph under development at Udaipur Solar Observatory. The control software is written in Visual Basic and exploits the Component Object Model (COM) components for a fast and flexible application development. The user can interact with the instrument modules through a Graphical User Interface (GUI) and can program the sequence of magnetograph operations. The integration of Interactive Data Language (IDL) ActiveX components in the interface provides a powerful tool for online visualization, analysis and processing of images.

Evaluating the potential energy landscape over single molecules at room temperature with lateral force microscopy

NASA Astrophysics Data System (ADS)

Weymouth, Alfred J.; Riegel, Elisabeth; Matencio, Sonia; Giessibl, Franz J.

2018-04-01

One of the challenges of AFM, in contrast to STM, is that the measured signal includes both long-range and short-range components. The most accurate method for removing long-range components is to measure both on and off an adsorbate and to subtract the difference. This on-off method is challenging at room temperature due to thermal drift. By moving to a non-contact scheme in which the lateral component of the force interaction is probed, the measurement is dominated by short-range interactions. We use frequency-modulation lateral force microscopy to measure individual PTCDA molecules adsorbed on Ag/Si(111)-( √{3 }×√{3 } ). By fitting the data to a model potential, we can extract the depth and width of the potential. When the tip is closer to the sample, a repulsive feature can be observed in the data.

A possible four-phase coexistence in a single-component system

PubMed Central

Akahane, Kenji; Russo, John; Tanaka, Hajime

2016-01-01

For different phases to coexist in equilibrium at constant temperature T and pressure P, the condition of equal chemical potential μ must be satisfied. This condition dictates that, for a single-component system, the maximum number of phases that can coexist is three. Historically this is known as the Gibbs phase rule, and is one of the oldest and venerable rules of thermodynamics. Here we make use of the fact that, by varying model parameters, the Gibbs phase rule can be generalized so that four phases can coexist even in single-component systems. To systematically search for the quadruple point, we use a monoatomic system interacting with a Stillinger–Weber potential with variable tetrahedrality. Our study indicates that the quadruple point provides flexibility in controlling multiple equilibrium phases and may be realized in systems with tunable interactions, which are nowadays feasible in several soft matter systems such as patchy colloids. PMID:27558452

Thermodynamic modelling of the C-U and B-U binary systems

NASA Astrophysics Data System (ADS)

Chevalier, P. Y.; Fischer, E.

2001-02-01

The thermodynamic modelling of the carbon-uranium (C-U) and boron-uranium (B-U) binary systems is being performed in the framework of the development of a thermodynamic database for nuclear materials, for increasing the basic knowledge of key phenomena which may occur in the event of a severe accident in a nuclear power plant. Applications are foreseen in the nuclear safety field to the physico-chemical interaction modelling, on the one hand the in-vessel core degradation producing the corium (fuel, zircaloy, steel, control rods) and on the other hand the ex-vessel molten corium-concrete interaction (MCCI). The key O-U-Zr ternary system, previously modelled, allows us to describe the first interaction of the fuel with zircaloy cladding. Then, the three binary systems Fe-U, Cr-U and Ni-U were modelled as a preliminary work for modelling the O-U-Zr-Fe-Cr-Ni multicomponent system, allowing us to introduce the steel components in the corium. In the existing database (TDBCR, thermodynamic data base for corium), Ag and In were introduced for modelling AIC (silver-indium-cadmium) control rods which are used in French pressurized water reactors (PWR). Elsewhere, B 4C is also used for control rods. That is why it was agreed to extend in the next years the database with two new components, B and C. Such a work needs the thermodynamic modelling of all the binary and pseudo-binary sub-systems resulting from the combination of B, B 2O 3 and C with the major components of TDBCR, O-U-Zr-Fe-Cr-Ni-Ag-In-Ba-La-Ru-Sr-Al-Ca-Mg-Si + Ar-H. The critical assessment of the very numerous experimental information available for the C-U and B-U binary systems was performed by using a classical optimization procedure and the Scientific Group Thermodata Europe (SGTE). New optimized Gibbs energy parameters are given, and comparisons between calculated and experimental equilibrium phase diagrams or thermodynamic properties are presented. The self-consistency obtained is quite satisfactory.

Pressor mechanism evaluation for phytochemical compounds using in silico compound-protein interaction prediction.

PubMed

He, Min; Cao, Dong-Sheng; Liang, Yi-Zeng; Li, Ya-Ping; Liu, Ping-Le; Xu, Qing-Song; Huang, Ren-Bin

2013-10-01

In this study, a method was applied to evaluate pressor mechanisms through compound-protein interactions. Our method assumed that the compounds with different pressor mechanisms should bind to different target proteins, and thereby these mechanisms could be differentiated using compound-protein interactions. Twenty-six phytochemical components and 46 tested target proteins related to blood pressure (BP) elevation were collected. Then, in silico compound-protein interactions prediction probabilities were calculated using a random forest model, which have been implemented in a web server, and the credibility was judged using related literature and other methods. Further, a heat map was constructed, it clearly showed different prediction probabilities accompanied with hierarchical clustering analysis results. Followed by a compound-protein interaction network was depicted according to the results, we can see the connectivity layout of phytochemical components with different target proteins within the BP elevation network, which guided the hypothesis generation of poly-pharmacology. Lastly, principal components analysis (PCA) was carried out upon the prediction probabilities, and pressor targets could be divided into three large classes: neurotransmitter receptors, hormones receptors and monoamine oxidases. In addition, steroid glycosides seem to be close to the region of hormone receptors, and a weak difference existed between them. This work explored the possibility for pharmacological or toxicological mechanism classification using compound-protein interactions. Such approaches could also be used to deduce pharmacological or toxicological mechanisms for uncharacterized compounds. Copyright © 2013 Elsevier Inc. All rights reserved.

Effects of mineral dust on global atmospheric nitrate concentrations

NASA Astrophysics Data System (ADS)

Karydis, V. A.; Tsimpidi, A. P.; Pozzer, A.; Astitha, M.; Lelieveld, J.

2016-02-01

This study assesses the chemical composition and global aerosol load of the major inorganic aerosol components, focusing on mineral dust and aerosol nitrate. The mineral dust aerosol components (i.e., Ca2+, Mg2+, K+, Na+) and their emissions are included in the ECHAM5/MESSy Atmospheric Chemistry model (EMAC). Gas/aerosol partitioning is simulated using the ISORROPIA-II thermodynamic equilibrium model that considers K+, Ca2+, Mg2+, NH4+, Na+, SO42-, NO3-, Cl-, and H2O aerosol components. Emissions of mineral dust are calculated online by taking into account the soil particle size distribution and chemical composition of different deserts worldwide. Presence of metallic ions can substantially affect the nitrate partitioning into the aerosol phase due to thermodynamic interactions. The model simulates highest fine aerosol nitrate concentration over urban and industrialized areas (1-3 µg m-3), while coarse aerosol nitrate is highest close to deserts (1-4 µg m-3). The influence of mineral dust on nitrate formation extends across southern Europe, western USA, and northeastern China. The tropospheric burden of aerosol nitrate increases by 44 % when considering interactions of nitrate with mineral dust. The calculated global average nitrate aerosol concentration near the surface increases by 36 %, while the coarse- and fine-mode concentrations of nitrate increase by 53 and 21 %, respectively. Other inorganic aerosol components are affected by reactive dust components as well (e.g., the tropospheric burden of chloride increases by 9 %, ammonium decreases by 41 %, and sulfate increases by 7 %). Sensitivity tests show that nitrate aerosol is most sensitive to the chemical composition of the emitted mineral dust, followed by the soil size distribution of dust particles, the magnitude of the mineral dust emissions, and the aerosol state assumption.

Estimating hydrologic budgets for six Persian Gulf watersheds, Iran

NASA Astrophysics Data System (ADS)

Hosseini, Majid; Ghafouri, Mohammad; Tabatabaei, MahmoudReza; Goodarzi, Masoud; Mokarian, Zeinab

2017-10-01

Estimation of the major components of the hydrologic budget is important for determining the impacts on the water supply and quality of either planned or proposed land management projects, vegetative changes, groundwater withdrawals, and reservoir management practices and plans. As acquisition of field data is costly and time consuming, models have been created to test various land use practices and their concomitant effects on the hydrologic budget of watersheds. To simulate such management scenarios realistically, a model should be able to simulate the individual components of the hydrologic budget. The main objective of this study is to perform the SWAT2012 model for estimation of hydrological budget in six subbasin of Persian Gulf watershed; Golgol, Baghan, Marghab Shekastian, Tangebirim and Daragah, which are located in south and south west of Iran during 1991-2009. In order to evaluate the performance of the model, hydrological data, soil map, land use map and digital elevation model (DEM) are obtained and prepared for each catchment to run the model. SWAT-CUP with SUFI2 program was used for simulation, uncertainty and validation with 95 Percent Prediction Uncertainty. Coefficient of determination ( R 2) and Nash-Sutcliffe coefficient (NS) were used for evaluation of the model simulation results. Comparison of measured and predicted values demonstrated that each component of the model gave reasonable output and that the interaction among components was realistic. The study has produced a technique with reliable capability for annual and monthly water budget components in Persian Gulf watershed.

Polyamines: naturally occurring small molecule modulators of electrostatic protein-protein interactions.

PubMed

Berwanger, Anja; Eyrisch, Susanne; Schuster, Inge; Helms, Volkhard; Bernhardt, Rita

2010-02-01

Modulations of protein-protein interactions are a key step in regulating protein function, especially in networks. Modulators of these interactions are supposed to be candidates for the development of novel drugs. Here, we describe the role of the small, polycationic and highly abundant natural polyamines that could efficiently bind to charged spots at protein interfaces as modulators of such protein-protein interactions. Using the mitochondrial cytochrome P45011A1 (CYP11A1) electron transfer system as a model, we have analyzed the capability of putrescine, spermidine, and spermine at physiologically relevant concentrations to affect the protein-protein interactions between adrenodoxin reductase (AdR), adrenodoxin (Adx), and CYP11A1. The actions of polyamines on the individual components, on their association/dissociation, on electron transfer, and on substrate conversion were examined. These studies revealed modulating effects of polyamines on distinct interactions and on the entire system in a complex way. Modulation via changed protein-protein interactions appeared plausible from docking experiments that suggested favourable high-affinity binding sites of polyamines (spermine>spermidine>putrescine) at the AdR-Adx interface. Our findings imply for the first time that small endogenous compounds are capable of interfering with distinct components of transient protein complexes and might control protein functions by modulating electrostatic protein-protein interactions.

The Madden-Julian Oscillation and the Indo-Pacific Warm Pool

NASA Astrophysics Data System (ADS)

Raymond, David J.; Fuchs, Željka

2018-04-01

A minimal model of the interaction of the Madden-Julian oscillation (MJO) with the Indo-Pacific warm pool is presented. This model is based on the linear superposition of the flow associated with a highly simplified treatment of the MJO plus the flow induced by the warm pool itself. Both of these components parameterize rainfall as proportional to the column water vapor, which in turn is governed by a linearized moisture equation in which WISHE (wind induced surface heat exchange) plays a governing role. The MJO component has maximum growth rate for planetary wavenumber 1 and is equatorially trapped with purely zonal winds. The warm pool component exhibits a complex flow pattern, differing significantly from the classical Gill model as a result of the mean easterly flow. The combination of the two produce a flow that reproduces many aspects of the observed global flow associated with the MJO.

Dissecting the role of milk components on gut microbiota composition

PubMed Central

Maga, Elizabeth A.; Weimer, Bart C.; Murray, James D.

2013-01-01

The composition of human milk is tailored to contribute to the development of the gastrointestinal (GI) tract of newborns and infants. Importantly, human milk contains the antimicrobial compounds lysozyme and lactoferrin that are thought to contribute to the formation of a health-promoting microbiota. As these protective factors are lacking in the milk of dairy animals, we genetically engineered goats expressing human lysozyme in their milk and have recently reported a new animal model to dissect out the role of milk components on gut microbiota formation. Using the pig as a more human-relevant animal model, we demonstrated that consumption of lysozyme-rich milk enriched the abundance of bacteria associated with GI health and decreased those associated with disease, much like human milk. This work demonstrated that the pig is a valid animal model for gut microbiome studies on the effects of dietary components on microbiota composition, host-microbe interactions and state of the intestine. PMID:23235404

Multidisciplinary model-based-engineering for laser weapon systems: recent progress

NASA Astrophysics Data System (ADS)

Coy, Steve; Panthaki, Malcolm

2013-09-01

We are working to develop a comprehensive, integrated software framework and toolset to support model-based engineering (MBE) of laser weapons systems. MBE has been identified by the Office of the Director, Defense Science and Engineering as one of four potentially "game-changing" technologies that could bring about revolutionary advances across the entire DoD research and development and procurement cycle. To be effective, however, MBE requires robust underlying modeling and simulation technologies capable of modeling all the pertinent systems, subsystems, components, effects, and interactions at any level of fidelity that may be required in order to support crucial design decisions at any point in the system development lifecycle. Very often the greatest technical challenges are posed by systems involving interactions that cut across two or more distinct scientific or engineering domains; even in cases where there are excellent tools available for modeling each individual domain, generally none of these domain-specific tools can be used to model the cross-domain interactions. In the case of laser weapons systems R&D these tools need to be able to support modeling of systems involving combined interactions among structures, thermal, and optical effects, including both ray optics and wave optics, controls, atmospheric effects, target interaction, computational fluid dynamics, and spatiotemporal interactions between lasing light and the laser gain medium. To address this problem we are working to extend Comet™, to add the addition modeling and simulation capabilities required for this particular application area. In this paper we will describe our progress to date.

Chemical synaptic and gap junctional interactions between principal neurons: partners in epileptogenesis.

PubMed

Traub, Roger D; Cunningham, Mark O; Whittington, Miles A

2011-08-01

Field potential signals, corresponding to electrographic seizures in cortical structures, often contain two components, which sometimes appear to be separable and other times to be superimposed. The first component consists of low-amplitude very fast oscillations (VFO, >70-80 Hz); the second component consists of larger amplitude transients, lasting tens to hundreds of ms, and variously called population spikes, EEG spikes, or bursts--terms chosen in part because of the cellular correlates of the field events. To first approximation, the two components arise because of distinctive types of cellular interactions: gap junctions for VFO (a model of which is reviewed in the following), and recurrent synaptic excitation and/or inhibition for the transients. With in vitro studies of epileptic human neocortical tissue, it is possible to elicit VFO alone, or VFO superimposed on a large transient, but not a large transient without the VFO. If such observations prove to be general, they would imply that gap junction-mediated interactions are the primary factor in epileptogenesis. It appears to be the case then, that in the setting of seizure initiation (but not necessarily under physiological conditions), the gain of gap junction-mediated circuits can actually be larger than the gain in excitatory synaptic circuits. Copyright © 2010 Elsevier Ltd. All rights reserved.

Chemical Synaptic and Gap Junctional Interactions Between Principal Neurons: Partners in Epileptogenesis

PubMed Central

Traub, Roger D.; Cunningham, Mark O.; Whittington, Miles A.

2010-01-01

Field potential signals, corresponding to electrographic seizures in cortical structures, often contain two components, which sometimes appear to be separable and other times to be superimposed. The first component consists of low-amplitude very fast oscillations (VFO, > 70–80 Hz); the second component consists of larger amplitude transients, lasting tens to hundreds of ms, and variously called population spikes, EEG spikes, or bursts – terms chosen in part because of the cellular correlates of the field events. To first approximation, the two components arise because of distinctive types of cellular interactions: gap junctions for VFO (a model of which is reviewed in the following), and recurrent synaptic excitation and/or inhibition for the transients. With in vitro studies of epileptic human neocortical tissue, it is possible to elicit VFO alone, or VFO superimposed on a large transient, but not a large transient without the VFO. If such observations prove to be general, they would imply that gap junction-mediated interactions are the primary factor in epileptogenesis. It appears to be the case then, that in the setting of seizure initiation (but not necessarily under physiological conditions), the gain of gap junction-mediated circuits can actually be larger than the gain in excitatory synaptic circuits. PMID:21168305

The Prediction of Key Cytoskeleton Components Involved in Glomerular Diseases Based on a Protein-Protein Interaction Network.

PubMed

Ding, Fangrui; Tan, Aidi; Ju, Wenjun; Li, Xuejuan; Li, Shao; Ding, Jie

2016-01-01

Maintenance of the physiological morphologies of different types of cells and tissues is essential for the normal functioning of each system in the human body. Dynamic variations in cell and tissue morphologies depend on accurate adjustments of the cytoskeletal system. The cytoskeletal system in the glomerulus plays a key role in the normal process of kidney filtration. To enhance the understanding of the possible roles of the cytoskeleton in glomerular diseases, we constructed the Glomerular Cytoskeleton Network (GCNet), which shows the protein-protein interaction network in the glomerulus, and identified several possible key cytoskeletal components involved in glomerular diseases. In this study, genes/proteins annotated to the cytoskeleton were detected by Gene Ontology analysis, and glomerulus-enriched genes were selected from nine available glomerular expression datasets. Then, the GCNet was generated by combining these two sets of information. To predict the possible key cytoskeleton components in glomerular diseases, we then examined the common regulation of the genes in GCNet in the context of five glomerular diseases based on their transcriptomic data. As a result, twenty-one cytoskeleton components as potential candidate were highlighted for consistently down- or up-regulating in all five glomerular diseases. And then, these candidates were examined in relation to existing known glomerular diseases and genes to determine their possible functions and interactions. In addition, the mRNA levels of these candidates were also validated in a puromycin aminonucleoside(PAN) induced rat nephropathy model and were also matched with existing Diabetic Nephropathy (DN) transcriptomic data. As a result, there are 15 of 21 candidates in PAN induced nephropathy model were consistent with our predication and also 12 of 21 candidates were matched with differentially expressed genes in the DN transcriptomic data. By providing a novel interaction network and prediction, GCNet contributes to improving the understanding of normal glomerular function and will be useful for detecting target cytoskeleton molecules of interest that may be involved in glomerular diseases in future studies.

The Prediction of Key Cytoskeleton Components Involved in Glomerular Diseases Based on a Protein-Protein Interaction Network

PubMed Central

Ju, Wenjun; Li, Xuejuan; Li, Shao; Ding, Jie

2016-01-01

Maintenance of the physiological morphologies of different types of cells and tissues is essential for the normal functioning of each system in the human body. Dynamic variations in cell and tissue morphologies depend on accurate adjustments of the cytoskeletal system. The cytoskeletal system in the glomerulus plays a key role in the normal process of kidney filtration. To enhance the understanding of the possible roles of the cytoskeleton in glomerular diseases, we constructed the Glomerular Cytoskeleton Network (GCNet), which shows the protein-protein interaction network in the glomerulus, and identified several possible key cytoskeletal components involved in glomerular diseases. In this study, genes/proteins annotated to the cytoskeleton were detected by Gene Ontology analysis, and glomerulus-enriched genes were selected from nine available glomerular expression datasets. Then, the GCNet was generated by combining these two sets of information. To predict the possible key cytoskeleton components in glomerular diseases, we then examined the common regulation of the genes in GCNet in the context of five glomerular diseases based on their transcriptomic data. As a result, twenty-one cytoskeleton components as potential candidate were highlighted for consistently down- or up-regulating in all five glomerular diseases. And then, these candidates were examined in relation to existing known glomerular diseases and genes to determine their possible functions and interactions. In addition, the mRNA levels of these candidates were also validated in a puromycin aminonucleoside(PAN) induced rat nephropathy model and were also matched with existing Diabetic Nephropathy (DN) transcriptomic data. As a result, there are 15 of 21 candidates in PAN induced nephropathy model were consistent with our predication and also 12 of 21 candidates were matched with differentially expressed genes in the DN transcriptomic data. By providing a novel interaction network and prediction, GCNet contributes to improving the understanding of normal glomerular function and will be useful for detecting target cytoskeleton molecules of interest that may be involved in glomerular diseases in future studies. PMID:27227331

Predictive performance models and multiple task performance

NASA Technical Reports Server (NTRS)

Wickens, Christopher D.; Larish, Inge; Contorer, Aaron

1989-01-01

Five models that predict how performance of multiple tasks will interact in complex task scenarios are discussed. The models are shown in terms of the assumptions they make about human operator divided attention. The different assumptions about attention are then empirically validated in a multitask helicopter flight simulation. It is concluded from this simulation that the most important assumption relates to the coding of demand level of different component tasks.

The development of interior noise and vibration criteria

NASA Technical Reports Server (NTRS)

Leatherwood, J. D.; Clevenson, S. A.; Stephens, D. G.

1990-01-01

A generalized model was developed for estimating passenger discomfort response to combined noise and vibration. This model accounts for broadband noise and vibration spectra and multiple axes of vibration as well as the interactive effects of combined noise and vibration. The model has the unique capability of transforming individual components of noise/vibration environment into subjective comfort units and then combining these comfort units to produce a total index of passenger discomfort and useful sub-indices that typify passenger comfort within the environment. An overview of the model development is presented including the methodology employed, major elements of the model, model applications, and a brief description of a commercially available portable ride comfort meter based directly upon the model algorithms. Also discussed are potential criteria formats that account for the interactive effects of noise and vibration on human discomfort response.

From Tabletop RPG to Interactive Storytelling: Definition of a Story Manager for Videogames

NASA Astrophysics Data System (ADS)

Delmas, Guylain; Champagnat, Ronan; Augeraud, Michel

Adding narrative in computer game is complicated because it may restrict player interactivity. Our aim is to design a controller that dynamically built a plot, through the game execution, centred on player's actions. Tabletop Role-playing games manage to deal with this goal. This paper presents a study of role-playing games, their organization, and the models commonly used for narrative generation. It then deduces a proposition of components and data structures for interactive storytelling in videogames. A prototype of a social game has been developed as example.

Behavioural phenotyping assays for mouse models of autism

PubMed Central

Silverman, Jill L.; Yang, Mu; Lord, Catherine; Crawley, Jacqueline N.

2011-01-01

Autism is a heterogeneous neurodevelopmental disorder of unknown aetiology that affects 1 in 100–150 individuals. Diagnosis is based on three categories of behavioural criteria: abnormal social interactions, communication deficits and repetitive behaviours. Strong evidence for a genetic basis has prompted the development of mouse models with targeted mutations in candidate genes for autism. As the diagnostic criteria for autism are behavioural, phenotyping these mouse models requires behavioural assays with high relevance to each category of the diagnostic symptoms. Behavioural neuroscientists are generating a comprehensive set of assays for social interaction, communication and repetitive behaviours to test hypotheses about the causes of austism. Robust phenotypes in mouse models hold great promise as translational tools for discovering effective treatments for components of autism spectrum disorders. PMID:20559336

Vapor mediated droplet interactions - models and mechanisms (Part 2)

NASA Astrophysics Data System (ADS)

Benusiglio, Adrien; Cira, Nate; Prakash, Manu

2014-11-01

When deposited on clean glass a two-component binary mixture of propylene glycol and water is energetically inclined to spread, as both pure liquids do. Instead the mixture forms droplets stabilized by evaporation induced surface tension gradients, giving them unique properties such as negligible hysteresis. When two of these special droplets are deposited several radii apart they attract each other. The vapor from one droplet destabilizes the other, resulting in an attraction force which brings both droplets together. We present a flux-based model for droplet stabilization and a model which connects the vapor profile to net force. These simple models capture the static and dynamic experimental trends, and our fundamental understanding of these droplets and their interactions allowed us to build autonomous fluidic machines.

Effect of interacting second- and third-order stimulus-dependent correlations on population-coding asymmetries.

PubMed

Montangie, Lisandro; Montani, Fernando

2016-10-01

Spike correlations among neurons are widely encountered in the brain. Although models accounting for pairwise interactions have proved able to capture some of the most important features of population activity at the level of the retina, the evidence shows that pairwise neuronal correlation analysis does not resolve cooperative population dynamics by itself. By means of a series expansion for short time scales of the mutual information conveyed by a population of neurons, the information transmission can be broken down into firing rate and correlational components. In a proposed extension of this framework, we investigate the information components considering both second- and higher-order correlations. We show that the existence of a mixed stimulus-dependent correlation term defines a new scenario for the interplay between pairwise and higher-than-pairwise interactions in noise and signal correlations that would lead either to redundancy or synergy in the information-theoretic sense.

Triple transition [ital Q][sub 1]([ital j][sub 1])+[ital Q][sub 1]([ital j][sub 2])+[ital Q][sub 1]([ital j][sub 3]) near 12 466 cm[sup --1] in compressed hydrogen

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

Moraldi, M.; Frommhold, L.

1995-01-16

We use the model of the overlap-induced, irreducible, ternary dipole (OITD) component of three interacting H[sub 2] molecules [Phys. Rev. A [bold 49], 4508 (1994)] to calculate the intensity of the triple [ital Q][sub 1] transition, observed by Reddy, Xiang, and Vaghese [following Letter, Phys. Rev. Lett. [bold 74], 367 (1995)] in compressed hydrogen gas in absorption near 12 466 cm[sup --1]. Such simultaneous transitions in three interacting molecules are thought to arise from irreducible, ternary dipole components. The calculated intensities agree with the measurement within a factor of 2 or 3, which shows once more that the OITD modelmore » is capable of describing ternary spectroscopic interaction in remarkable detail.« less

Water resources planning based on complex system dynamics: A case study of Tianjin city

NASA Astrophysics Data System (ADS)

Zhang, X. H.; Zhang, H. W.; Chen, B.; Chen, G. Q.; Zhao, X. H.

2008-12-01

A complex system dynamic (SD) model focusing on water resources, termed as TianjinSD, is developed for the integrated and scientific management of the water resources of Tianjin, which contains information feedback that governs interactions in the system and is capable of synthesizing component-level knowledge into system behavior simulation at an integrated level, thus presenting reasonable predictive results for policy-making on water resources allocation and management. As for the Tianjin city, interactions among 96 components for 12 years are explored and four planning alternatives are chosen, one of which is based on the conventional mode assuming that the existing pattern of human activities will be prevailed, while the others are alternative planning designs based on the interaction of local authorities and planning researchers. Optimal mode is therefore obtained according to different scenarios when compared the simulation results for evaluation of different decisions and dynamic consequences.

Water Energy Simulation Toolset

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

Nguyen, Thuy; Jeffers, Robert

The Water-Energy Simulation Toolset (WEST) is an interactive simulation model that helps visualize impacts of different stakeholders on water quantity and quality of a watershed. The case study is applied for the Snake River Basin with the fictional name Cutthroat River Basin. There are four groups of stakeholders of interest: hydropower, agriculture, flood control, and environmental protection. Currently, the quality component depicts nitrogen-nitrate contaminant. Users can easily interact with the model by changing certain inputs (climate change, fertilizer inputs, etc.) to observe the change over the entire system. Users can also change certain parameters to test their management policy.

Aerothermal modeling program. Phase 2, element B: Flow interaction experiment

NASA Technical Reports Server (NTRS)

Nikjooy, M.; Mongia, H. C.; Murthy, S. N. B.; Sullivan, J. P.

1987-01-01

NASA has instituted an extensive effort to improve the design process and data base for the hot section components of gas turbine engines. The purpose of element B is to establish a benchmark quality data set that consists of measurements of the interaction of circular jets with swirling flow. Such flows are typical of those that occur in the primary zone of modern annular combustion liners. Extensive computations of the swirling flows are to be compared with the measurements for the purpose of assessing the accuracy of current physical models used to predict such flows.

Scaling cosmology with variable dark-energy equation of state

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

Castro, David R.; Velten, Hermano; Zimdahl, Winfried, E-mail: drodriguez-ufes@hotmail.com, E-mail: velten@physik.uni-bielefeld.de, E-mail: winfried.zimdahl@pq.cnpq.br

2012-06-01

Interactions between dark matter and dark energy which result in a power-law behavior (with respect to the cosmic scale factor) of the ratio between the energy densities of the dark components (thus generalizing the ΛCDM model) have been considered as an attempt to alleviate the cosmic coincidence problem phenomenologically. We generalize this approach by allowing for a variable equation of state for the dark energy within the CPL-parametrization. Based on analytic solutions for the Hubble rate and using the Constitution and Union2 SNIa sets, we present a statistical analysis and classify different interacting and non-interacting models according to the Akaikemore » (AIC) and the Bayesian (BIC) information criteria. We do not find noticeable evidence for an alleviation of the coincidence problem with the mentioned type of interaction.« less

Single- and mixture toxicity of three organic UV-filters, ethylhexyl methoxycinnamate, octocrylene, and avobenzone on Daphnia magna.

PubMed

Park, Chang-Beom; Jang, Jiyi; Kim, Sanghun; Kim, Young Jun

2017-03-01

In freshwater environments, aquatic organisms are generally exposed to mixtures of various chemical substances. In this study, we tested the toxicity of three organic UV-filters (ethylhexyl methoxycinnamate, octocrylene, and avobenzone) to Daphnia magna in order to evaluate the combined toxicity of these substances when in they occur in a mixture. The values of effective concentrations (ECx) for each UV-filter were calculated by concentration-response curves; concentration-combinations of three different UV-filters in a mixture were determined by the fraction of components based on EC 25 values predicted by concentration addition (CA) model. The interaction between the UV-filters were also assessed by model deviation ratio (MDR) using observed and predicted toxicity values obtained from mixture-exposure tests and CA model. The results from this study indicated that observed ECx mix (e.g., EC 10mix , EC 25mix , or EC 50mix ) values obtained from mixture-exposure tests were higher than predicted ECx mix (e.g., EC 10mix , EC 25mix , or EC 50mix ) values calculated by CA model. MDR values were also less than a factor of 1.0 in a mixtures of three different UV-filters. Based on these results, we suggest for the first time a reduction of toxic effects in the mixtures of three UV-filters, caused by antagonistic action of the components. Our findings from this study will provide important information for hazard or risk assessment of organic UV-filters, when they existed together in the aquatic environment. To better understand the mixture toxicity and the interaction of components in a mixture, further studies for various combinations of mixture components are also required. Copyright © 2016 Elsevier Inc. All rights reserved.

First-order reversal curves of single domain particles: diluted random assemblages and chains

NASA Astrophysics Data System (ADS)

Egli, R.

2009-04-01

Exact magnetic models can be used to calculate first-order reversal curves (FORC) of single domain (SD) particle assemblages, as shown by Newell [2005] for the case of isolated Stoner-Wohlfarth particles. After overcoming experimental difficulties, a FORC diagram sharing many similarities to Newell's model has been measured on a lake sediment sample (see A.P. Chen et al., "Quantification of magnetofossils using first-order reversal curves", EGU General Assembly 2009, Abstracts Vol. 11, EGU2009-10719). This sample contains abundant magnetofossils, as shown by coercivity analysis and electron microscopy, therefore suggesting that well dispersed, intact magnetosome chains are the main SD carriers. Subtle differences between the reversible and the irreversible contributions of the measured FORC distribution suggest that magnetosome chains might not be correctly described by the Stoner-Wohlfarth model. To better understand the hysteresis properties of such chains, a simple magnetic model has been implemented, taking dipole-dipole interactions between particles within the same chain into account. The model results depend on the magnetosome elongation, the number of magnetosomes in a chain, and the gap between them. If the chain axis is subparallel to the applied field, the magnetic moment reverses by a pseudo-fanning mode, which is replaced by a pseudo-coherent rotation mode at greater angles. These reversal modes are intrinsically different from coherent rotation assumed Stoner-Wohlfarth model, resulting in FORC diagrams with a smaller reversible component. On the other hand, isolated authigenic SD particles can precipitate in the sediment matrix, as it might occur for pedogenic magnetite. In this case, an assembly of randomly located particles provides a possible model for the resulting FORC diagram. If the concentration of the particles is small, each particle is affected by a random interaction field whose statistical distribution can be calculated from first principles. In this case, the irreversible component of the FORC diagram, which is described by a Dirac delta function in the non-interacting case, converts into a continuous function that directly reflects the distribution of interaction fields. Such models provide a way to identify and characterize authigenic SD particles in sediments, and in some case allow one to isolate their magnetic contribution from that of other magnetic components. Newell, A.J. (2005), A high-precision model of first-order reversal curve (FORC) functions for single-domain ferromagnets with uniaxial anisotropy, Gechem. Geophys. Geosyst., 6, Q05010, doi:10.1029/2004GC00877.

Dynamic train-track interaction at high vehicle speeds—Modelling of wheelset dynamics and wheel rotation

NASA Astrophysics Data System (ADS)

Torstensson, P. T.; Nielsen, J. C. O.; Baeza, L.

2011-10-01

Vertical dynamic train-track interaction at high vehicle speeds is investigated in a frequency range from about 20 Hz to 2.5 kHz. The inertial effects due to wheel rotation are accounted for in the vehicle model by implementing a structural dynamics model of a rotating wheelset. Calculated wheel-rail contact forces using the flexible, rotating wheelset model are compared with contact forces based on rigid, non-rotating models. For a validation of the train-track interaction model, calculated contact forces are compared with contact forces measured using an instrumented wheelset. When the system is excited at a frequency where two different wheelset mode shapes, due to the wheel rotation, have coinciding resonance frequencies, significant differences are found in the contact forces calculated with the rotating and non-rotating wheelset models. Further, the use of a flexible, rotating wheelset model is recommended for load cases leading to large magnitude contact force components in the high-frequency range (above 1.5 kHz). In particular, the influence of the radial wheel eigenmodes with two or three nodal diameters is significant.

Computational model of precision grip in Parkinson's disease: a utility based approach

PubMed Central

Gupta, Ankur; Balasubramani, Pragathi P.; Chakravarthy, V. Srinivasa

2013-01-01

We propose a computational model of Precision Grip (PG) performance in normal subjects and Parkinson's Disease (PD) patients. Prior studies on grip force generation in PD patients show an increase in grip force during ON medication and an increase in the variability of the grip force during OFF medication (Ingvarsson et al., 1997; Fellows et al., 1998). Changes in grip force generation in dopamine-deficient PD conditions strongly suggest contribution of the Basal Ganglia, a deep brain system having a crucial role in translating dopamine signals to decision making. The present approach is to treat the problem of modeling grip force generation as a problem of action selection, which is one of the key functions of the Basal Ganglia. The model consists of two components: (1) the sensory-motor loop component, and (2) the Basal Ganglia component. The sensory-motor loop component converts a reference position and a reference grip force, into lift force and grip force profiles, respectively. These two forces cooperate in grip-lifting a load. The sensory-motor loop component also includes a plant model that represents the interaction between two fingers involved in PG, and the object to be lifted. The Basal Ganglia component is modeled using Reinforcement Learning with the significant difference that the action selection is performed using utility distribution instead of using purely Value-based distribution, thereby incorporating risk-based decision making. The proposed model is able to account for the PG results from normal and PD patients accurately (Ingvarsson et al., 1997; Fellows et al., 1998). To our knowledge the model is the first model of PG in PD conditions. PMID:24348373

What is reflection? A conceptual analysis of major definitions and a proposal of a five-component model.

PubMed

Nguyen, Quoc Dinh; Fernandez, Nicolas; Karsenti, Thierry; Charlin, Bernard

2014-12-01

Although reflection is considered a significant component of medical education and practice, the literature does not provide a consensual definition or model for it. Because reflection has taken on multiple meanings, it remains difficult to operationalise. A standard definition and model are needed to improve the development of practical applications of reflection. This study was conducted in order to identify, explore and analyse the most influential conceptualisations of reflection, and to develop a new theory-informed and unified definition and model of reflection. A systematic review was conducted to identify the 15 most cited authors in papers on reflection published during the period from 2008 to 2012. The authors' definitions and models were extracted. An exploratory thematic analysis was carried out and identified seven initial categories. Categories were clustered and reworded to develop an integrative definition and model of reflection, which feature core components that define reflection and extrinsic elements that influence instances of reflection. Following our review and analysis, five core components of reflection and two extrinsic elements were identified as characteristics of the reflective thinking process. Reflection is defined as the process of engaging the self (S) in attentive, critical, exploratory and iterative (ACEI) interactions with one's thoughts and actions (TA), and their underlying conceptual frame (CF), with a view to changing them and a view on the change itself (VC). Our conceptual model consists of the defining core components, supplemented with the extrinsic elements that influence reflection. This article presents a new theory-informed, five-component definition and model of reflection. We believe these have advantages over previous models in terms of helping to guide the further study, learning, assessment and teaching of reflection. © 2014 John Wiley & Sons Ltd.

Two-wave model of the muscle contraction.

PubMed

Molski, Marcin

2009-05-01

The Matsuno model of the muscle contraction is considered in the framework of the two-wave Corben's theory of composite objects built up of both time- and space-like components. It has been proved that during muscle contraction the locally coherent aggregates distributed along the actin filament interact by means of space-like fields, which are solutions of the relativistic Feinberg equation. The existence of such interactions and lack of decoherence are conditions sine qua non for appearance of the quantum entanglement between actin monomers in an ATP-activated filament. A possible role of a quantum potential in the muscle contraction is discussed and the mass of the carrier of space-like interactions is estimated m0' = 7.3 x 10(-32) g (46 eV).

Proates a computer modelling system for power plant: Its description and application to heatrate improvement within PowerGen

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

Green, C.H.; Ready, A.B.; Rea, J.

1995-06-01

Versions of the computer program PROATES (PROcess Analysis for Thermal Energy Systems) have been used since 1979 to analyse plant performance improvement proposals relating to existing plant and also to evaluate new plant designs. Several plant modifications have been made to improve performance based on the model predictions and the predicted performance has been realised in practice. The program was born out of a need to model the overall steady state performance of complex plant to enable proposals to change plant component items or operating strategy to be evaluated. To do this with confidence it is necessary to model themore » multiple thermodynamic interactions between the plant components. The modelling system is modular in concept allowing the configuration of individual plant components to represent any particular power plant design. A library exists of physics based modules which have been extensively validated and which provide representations of a wide range of boiler, turbine and CW system components. Changes to model data and construction is achieved via a user friendly graphical model editing/analysis front-end with results being presented via the computer screen or hard copy. The paper describes briefly the modelling system but concentrates mainly on the application of the modelling system to assess design re-optimisation, firing with different fuels and the re-powering of an existing plant.« less

The dynamical core, physical parameterizations, and basic simulation characteristics of the atmospheric component AM3 of the GFDL global coupled model CM3

USGS Publications Warehouse

Donner, L.J.; Wyman, B.L.; Hemler, R.S.; Horowitz, L.W.; Ming, Y.; Zhao, M.; Golaz, J.-C.; Ginoux, P.; Lin, S.-J.; Schwarzkopf, M.D.; Austin, J.; Alaka, G.; Cooke, W.F.; Delworth, T.L.; Freidenreich, S.M.; Gordon, C.T.; Griffies, S.M.; Held, I.M.; Hurlin, W.J.; Klein, S.A.; Knutson, T.R.; Langenhorst, A.R.; Lee, H.-C.; Lin, Y.; Magi, B.I.; Malyshev, S.L.; Milly, P.C.D.; Naik, V.; Nath, M.J.; Pincus, R.; Ploshay, J.J.; Ramaswamy, V.; Seman, C.J.; Shevliakova, E.; Sirutis, J.J.; Stern, W.F.; Stouffer, R.J.; Wilson, R.J.; Winton, M.; Wittenberg, A.T.; Zeng, F.

2011-01-01

The Geophysical Fluid Dynamics Laboratory (GFDL) has developed a coupled general circulation model (CM3) for the atmosphere, oceans, land, and sea ice. The goal of CM3 is to address emerging issues in climate change, including aerosol-cloud interactions, chemistry-climate interactions, and coupling between the troposphere and stratosphere. The model is also designed to serve as the physical system component of earth system models and models for decadal prediction in the near-term future-for example, through improved simulations in tropical land precipitation relative to earlier-generation GFDL models. This paper describes the dynamical core, physical parameterizations, and basic simulation characteristics of the atmospheric component (AM3) of this model. Relative to GFDL AM2, AM3 includes new treatments of deep and shallow cumulus convection, cloud droplet activation by aerosols, subgrid variability of stratiform vertical velocities for droplet activation, and atmospheric chemistry driven by emissions with advective, convective, and turbulent transport. AM3 employs a cubed-sphere implementation of a finite-volume dynamical core and is coupled to LM3, a new land model with ecosystem dynamics and hydrology. Its horizontal resolution is approximately 200 km, and its vertical resolution ranges approximately from 70 m near the earth's surface to 1 to 1.5 km near the tropopause and 3 to 4 km in much of the stratosphere. Most basic circulation features in AM3 are simulated as realistically, or more so, as in AM2. In particular, dry biases have been reduced over South America. In coupled mode, the simulation of Arctic sea ice concentration has improved. AM3 aerosol optical depths, scattering properties, and surface clear-sky downward shortwave radiation are more realistic than in AM2. The simulation of marine stratocumulus decks remains problematic, as in AM2. The most intense 0.2% of precipitation rates occur less frequently in AM3 than observed. The last two decades of the twentieth century warm in CM3 by 0.328C relative to 1881-1920. The Climate Research Unit (CRU) and Goddard Institute for Space Studies analyses of observations show warming of 0.568 and 0.528C, respectively, over this period. CM3 includes anthropogenic cooling by aerosol-cloud interactions, and its warming by the late twentieth century is somewhat less realistic than in CM2.1, which warmed 0.668C but did not include aerosol-cloud interactions. The improved simulation of the direct aerosol effect (apparent in surface clear-sky downward radiation) in CM3 evidently acts in concert with its simulation of cloud-aerosol interactions to limit greenhouse gas warming. ?? 2011 American Meteorological Society.

Flow Analysis of a Gas Turbine Low- Pressure Subsystem

NASA Technical Reports Server (NTRS)

Veres, Joseph P.

1997-01-01

The NASA Lewis Research Center is coordinating a project to numerically simulate aerodynamic flow in the complete low-pressure subsystem (LPS) of a gas turbine engine. The numerical model solves the three-dimensional Navier-Stokes flow equations through all components within the low-pressure subsystem as well as the external flow around the engine nacelle. The Advanced Ducted Propfan Analysis Code (ADPAC), which is being developed jointly by Allison Engine Company and NASA, is the Navier-Stokes flow code being used for LPS simulation. The majority of the LPS project is being done under a NASA Lewis contract with Allison. Other contributors to the project are NYMA and the University of Toledo. For this project, the Energy Efficient Engine designed by GE Aircraft Engines is being modeled. This engine includes a low-pressure system and a high-pressure system. An inlet, a fan, a booster stage, a bypass duct, a lobed mixer, a low-pressure turbine, and a jet nozzle comprise the low-pressure subsystem within this engine. The tightly coupled flow analysis evaluates aerodynamic interactions between all components of the LPS. The high-pressure core engine of this engine is simulated with a one-dimensional thermodynamic cycle code in order to provide boundary conditions to the detailed LPS model. This core engine consists of a high-pressure compressor, a combustor, and a high-pressure turbine. The three-dimensional LPS flow model is coupled to the one-dimensional core engine model to provide a "hybrid" flow model of the complete gas turbine Energy Efficient Engine. The resulting hybrid engine model evaluates the detailed interaction between the LPS components at design and off-design engine operating conditions while considering the lumped-parameter performance of the core engine.

Patient-Clinician Communication About Pain: A Conceptual Model and Narrative Review.

PubMed

Henry, Stephen G; Matthias, Marianne S

2018-02-01

Productive patient-clinician communication is an important component of effective pain management, but we know little about how patients and clinicians actually talk about pain in clinical settings and how it might be improved to produce better patient outcomes. The objective of this review was to create a conceptual model of patient-clinician communication about noncancer pain, review and synthesize empirical research in this area, and identify priorities for future research. A conceptual model was developed that drew on existing pain and health communication research. CINAHL, EMBASE, and PubMed were searched to find studies reporting empirical data on patient-clinician communication about noncancer pain; results were supplemented with manual searches. Studies were categorized and analyzed to identify crosscutting themes and inform model development. The conceptual model comprised the following components: contextual factors, clinical interaction, attitudes and beliefs, and outcomes. Thirty-nine studies met inclusion criteria and were analyzed based on model components. Studies varied widely in quality, methodology, and sample size. Two provisional conclusions were identified: contrary to what is often reported in the literature, discussions about analgesics are most frequently characterized by patient-clinician agreement, and self-presentation during patient-clinician interactions plays an important role in communication about pain and opioids. Published studies on patient-clinician communication about noncancer pain are few and diverse. The conceptual model presented here can help to identify knowledge gaps and guide future research on communication about pain. Investigating the links between communication and pain-related outcomes is an important priority for future research. © 2018 American Academy of Pain Medicine. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

A perfectly conducting surface in electrodynamics with Lorentz symmetry breaking

NASA Astrophysics Data System (ADS)

Borges, L. H. C.; Barone, F. A.

2017-10-01

In this paper we consider a model which exhibits explicit Lorentz symmetry breaking due to the presence of a single background vector v^{μ } coupled to the gauge field. We investigate such a theory in the vicinity of a perfectly conducting plate for different configurations of v^{μ }. First we consider no restrictions on the components of the background vector and we treat it perturbatively up to second order. Next, we treat v^{μ } exactly for two special cases: the first one is when it has only components parallel to the plate, and the second one when it has a single component perpendicular to the plate. For all these configurations, the propagator for the gauge field and the interaction force between the plate and a point-like electric charge are computed. Surprisingly, it is shown that the image method is valid in our model and we argue that it is a non-trivial result. We show there arises a torque on the mirror with respect to its positioning in the background field when it interacts with a point-like charge. It is a new effect with no counterpart in theories with Lorentz symmetry in the presence of a perfect mirror.

Accounting for water management issues within hydrological simulation: Alternative modelling options and a network optimization approach

NASA Astrophysics Data System (ADS)

Efstratiadis, Andreas; Nalbantis, Ioannis; Rozos, Evangelos; Koutsoyiannis, Demetris

2010-05-01

In mixed natural and artificialized river basins, many complexities arise due to anthropogenic interventions in the hydrological cycle, including abstractions from surface water bodies, groundwater pumping or recharge and water returns through drainage systems. Typical engineering approaches adopt a multi-stage modelling procedure, with the aim to handle the complexity of process interactions and the lack of measured abstractions. In such context, the entire hydrosystem is separated into natural and artificial sub-systems or components; the natural ones are modelled individually, and their predictions (i.e. hydrological fluxes) are transferred to the artificial components as inputs to a water management scheme. To account for the interactions between the various components, an iterative procedure is essential, whereby the outputs of the artificial sub-systems (i.e. abstractions) become inputs to the natural ones. However, this strategy suffers from multiple shortcomings, since it presupposes that pure natural sub-systems can be located and that sufficient information is available for each sub-system modelled, including suitable, i.e. "unmodified", data for calibrating the hydrological component. In addition, implementing such strategy is ineffective when the entire scheme runs in stochastic simulation mode. To cope with the above drawbacks, we developed a generalized modelling framework, following a network optimization approach. This originates from the graph theory, which has been successfully implemented within some advanced computer packages for water resource systems analysis. The user formulates a unified system which is comprised of the hydrographical network and the typical components of a water management network (aqueducts, pumps, junctions, demand nodes etc.). Input data for the later include hydraulic properties, constraints, targets, priorities and operation costs. The real-world system is described through a conceptual graph, whose dummy properties are the conveyance capacity and the unit cost of each link. Unit costs are either real or artificial, and positive or negative. Positive costs are set to prohibit undesirable fluxes and negative ones to force fulfilling water demands for various uses. The assignment of costs is based on a recursive algorithm that implements the physical constraints and the user-specified hierarchy for the water uses. Referring to the desired management policy, an optimal allocation is achieved regarding the unknown fluxes within the hydrosystem (flows, abstractions, water losses) by minimizing the total transportation cost through the graph. The mathematical structure of the problem enables use of accurate and exceptionally fast solvers. The proposed methodology is effective, efficient and easy to implement, in order to link on-line multiple modelling components, thus ensuring a comprehensive overview of the process interactions in complex and heavily modified hydrosystems. It is applicable to hydrological simulators of the semi-distributed type, in which it allows integrating groundwater models and flood routing schemes within decision support modules. The methodology is implemented within the HYGROGEIOS computer package, which is illustrated by example applications in modified river basins in Greece.

Dynamics of translational friction in needle-tissue interaction during needle insertion.

PubMed

Asadian, Ali; Patel, Rajni V; Kermani, Mehrdad R

2014-01-01

In this study, a distributed approach to account for dynamic friction during needle insertion in soft tissue is presented. As is well known, friction is a complex nonlinear phenomenon. It appears that classical or static models are unable to capture some of the observations made in systems subjected to significant frictional effects. In needle insertion, translational friction would be a matter of importance when the needle is very flexible, or a stop-and-rotate motion profile at low insertion velocities is implemented, and thus, the system is repeatedly transitioned from a pre-sliding to a sliding mode and vice versa. In order to characterize friction components, a distributed version of the LuGre model in the state-space representation is adopted. This method also facilitates estimating cutting force in an intra-operative manner. To evaluate the performance of the proposed family of friction models, experiments were conducted on homogeneous artificial phantoms and animal tissue. The results illustrate that our approach enables us to represent the main features of friction which is a major force component in needle-tissue interaction during needle-based interventions.

A Model for Generation of Martian Surface Dust, Soil and Rock Coatings: Physical vs. Chemical Interactions, and Palagonitic Plus Hydrothermal Alteration

NASA Technical Reports Server (NTRS)

Bishop, J. L.; Murchie, S.; Pieters, C.; Zent, A.

1999-01-01

This model is one of many possible scenarios to explain the generation of the current surface material on Mars using chemical, magnetic and spectroscopic data from Mars and geologic analogs from terrestrial sites. One basic premise is that there are physical and chemical interactions of the atmospheric dust particles and that these two processes create distinctly different results. Physical processes distribute dust particles on rocks, forming physical rock coatings, and on the surface between rocks forming soil units; these are reversible processes. Chemical reactions of the dust/soil particles create alteration rinds on rock surfaces or duricrust surface units, both of which are relatively permanent materials. According to this model the mineral components of the dust/soil particles are derived from a combination of "typical" palagonitic weathering of volcanic ash and hydrothermally altered components, primarily from steam vents or fumeroles. Both of these altered materials are composed of tiny particles, about 1 micron or smaller, that are aggregates of silicates and iron oxide/oxyhydroxide/sulfate phases. Additional information is contained in the original extended abstract.

Towards a Best Practice Approach in PBPK Modeling: Case Example of Developing a Unified Efavirenz Model Accounting for Induction of CYPs 3A4 and 2B6

PubMed Central

Ke, A; Barter, Z; Rowland‐Yeo, K

2016-01-01

In this study, we present efavirenz physiologically based pharmacokinetic (PBPK) model development as an example of our best practice approach that uses a stepwise approach to verify the different components of the model. First, a PBPK model for efavirenz incorporating in vitro and clinical pharmacokinetic (PK) data was developed to predict exposure following multiple dosing (600 mg q.d.). Alfentanil i.v. and p.o. drug‐drug interaction (DDI) studies were utilized to evaluate and refine the CYP3A4 induction component in the liver and gut. Next, independent DDI studies with substrates of CYP3A4 (maraviroc, atazanavir, and clarithromycin) and CYP2B6 (bupropion) verified the induction components of the model (area under the curve [AUC] ratios within 1.0–1.7‐fold of observed). Finally, the model was refined to incorporate the fractional contribution of enzymes, including CYP2B6, propagating autoinduction into the model (Racc 1.7 vs. 1.7 observed). This validated mechanistic model can now be applied in clinical pharmacology studies to prospectively assess both the victim and perpetrator DDI potential of efavirenz. PMID:27435752

Object-oriented approach for gas turbine engine simulation

NASA Technical Reports Server (NTRS)

Curlett, Brian P.; Felder, James L.

1995-01-01

An object-oriented gas turbine engine simulation program was developed. This program is a prototype for a more complete, commercial grade engine performance program now being proposed as part of the Numerical Propulsion System Simulator (NPSS). This report discusses architectural issues of this complex software system and the lessons learned from developing the prototype code. The prototype code is a fully functional, general purpose engine simulation program, however, only the component models necessary to model a transient compressor test rig have been written. The production system will be capable of steady state and transient modeling of almost any turbine engine configuration. Chief among the architectural considerations for this code was the framework in which the various software modules will interact. These modules include the equation solver, simulation code, data model, event handler, and user interface. Also documented in this report is the component based design of the simulation module and the inter-component communication paradigm. Object class hierarchies for some of the code modules are given.

An interactive environment for the analysis of large Earth observation and model data sets

NASA Technical Reports Server (NTRS)

Bowman, Kenneth P.; Walsh, John E.; Wilhelmson, Robert B.

1993-01-01

We propose to develop an interactive environment for the analysis of large Earth science observation and model data sets. We will use a standard scientific data storage format and a large capacity (greater than 20 GB) optical disk system for data management; develop libraries for coordinate transformation and regridding of data sets; modify the NCSA X Image and X DataSlice software for typical Earth observation data sets by including map transformations and missing data handling; develop analysis tools for common mathematical and statistical operations; integrate the components described above into a system for the analysis and comparison of observations and model results; and distribute software and documentation to the scientific community.

An interactive environment for the analysis of large Earth observation and model data sets

NASA Technical Reports Server (NTRS)

Bowman, Kenneth P.; Walsh, John E.; Wilhelmson, Robert B.

1992-01-01

We propose to develop an interactive environment for the analysis of large Earth science observation and model data sets. We will use a standard scientific data storage format and a large capacity (greater than 20 GB) optical disk system for data management; develop libraries for coordinate transformation and regridding of data sets; modify the NCSA X Image and X Data Slice software for typical Earth observation data sets by including map transformations and missing data handling; develop analysis tools for common mathematical and statistical operations; integrate the components described above into a system for the analysis and comparison of observations and model results; and distribute software and documentation to the scientific community.

Psychological Empowerment Among Urban Youth: Measurement Model and Associations with Youth Outcomes.

PubMed

Eisman, Andria B; Zimmerman, Marc A; Kruger, Daniel; Reischl, Thomas M; Miller, Alison L; Franzen, Susan P; Morrel-Samuels, Susan

2016-12-01

Empowerment-based strategies have become widely used method to address health inequities and promote social change. Few researchers, however, have tested theoretical models of empowerment, including multidimensional, higher-order models. We test empirically a multidimensional, higher-order model of psychological empowerment (PE), guided by Zimmerman's conceptual framework including three components of PE: intrapersonal, interactional, and behavioral. We also investigate if PE is associated with positive and negative outcomes among youth. The sample included 367 middle school youth aged 11-16 (M = 12.71; SD = 0.91); 60% female, 32% (n = 117) white youth, 46% (n = 170) African-American youth, and 22% (n = 80) identifying as mixed race, Asian-American, Latino, Native American, or other ethnic/racial group; schools reported 61-75% free/reduced lunch students. Our results indicated that each of the latent factors for the three PE components demonstrate a good fit with the data. Our results also indicated that these components loaded on to a higher-order PE factor (X 2  = 32.68; df: 22; p = .07; RMSEA: 0.04; 95% CI: .00, .06; CFI: 0.99). We found that the second-order PE factor was negatively associated with aggressive behavior and positively associated with prosocial engagement. Our results suggest that empowerment-focused programs would benefit from incorporating components addressing how youth think about themselves in relation to their social contexts (intrapersonal), understanding social and material resources needed to achieve specific goals (interactional), and actions taken to influence outcomes (behavioral). Our results also suggest that integrating the three components and promoting PE may help increase likelihood of positive behaviors (e.g., prosocial involvement); we did not find an association between PE and aggressive behavior. Implications and future directions for empowerment research are discussed. © Society for Community Research and Action 2016.

The AgroEcoSystem (AgES) response-function model simulates layered soil water dynamics in semi-arid Colorado: sensitivity and calibration

USDA-ARS?s Scientific Manuscript database

Simulation of vertical soil hydrology is a critical component of simulating even more complex soil water dynamics in space and time, including land-atmosphere and subsurface interactions. The AgroEcoSystem (AgES) model is defined here as a single land unit implementation of the full AgES-W (Watershe...

The Enhancement of Mathematical Critical Thinking Ability of Aliyah Madrasas Student Model Using Gorontalo by Interactive Learning Setting Cooperative Model

ERIC Educational Resources Information Center

Husnaeni

2016-01-01

Critical thinking ability of students' mathematical is a component that must be mastered by the student. Learn to think critically means using mental processes, such as attention, categorize, selection, and rate/decide. Critical thinking ability in giving proper guidance in thinking and working, and assist in determining the relationship between…

Diffusiophoretic self-propulsion for partially catalytic spherical colloids.

PubMed

de Graaf, Joost; Rempfer, Georg; Holm, Christian

2015-04-01

Colloidal spheres with a partial platinum surface coating perform autophoretic motion when suspended in hydrogen peroxide solution. We present a theoretical analysis of the self-propulsion velocity of these particles using a continuum multi-component, self-diffusiophoretic model. With this model as a basis, we show how the slip-layer approximation can be derived and in which limits it holds. First, we consider the differences between the full multi-component model and the slip-layer approximation. Then the slip model is used to demonstrate and explore the sensitive nature of the particle's velocity on the details of the molecule-surface interaction. We find a strong asymmetry in the dependence of the colloid's velocity as a function of the level of catalytic coating, when there is a different interaction between the solute and solvent molecules and the inert and catalytic part of the colloid, respectively. The direction of motion can even be reversed by varying the level of the catalytic coating. Finally, we investigate the robustness of these results with respect to variations in the reaction rate near the edge between the catalytic and inert parts of the particle. Our results are of significant interest to the interpretation of experimental results on the motion of self-propelled particles.

Discrete Element Framework for Modelling Extracellular Matrix, Deformable Cells and Subcellular Components

PubMed Central

Gardiner, Bruce S.; Wong, Kelvin K. L.; Joldes, Grand R.; Rich, Addison J.; Tan, Chin Wee; Burgess, Antony W.; Smith, David W.

2015-01-01

This paper presents a framework for modelling biological tissues based on discrete particles. Cell components (e.g. cell membranes, cell cytoskeleton, cell nucleus) and extracellular matrix (e.g. collagen) are represented using collections of particles. Simple particle to particle interaction laws are used to simulate and control complex physical interaction types (e.g. cell-cell adhesion via cadherins, integrin basement membrane attachment, cytoskeletal mechanical properties). Particles may be given the capacity to change their properties and behaviours in response to changes in the cellular microenvironment (e.g., in response to cell-cell signalling or mechanical loadings). Each particle is in effect an ‘agent’, meaning that the agent can sense local environmental information and respond according to pre-determined or stochastic events. The behaviour of the proposed framework is exemplified through several biological problems of ongoing interest. These examples illustrate how the modelling framework allows enormous flexibility for representing the mechanical behaviour of different tissues, and we argue this is a more intuitive approach than perhaps offered by traditional continuum methods. Because of this flexibility, we believe the discrete modelling framework provides an avenue for biologists and bioengineers to explore the behaviour of tissue systems in a computational laboratory. PMID:26452000

Discrete Element Framework for Modelling Extracellular Matrix, Deformable Cells and Subcellular Components.

PubMed

Gardiner, Bruce S; Wong, Kelvin K L; Joldes, Grand R; Rich, Addison J; Tan, Chin Wee; Burgess, Antony W; Smith, David W

2015-10-01

This paper presents a framework for modelling biological tissues based on discrete particles. Cell components (e.g. cell membranes, cell cytoskeleton, cell nucleus) and extracellular matrix (e.g. collagen) are represented using collections of particles. Simple particle to particle interaction laws are used to simulate and control complex physical interaction types (e.g. cell-cell adhesion via cadherins, integrin basement membrane attachment, cytoskeletal mechanical properties). Particles may be given the capacity to change their properties and behaviours in response to changes in the cellular microenvironment (e.g., in response to cell-cell signalling or mechanical loadings). Each particle is in effect an 'agent', meaning that the agent can sense local environmental information and respond according to pre-determined or stochastic events. The behaviour of the proposed framework is exemplified through several biological problems of ongoing interest. These examples illustrate how the modelling framework allows enormous flexibility for representing the mechanical behaviour of different tissues, and we argue this is a more intuitive approach than perhaps offered by traditional continuum methods. Because of this flexibility, we believe the discrete modelling framework provides an avenue for biologists and bioengineers to explore the behaviour of tissue systems in a computational laboratory.

Automatic determination of fault effects on aircraft functionality

NASA Technical Reports Server (NTRS)

Feyock, Stefan

1989-01-01

The problem of determining the behavior of physical systems subsequent to the occurrence of malfunctions is discussed. It is established that while it was reasonable to assume that the most important fault behavior modes of primitive components and simple subsystems could be known and predicted, interactions within composite systems reached levels of complexity that precluded the use of traditional rule-based expert system techniques. Reasoning from first principles, i.e., on the basis of causal models of the physical system, was required. The first question that arises is, of course, how the causal information required for such reasoning should be represented. The bond graphs presented here occupy a position intermediate between qualitative and quantitative models, allowing the automatic derivation of Kuipers-like qualitative constraint models as well as state equations. Their most salient feature, however, is that entities corresponding to components and interactions in the physical system are explicitly represented in the bond graph model, thus permitting systematic model updates to reflect malfunctions. Researchers show how this is done, as well as presenting a number of techniques for obtaining qualitative information from the state equations derivable from bond graph models. One insight is the fact that one of the most important advantages of the bond graph ontology is the highly systematic approach to model construction it imposes on the modeler, who is forced to classify the relevant physical entities into a small number of categories, and to look for two highly specific types of interactions among them. The systematic nature of bond graph model construction facilitates the process to the point where the guidelines are sufficiently specific to be followed by modelers who are not domain experts. As a result, models of a given system constructed by different modelers will have extensive similarities. Researchers conclude by pointing out that the ease of updating bond graph models to reflect malfunctions is a manifestation of the systematic nature of bond graph construction, and the regularity of the relationship between bond graph models and physical reality.

Paleozoic fluid history of the Michigan Basin: Evidence from dolomite geochemistry in the Middle Ordovician St. Peter Sandstone

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

Winter, B.L.; Johnson, C.M.; Simo, J.A.

1995-04-03

The isotope (Sr and O) and elemental (Mg, Ca, Mn, Fe, and Sr) compositions of the various dolomites in the Middle Ordovician St. Peter Sandstone in the Michigan Basin are determined and the variations are modeled in terms of fluid-rock interaction or as mixing relations. These geochemical models, combined with the paragenetic sequence of the dolomites and late anhydrite cement, suggest the existence of at least four distinct diagenetic fluids in the St. Peter Sandstone during the paleozoic. Fluid 1 has a composition consistent with a modified older (pre-Middle Ordovician) seawater origin, which indicates that the flow path for thismore » fluid had a major upward component. This fluid resulted in the first and volumetrically most important burial dolomitization event, producing dolomite in both carbonate and quartz sandstone lithofacies in the St. Peter Sandstone. Fluid 2 has a composition consistent with a modified Middle to early Late Ordovician seawater origin, suggesting a major downward component for fluid flow. Fluid 2 produced dolomite cement in the carbonate lithofacies that postdates Fluid 1 dolomite. The composition of Fluid 3 is best interpreted to reflect a heated, deep basinal brine that had previously interacted with the K-feldspar-rich rocks near the Cambrian-Precambrian unconformity in the Michigan Basin, indicating a major upward component for fluid flow. Fluid 3 produced dolomite cement in quartz sandstone lithofacies that postdates Fluid 1 dolomite. Fluid 4 resulted in precipitation of late anhydrite in fractures. The {sup 87}Sr/{sup 86}Sr ratio of the anhydrite is consistent with Fluid 4 originating as a dilute fluid that interacted extensively with Silurian gypsum in the Michigan Basin; this indicates that the flow path of Fluid 4 had a major downward component.« less

Risk assessment of flange climb derailment of a rail vehicle

NASA Astrophysics Data System (ADS)

Vlakhova, A. V.

2015-01-01

We study the wheel flange climb onto the railhead, which is one of the most dangerous regimes of motion and can lead to derailment. The tangential components of the wheel-rail interaction forces are described by the creep model with small slips taken into account. We pass to the limit of infinite rigidity of the interacting bodies (zero slip velocities). It is shown that, in the actual service conditions of rail vehicle motion, neglecting the wheel-rail slip is not justified; namely, the limit model is determined by the primary Dirac constraints, i.e., finite relations between coordinates and momenta arising owing to the system Lagrangian degeneration. The obtained nonclassical model allows one to study the efficiency of some railway motion safety criteria and analytically estimate derailment conditions, which depend on the flange shape, the track curvature radius, the height of the vehicle center of mass, the wheel-rail interaction forces, the coefficients of friction of the interacting surfaces, and the external perturbation forces and moments.

A MODEL FOR DIFFUSION CONTROLLED BIOAVAILABILITY OF CRUDE OIL COMPONENTS

EPA Science Inventory

Crude oil is a complex mixture of several different structural classes of compounds including alkanes, aromatics, heterocyclic polar compounds, and asphaltenes. The rate and extent of microbial degradation of crude oil depends on the interaction between the physical and biochemi...

The Changing Climate.

ERIC Educational Resources Information Center

Schneider, Stephen H.

1989-01-01

Discusses the global change of climate. Presents the trend of climate change with graphs. Describes mathematical climate models including expressions for the interacting components of the ocean-atmosphere system and equations representing the basic physical laws governing their behavior. Provides three possible responses on the change. (YP)

Mechanical impedance and acoustic mobility measurement techniques of specifying vibration environments

NASA Technical Reports Server (NTRS)

Kao, G. C.

1973-01-01

Method has been developed for predicting interaction between components and corresponding support structures subjected to acoustic excitations. Force environments determined in spectral form are called force spectra. Force-spectra equation is determined based on one-dimensional structural impedance model.

Generalized entropy formalism and a new holographic dark energy model

NASA Astrophysics Data System (ADS)

Sayahian Jahromi, A.; Moosavi, S. A.; Moradpour, H.; Morais Graça, J. P.; Lobo, I. P.; Salako, I. G.; Jawad, A.

2018-05-01

Recently, the Rényi and Tsallis generalized entropies have extensively been used in order to study various cosmological and gravitational setups. Here, using a special type of generalized entropy, a generalization of both the Rényi and Tsallis entropy, together with holographic principle, we build a new model for holographic dark energy. Thereinafter, considering a flat FRW universe, filled by a pressureless component and the new obtained dark energy model, the evolution of cosmos has been investigated showing satisfactory results and behavior. In our model, the Hubble horizon plays the role of IR cutoff, and there is no mutual interaction between the cosmos components. Our results indicate that the generalized entropy formalism may open a new window to become more familiar with the nature of spacetime and its properties.

[Market-based medicine or patient-based medicine?].

PubMed

Justich, Pablo R

2015-04-01

The health care has evolved over the centuries from a theocentric model to a model centered on man, environment and society. The process of neoliberal globalization has changed the relationship between the components of the health system and population. The active participation of organizations such as the World Trade Organization, the International Monetary Fund and the World Bank by the techno-medical industrial complex tends to make the health care in a model focused on economy. This, impacts negatively on all components in the process of health care and have an adverse effect on the humanized care. The analysis of each sector in particular and their interactions shows the effects of this change. Alternatives are proposed for each sector to contribute to a model of care focused on the patient, their family and the social environment.

Reliable prediction of three-body intermolecular interactions using dispersion-corrected second-order Møller-Plesset perturbation theory

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

Huang, Yuanhang; Beran, Gregory J. O., E-mail: gregory.beran@ucr.edu

2015-07-28

Three-body and higher intermolecular interactions can play an important role in molecular condensed phases. Recent benchmark calculations found problematic behavior for many widely used density functional approximations in treating 3-body intermolecular interactions. Here, we demonstrate that the combination of second-order Møller-Plesset (MP2) perturbation theory plus short-range damped Axilrod-Teller-Muto (ATM) dispersion accurately describes 3-body interactions with reasonable computational cost. The empirical damping function used in the ATM dispersion term compensates both for the absence of higher-order dispersion contributions beyond the triple-dipole ATM term and non-additive short-range exchange terms which arise in third-order perturbation theory and beyond. Empirical damping enables this simplemore » model to out-perform a non-expanded coupled Kohn-Sham dispersion correction for 3-body intermolecular dispersion. The MP2 plus ATM dispersion model approaches the accuracy of O(N{sup 6}) methods like MP2.5 or even spin-component-scaled coupled cluster models for 3-body intermolecular interactions with only O(N{sup 5}) computational cost.« less

Orphan receptor GPR179 forms macromolecular complexes with components of metabotropic signaling cascade in retina ON-bipolar neurons.

PubMed

Orlandi, Cesare; Cao, Yan; Martemyanov, Kirill A

2013-10-29

In the mammalian retina, synaptic transmission between light-excited rod photoreceptors and downstream ON-bipolar neurons is indispensable for dim vision, and disruption of this process leads to congenital stationary night blindness in human patients. The ON-bipolar neurons use the metabotropic signaling cascade, initiated by the mGluR6 receptor, to generate depolarizing responses to light-induced changes in neurotransmitter glutamate release from the photoreceptor axonal terminals. Evidence for the identity of the components involved in transducing these signals is growing rapidly. Recently, the orphan receptor, GPR179, a member of the G protein-coupled receptor (GPCR) superfamily, has been shown to be indispensable for the synaptic responses of ON-bipolar cells. In our study, we investigated the interaction of GPR179 with principle components of the signal transduction cascade. We used immunoprecipitation and proximity ligation assays in transfected cells and native retinas to characterize the protein-protein interactions involving GPR179. The influence of cascade components on GPR179 localization was examined through immunohistochemical staining of the retinas from genetic mouse models. We demonstrated that, in mouse retinas, GPR179 forms physical complexes with the main components of the metabotropic cascade, recruiting mGluR6, TRPM1, and the RGS proteins. Elimination of mGluR6 or RGS proteins, but not TRPM1, detrimentally affects postsynaptic targeting or GPR179 expression. These observations suggest that the mGluR6 signaling cascade is scaffolded as a macromolecular complex in which the interactions between the components ensure the optimal spatiotemporal characteristics of signal transduction.

A review on vegetation models and applicability to climate simulations at regional scale

NASA Astrophysics Data System (ADS)

Myoung, Boksoon; Choi, Yong-Sang; Park, Seon Ki

2011-11-01

The lack of accurate representations of biospheric components and their biophysical and biogeochemical processes is a great source of uncertainty in current climate models. The interactions between terrestrial ecosystems and the climate include exchanges not only of energy, water and momentum, but also of carbon and nitrogen. Reliable simulations of these interactions are crucial for predicting the potential impacts of future climate change and anthropogenic intervention on terrestrial ecosystems. In this paper, two biogeographical (Neilson's rule-based model and BIOME), two biogeochemical (BIOME-BGC and PnET-BGC), and three dynamic global vegetation models (Hybrid, LPJ, and MC1) were reviewed and compared in terms of their biophysical and physiological processes. The advantages and limitations of the models were also addressed. Lastly, the applications of the dynamic global vegetation models to regional climate simulations have been discussed.

Knowing and acting in the clinical workplace: trainees' perspectives on modelling and feedback.

PubMed

Stegeman, J H; Schoten, E J; Terpstra, O T

2013-10-01

In this article we discuss clinical workplace learning using a dual approach: a theoretical one and an empirical one. Drawing on the philosophical work of Aristotle, Polanyi and Schön we posit that the 'knowing and acting' underpinning day-to-day medical practice is personal and embraces by nature a tacit dimension. Consequently, imparting and acquiring this knowledge type necessitates personal interaction between trainer and trainee. The tacit dimension particularly influences modelling and feedback. In our empirical exploration we explore these educational routes in two disparate disciplines: surgery and paediatrics. We use a longitudinal design with in-depth interviewing. Our conclusion on modelling is: modelling is a dynamic and fragmented process reflecting discipline bound characteristics and working styles. On feedback it is: 'feedback' serves as vehicle for three distinctive forms of commenting on performance, each holding a specific power of expression for learning. We propose to view clinical workplace learning as: an interactive master-apprenticeship model encompassing modelling and feedback as natural educational routes. We conceptualise modelling and feedback as 'function' of interaction (developing grounded theory). Modelling function and feedback function may serve to study these routes as didactical components of ongoing interaction between trainer and trainee rather than an educator-driven series of unrelated events.

Probing eukaryotic cell mechanics via mesoscopic simulations

PubMed Central

Shang, Menglin; Lim, Chwee Teck

2017-01-01

Cell mechanics has proven to be important in many biological processes. Although there is a number of experimental techniques which allow us to study mechanical properties of cell, there is still a lack of understanding of the role each sub-cellular component plays during cell deformations. We present a new mesoscopic particle-based eukaryotic cell model which explicitly describes cell membrane, nucleus and cytoskeleton. We employ Dissipative Particle Dynamics (DPD) method that provides us with the unified framework for modeling of a cell and its interactions in the flow. Data from micropipette aspiration experiments were used to define model parameters. The model was validated using data from microfluidic experiments. The validated model was then applied to study the impact of the sub-cellular components on the cell viscoelastic response in micropipette aspiration and microfluidic experiments. PMID:28922399

A computational framework for modeling targets as complex adaptive systems

NASA Astrophysics Data System (ADS)

Santos, Eugene; Santos, Eunice E.; Korah, John; Murugappan, Vairavan; Subramanian, Suresh

2017-05-01

Modeling large military targets is a challenge as they can be complex systems encompassing myriad combinations of human, technological, and social elements that interact, leading to complex behaviors. Moreover, such targets have multiple components and structures, extending across multiple spatial and temporal scales, and are in a state of change, either in response to events in the environment or changes within the system. Complex adaptive system (CAS) theory can help in capturing the dynamism, interactions, and more importantly various emergent behaviors, displayed by the targets. However, a key stumbling block is incorporating information from various intelligence, surveillance and reconnaissance (ISR) sources, while dealing with the inherent uncertainty, incompleteness and time criticality of real world information. To overcome these challenges, we present a probabilistic reasoning network based framework called complex adaptive Bayesian Knowledge Base (caBKB). caBKB is a rigorous, overarching and axiomatic framework that models two key processes, namely information aggregation and information composition. While information aggregation deals with the union, merger and concatenation of information and takes into account issues such as source reliability and information inconsistencies, information composition focuses on combining information components where such components may have well defined operations. Since caBKBs can explicitly model the relationships between information pieces at various scales, it provides unique capabilities such as the ability to de-aggregate and de-compose information for detailed analysis. Using a scenario from the Network Centric Operations (NCO) domain, we will describe how our framework can be used for modeling targets with a focus on methodologies for quantifying NCO performance metrics.

The extracellular phage-host interactions involved in the bacteriophage LL-H infection of Lactobacillus delbrueckii ssp. lactis ATCC 15808

PubMed Central

Munsch-Alatossava, Patricia; Alatossava, Tapani

2013-01-01

The complete genome sequence of Lactobacillus bacteriophage LL-H was determined in 1996. Accordingly, LL-H has been used as a model phage for the infection of dairy Lactobacillus, specifically for thermophilic Lactobacillus delbrueckii ssp. lactis host strains, such as ATCC 15808. One of the major goals of phage LL-H research consisted of the characterization of the first phage-host interactions at the level of phage adsorption and phage DNA injection steps to determine effective and practical methods to minimize the risks associated with the appearance and attack of phages in the manufacture of yogurt, and Swiss or Italian hard type cheeses, which typically use thermophilic lactic acid bacteria starter cultures containing L. delbrueckii strains among others. This mini review article summarizes the present data concerning (i) the special features, particle structure, and components of phage LL-H and (ii) the structure and properties of lipoteichoic acids (LTAs), which are the phage LL-H receptor components of L. delbrueckii ssp. lactis host strains. Moreover, a model of the first, extracellular, phage-host interactions for the infection of L. delbrueckii ssp. lactis ATCC 15808 by phage LL-H is presented and further discussed. PMID:24400001

Positional cloning in mice and its use for molecular dissection of inflammatory arthritis.

PubMed

Abe, Koichiro; Yu, Philipp

2009-02-01

One of the upcoming next quests in the field of genetics might be molecular dissection of the genetic and environmental components of human complex diseases. In humans, however, there are certain experimental limitations for identification of a single component of the complex interactions by genetic analyses. Experimental animals offer simplified models for genetic and environmental interactions in human complex diseases. In particular, mice are the best mammalian models because of a long history and ample experience for genetic analyses. Forward genetics, which includes genetic screen and subsequent positional cloning of the causative genes, is a powerful strategy to dissect a complex phenomenon without preliminarily molecular knowledge of the process. In this review, first, we describe a general scheme of positional cloning in mice. Next, recent accomplishments on the patho-mechanisms of inflammatory arthritis by forward genetics approaches are introduced; Positional cloning effort for skg, Ali5, Ali18, cmo, and lupo mutants are provided as examples for the application to human complex diseases. As seen in the examples, the identification of genetic factors by positional cloning in the mouse have potential in solving molecular complexity of gene-environment interactions in human complex diseases.

The extracellular phage-host interactions involved in the bacteriophage LL-H infection of Lactobacillus delbrueckii ssp. lactis ATCC 15808.

PubMed

Munsch-Alatossava, Patricia; Alatossava, Tapani

2013-12-24

The complete genome sequence of Lactobacillus bacteriophage LL-H was determined in 1996. Accordingly, LL-H has been used as a model phage for the infection of dairy Lactobacillus, specifically for thermophilic Lactobacillus delbrueckii ssp. lactis host strains, such as ATCC 15808. One of the major goals of phage LL-H research consisted of the characterization of the first phage-host interactions at the level of phage adsorption and phage DNA injection steps to determine effective and practical methods to minimize the risks associated with the appearance and attack of phages in the manufacture of yogurt, and Swiss or Italian hard type cheeses, which typically use thermophilic lactic acid bacteria starter cultures containing L. delbrueckii strains among others. This mini review article summarizes the present data concerning (i) the special features, particle structure, and components of phage LL-H and (ii) the structure and properties of lipoteichoic acids (LTAs), which are the phage LL-H receptor components of L. delbrueckii ssp. lactis host strains. Moreover, a model of the first, extracellular, phage-host interactions for the infection of L. delbrueckii ssp. lactis ATCC 15808 by phage LL-H is presented and further discussed.

Constraining the interaction between dark sectors with future HI intensity mapping observations

NASA Astrophysics Data System (ADS)

Xu, Xiaodong; Ma, Yin-Zhe; Weltman, Amanda

2018-04-01

We study a model of interacting dark matter and dark energy, in which the two components are coupled. We calculate the predictions for the 21-cm intensity mapping power spectra, and forecast the detectability with future single-dish intensity mapping surveys (BINGO, FAST and SKA-I). Since dark energy is turned on at z ˜1 , which falls into the sensitivity range of these radio surveys, the HI intensity mapping technique is an efficient tool to constrain the interaction. By comparing with current constraints on dark sector interactions, we find that future radio surveys will produce tight and reliable constraints on the coupling parameters.

Learning of embodied interaction dynamics with recurrent neural networks: some exploratory experiments.

PubMed

Oubbati, Mohamed; Kord, Bahram; Koprinkova-Hristova, Petia; Palm, Günther

2014-04-01

The new tendency of artificial intelligence suggests that intelligence must be seen as a result of the interaction between brains, bodies and environments. This view implies that designing sophisticated behaviour requires a primary focus on how agents are functionally coupled to their environments. Under this perspective, we present early results with the application of reservoir computing as an efficient tool to understand how behaviour emerges from interaction. Specifically, we present reservoir computing models, that are inspired by imitation learning designs, to extract the essential components of behaviour that results from agent-environment interaction dynamics. Experimental results using a mobile robot are reported to validate the learning architectures.

Learning of embodied interaction dynamics with recurrent neural networks: some exploratory experiments

NASA Astrophysics Data System (ADS)

Oubbati, Mohamed; Kord, Bahram; Koprinkova-Hristova, Petia; Palm, Günther

2014-04-01

The new tendency of artificial intelligence suggests that intelligence must be seen as a result of the interaction between brains, bodies and environments. This view implies that designing sophisticated behaviour requires a primary focus on how agents are functionally coupled to their environments. Under this perspective, we present early results with the application of reservoir computing as an efficient tool to understand how behaviour emerges from interaction. Specifically, we present reservoir computing models, that are inspired by imitation learning designs, to extract the essential components of behaviour that results from agent-environment interaction dynamics. Experimental results using a mobile robot are reported to validate the learning architectures.

The Poisson-Helmholtz-Boltzmann model.

PubMed

Bohinc, K; Shrestha, A; May, S

2011-10-01

We present a mean-field model of a one-component electrolyte solution where the mobile ions interact not only via Coulomb interactions but also through a repulsive non-electrostatic Yukawa potential. Our choice of the Yukawa potential represents a simple model for solvent-mediated interactions between ions. We employ a local formulation of the mean-field free energy through the use of two auxiliary potentials, an electrostatic and a non-electrostatic potential. Functional minimization of the mean-field free energy leads to two coupled local differential equations, the Poisson-Boltzmann equation and the Helmholtz-Boltzmann equation. Their boundary conditions account for the sources of both the electrostatic and non-electrostatic interactions on the surface of all macroions that reside in the solution. We analyze a specific example, two like-charged planar surfaces with their mobile counterions forming the electrolyte solution. For this system we calculate the pressure between the two surfaces, and we analyze its dependence on the strength of the Yukawa potential and on the non-electrostatic interactions of the mobile ions with the planar macroion surfaces. In addition, we demonstrate that our mean-field model is consistent with the contact theorem, and we outline its generalization to arbitrary interaction potentials through the use of a Laplace transformation. © EDP Sciences / Società Italiana di Fisica / Springer-Verlag 2011

Gender, position of authority, and the risk of depression and post-traumatic stress disorder among a national sample of U.S. Reserve Component Personnel

PubMed Central

Cohen, Gregory H.; Sampson, Laura A.; Fink, David S.; Wang, Jing; Russell, Dale; Gifford, Robert; Fullerton, Carol; Ursano, Robert; Galea, Sandro

2016-01-01

BACKGROUND Recent United States military operations in Iraq and Afghanistan have seen dramatic increases in the proportion of women serving, and the breadth of their occupational roles. General population studies suggest that women, compared to men, and persons with lower, as compared to higher, social position may be at greater risk of post-traumatic stress disorder (PTSD) and depression. However, these relations remain unclear in military populations. Accordingly, we aimed to estimate the effects of (1) gender, (2) military authority (i.e., rank) and (3) the interaction of gender and military authority upon: (a) risk of most-recent-deployment-related PTSD, and (b) risk of depression since most-recent-deployment. METHODS Using a nationally representative sample of 1024 previously deployed Reserve Component personnel surveyed in 2010, we constructed multivariable logistic regression models to estimate effects of interest. RESULTS Weighted multivariable logistic regression models demonstrated no statistically significant associations between gender or authority, and either PTSD or depression. Interaction models demonstrated multiplicative statistical interaction between gender and authority for PTSD (beta= −2.37;p=0.01), and depression (beta=-1.21; p=0.057). Predicted probabilities of PTSD and depression, respectively, were lowest in male officers (0.06, 0.09), followed by male enlisted (0.07, 0.14), female enlisted (0.07, 0.15), and female officers (0.30, 0.25). CONCLUSIONS Female officers in the Reserve Component may be at greatest risk for PTSD and depression following deployment, relative to their male and enlisted counterparts, and this relation is not explained by deployment trauma exposure. Future studies may fruitfully examine whether social support, family responsibilities peri-deployment, or contradictory class status may explain these findings. PMID:26899583

Simplifying and upscaling water resources systems models that combine natural and engineered components

NASA Astrophysics Data System (ADS)

McIntyre, N.; Keir, G.

2014-12-01

Water supply systems typically encompass components of both natural systems (e.g. catchment runoff, aquifer interception) and engineered systems (e.g. process equipment, water storages and transfers). Many physical processes of varying spatial and temporal scales are contained within these hybrid systems models. The need to aggregate and simplify system components has been recognised for reasons of parsimony and comprehensibility; and the use of probabilistic methods for modelling water-related risks also prompts the need to seek computationally efficient up-scaled conceptualisations. How to manage the up-scaling errors in such hybrid systems models has not been well-explored, compared to research in the hydrological process domain. Particular challenges include the non-linearity introduced by decision thresholds and non-linear relations between water use, water quality, and discharge strategies. Using a case study of a mining region, we explore the nature of up-scaling errors in water use, water quality and discharge, and we illustrate an approach to identification of a scale-adjusted model including an error model. Ways forward for efficient modelling of such complex, hybrid systems are discussed, including interactions with human, energy and carbon systems models.