Science.gov

Sample records for models functional

  1. Functional Generalized Additive Models.

    PubMed

    McLean, Mathew W; Hooker, Giles; Staicu, Ana-Maria; Scheipl, Fabian; Ruppert, David

    2014-01-01

    We introduce the functional generalized additive model (FGAM), a novel regression model for association studies between a scalar response and a functional predictor. We model the link-transformed mean response as the integral with respect to t of F{X(t), t} where F(·,·) is an unknown regression function and X(t) is a functional covariate. Rather than having an additive model in a finite number of principal components as in Müller and Yao (2008), our model incorporates the functional predictor directly and thus our model can be viewed as the natural functional extension of generalized additive models. We estimate F(·,·) using tensor-product B-splines with roughness penalties. A pointwise quantile transformation of the functional predictor is also considered to ensure each tensor-product B-spline has observed data on its support. The methods are evaluated using simulated data and their predictive performance is compared with other competing scalar-on-function regression alternatives. We illustrate the usefulness of our approach through an application to brain tractography, where X(t) is a signal from diffusion tensor imaging at position, t, along a tract in the brain. In one example, the response is disease-status (case or control) and in a second example, it is the score on a cognitive test. R code for performing the simulations and fitting the FGAM can be found in supplemental materials available online. PMID:24729671

  2. Modelling of graphene functionalization.

    PubMed

    Pykal, Martin; Jurečka, Petr; Karlický, František; Otyepka, Michal

    2016-03-01

    Graphene has attracted great interest because of its remarkable properties and numerous potential applications. A comprehensive understanding of its structural and dynamic properties and those of its derivatives will be required to enable the design and optimization of sophisticated new nanodevices. While it is challenging to perform experimental studies on nanoscale systems at the atomistic level, this is the 'native' scale of computational chemistry. Consequently, computational methods are increasingly being used to complement experimental research in many areas of chemistry and nanotechnology. However, it is difficult for non-experts to get to grips with the plethora of computational tools that are available and their areas of application. This perspective briefly describes the available theoretical methods and models for simulating graphene functionalization based on quantum and classical mechanics. The benefits and drawbacks of the individual methods are discussed, and we provide numerous examples showing how computational methods have provided new insights into the physical and chemical features of complex systems including graphene and graphene derivatives. We believe that this overview will help non-expert readers to understand this field and its great potential. PMID:26323438

  3. Modeling Protein Domain Function

    ERIC Educational Resources Information Center

    Baker, William P.; Jones, Carleton "Buck"; Hull, Elizabeth

    2007-01-01

    This simple but effective laboratory exercise helps students understand the concept of protein domain function. They use foam beads, Styrofoam craft balls, and pipe cleaners to explore how domains within protein active sites interact to form a functional protein. The activity allows students to gain content mastery and an understanding of the…

  4. Computational Models for Neuromuscular Function

    PubMed Central

    Valero-Cuevas, Francisco J.; Hoffmann, Heiko; Kurse, Manish U.; Kutch, Jason J.; Theodorou, Evangelos A.

    2011-01-01

    Computational models of the neuromuscular system hold the potential to allow us to reach a deeper understanding of neuromuscular function and clinical rehabilitation by complementing experimentation. By serving as a means to distill and explore specific hypotheses, computational models emerge from prior experimental data and motivate future experimental work. Here we review computational tools used to understand neuromuscular function including musculoskeletal modeling, machine learning, control theory, and statistical model analysis. We conclude that these tools, when used in combination, have the potential to further our understanding of neuromuscular function by serving as a rigorous means to test scientific hypotheses in ways that complement and leverage experimental data. PMID:21687779

  5. Model-based Utility Functions

    NASA Astrophysics Data System (ADS)

    Hibbard, Bill

    2012-05-01

    Orseau and Ring, as well as Dewey, have recently described problems, including self-delusion, with the behavior of agents using various definitions of utility functions. An agent's utility function is defined in terms of the agent's history of interactions with its environment. This paper argues, via two examples, that the behavior problems can be avoided by formulating the utility function in two steps: 1) inferring a model of the environment from interactions, and 2) computing utility as a function of the environment model. Basing a utility function on a model that the agent must learn implies that the utility function must initially be expressed in terms of specifications to be matched to structures in the learned model. These specifications constitute prior assumptions about the environment so this approach will not work with arbitrary environments. But the approach should work for agents designed by humans to act in the physical world. The paper also addresses the issue of self-modifying agents and shows that if provided with the possibility to modify their utility functions agents will not choose to do so, under some usual assumptions.

  6. Transfer Function Identification Using Orthogonal Fourier Transform Modeling Functions

    NASA Technical Reports Server (NTRS)

    Morelli, Eugene A.

    2013-01-01

    A method for transfer function identification, including both model structure determination and parameter estimation, was developed and demonstrated. The approach uses orthogonal modeling functions generated from frequency domain data obtained by Fourier transformation of time series data. The method was applied to simulation data to identify continuous-time transfer function models and unsteady aerodynamic models. Model fit error, estimated model parameters, and the associated uncertainties were used to show the effectiveness of the method for identifying accurate transfer function models from noisy data.

  7. Function Model for Community Health Service Information

    NASA Astrophysics Data System (ADS)

    Yang, Peng; Pan, Feng; Liu, Danhong; Xu, Yongyong

    In order to construct a function model of community health service (CHS) information for development of CHS information management system, Integration Definition for Function Modeling (IDEF0), an IEEE standard which is extended from Structured Analysis and Design(SADT) and now is a widely used function modeling method, was used to classifying its information from top to bottom. The contents of every level of the model were described and coded. Then function model for CHS information, which includes 4 super-classes, 15 classes and 28 sub-classed of business function, 43 business processes and 168 business activities, was established. This model can facilitate information management system development and workflow refinement.

  8. Robust, Adaptive Functional Regression in Functional Mixed Model Framework

    PubMed Central

    Zhu, Hongxiao; Brown, Philip J.; Morris, Jeffrey S.

    2012-01-01

    Functional data are increasingly encountered in scientific studies, and their high dimensionality and complexity lead to many analytical challenges. Various methods for functional data analysis have been developed, including functional response regression methods that involve regression of a functional response on univariate/multivariate predictors with nonparametrically represented functional coefficients. In existing methods, however, the functional regression can be sensitive to outlying curves and outlying regions of curves, so is not robust. In this paper, we introduce a new Bayesian method, robust functional mixed models (R-FMM), for performing robust functional regression within the general functional mixed model framework, which includes multiple continuous or categorical predictors and random effect functions accommodating potential between-function correlation induced by the experimental design. The underlying model involves a hierarchical scale mixture model for the fixed effects, random effect and residual error functions. These modeling assumptions across curves result in robust nonparametric estimators of the fixed and random effect functions which down-weight outlying curves and regions of curves, and produce statistics that can be used to flag global and local outliers. These assumptions also lead to distributions across wavelet coefficients that have outstanding sparsity and adaptive shrinkage properties, with great flexibility for the data to determine the sparsity and the heaviness of the tails. Together with the down-weighting of outliers, these within-curve properties lead to fixed and random effect function estimates that appear in our simulations to be remarkably adaptive in their ability to remove spurious features yet retain true features of the functions. We have developed general code to implement this fully Bayesian method that is automatic, requiring the user to only provide the functional data and design matrices. It is efficient

  9. Functional Risk Modeling for Lunar Surface Systems

    NASA Technical Reports Server (NTRS)

    Thomson, Fraser; Mathias, Donovan; Go, Susie; Nejad, Hamed

    2010-01-01

    We introduce an approach to risk modeling that we call functional modeling , which we have developed to estimate the capabilities of a lunar base. The functional model tracks the availability of functions provided by systems, in addition to the operational state of those systems constituent strings. By tracking functions, we are able to identify cases where identical functions are provided by elements (rovers, habitats, etc.) that are connected together on the lunar surface. We credit functional diversity in those cases, and in doing so compute more realistic estimates of operational mode availabilities. The functional modeling approach yields more realistic estimates of the availability of the various operational modes provided to astronauts by the ensemble of surface elements included in a lunar base architecture. By tracking functional availability the effects of diverse backup, which often exists when two or more independent elements are connected together, is properly accounted for.

  10. Bootstrapped models for intrinsic random functions

    SciTech Connect

    Campbell, K.

    1987-01-01

    The use of intrinsic random function stochastic models as a basis for estimation in geostatistical work requires the identification of the generalized covariance function of the underlying process, and the fact that this function has to be estimated from the data introduces an additional source of error into predictions based on the model. This paper develops the sample reuse procedure called the ''bootstrap'' in the context of intrinsic random functions to obtain realistic estimates of these errors. Simulation results support the conclusion that bootstrap distributions of functionals of the process, as well as of their ''kriging variance,'' provide a reasonable picture of the variability introduced by imperfect estimation of the generalized covariance function.

  11. Bootstrapped models for intrinsic random functions

    SciTech Connect

    Campbell, K.

    1988-08-01

    Use of intrinsic random function stochastic models as a basis for estimation in geostatistical work requires the identification of the generalized covariance function of the underlying process. The fact that this function has to be estimated from data introduces an additional source of error into predictions based on the model. This paper develops the sample reuse procedure called the bootstrap in the context of intrinsic random functions to obtain realistic estimates of these errors. Simulation results support the conclusion that bootstrap distributions of functionals of the process, as well as their kriging variance, provide a reasonable picture of variability introduced by imperfect estimation of the generalized covariance function.

  12. Mouse models of PAK function.

    PubMed

    Kelly, Mollie L; Chernoff, Jonathan

    2012-04-01

    p21-activated kinases are a family of highly conserved protein serine/threonine kinases that are increasingly recognized as playing essential roles in a variety of key signaling processes. Genetic analyses in mice, using constitutive or regulated gene disruption, have provided important new insights into PAK function. In this paper, we review the genetic analysis of all six PAK genes in mice. These data address the singular and redundant functions of the various PAK genes and suggest therapeutic possibilities for small molecule PAK inhibitors or activators. PMID:23162740

  13. Modeling of functional brain imaging data

    NASA Astrophysics Data System (ADS)

    Horwitz, Barry

    1999-03-01

    The richness and complexity of data sets obtained from functional neuroimaging studies of human cognitive behavior, using techniques such as positron emission tomography and functional magnetic resonance imaging, have until recently not been exploited by computational neural modeling methods. In this article, following a brief introduction to functional neuroimaging methodology, two neural modeling approaches for use with functional brain imaging data are described. One, which uses structural equation modeling, examines the effective functional connections between various brain regions during specific cognitive tasks. The second employs large-scale neural modeling to relate functional neuroimaging signals in multiple, interconnected brain regions to the underlying neurobiological time-varying activities in each region. These two modeling procedures are illustrated using a visual processing paradigm.

  14. Response Surface Modeling Using Multivariate Orthogonal Functions

    NASA Technical Reports Server (NTRS)

    Morelli, Eugene A.; DeLoach, Richard

    2001-01-01

    A nonlinear modeling technique was used to characterize response surfaces for non-dimensional longitudinal aerodynamic force and moment coefficients, based on wind tunnel data from a commercial jet transport model. Data were collected using two experimental procedures - one based on modem design of experiments (MDOE), and one using a classical one factor at a time (OFAT) approach. The nonlinear modeling technique used multivariate orthogonal functions generated from the independent variable data as modeling functions in a least squares context to characterize the response surfaces. Model terms were selected automatically using a prediction error metric. Prediction error bounds computed from the modeling data alone were found to be- a good measure of actual prediction error for prediction points within the inference space. Root-mean-square model fit error and prediction error were less than 4 percent of the mean response value in all cases. Efficacy and prediction performance of the response surface models identified from both MDOE and OFAT experiments were investigated.

  15. Meson wave function from holographic models

    SciTech Connect

    Vega, Alfredo; Schmidt, Ivan; Branz, Tanja; Gutsche, Thomas; Lyubovitskij, Valery E.

    2009-09-01

    We consider the light-front wave function for the valence quark state of mesons using the AdS/CFT correspondence, as has been suggested by Brodsky and Teramond. Two kinds of wave functions, obtained in different holographic Soft-Wall models, are discussed.

  16. The NJL Model for Quark Fragmentation Functions

    SciTech Connect

    T. Ito, W. Bentz, I. Cloet, A W Thomas, K. Yazaki

    2009-10-01

    A description of fragmentation functions which satisfy the momentum and isospin sum rules is presented in an effective quark theory. Concentrating on the pion fragmentation function, we first explain the reason why the elementary (lowest order) fragmentation process q → qπ is completely inadequate to describe the empirical data, although the “crossed” process π → qq describes the quark distribution functions in the pion reasonably well. Then, taking into account cascade-like processes in a modified jet-model approach, we show that the momentum and isospin sum rules can be satisfied naturally without introducing any ad-hoc parameters. We present numerical results for the Nambu-Jona-Lasinio model in the invariant mass regularization scheme, and compare the results with the empirical parametrizations. We argue that this NJL-jet model provides a very useful framework to calculate the fragmentation functions in an effective chiral quark theory.

  17. Forward and reverse transfer function model synthesis

    NASA Technical Reports Server (NTRS)

    Houghton, J. R.

    1985-01-01

    A process for synthesizing a mathematical model for a linear mechanical system using the forward and reverse Fourier transform functions is described. The differential equation for a system model is given. The Bode conversion of the differential equation, and the frequency and time-domain optimization matching of the model to the forward and reverse transform functions using the geometric simplex method of Nelder and Mead (1965) are examined. The effect of the window function on the linear mechanical system is analyzed. The model is applied to two examples; in one the signal damps down before the end of the time window and in the second the signal has significant energy at the end of the time window.

  18. Understanding human functioning using graphical models

    PubMed Central

    2010-01-01

    Background Functioning and disability are universal human experiences. However, our current understanding of functioning from a comprehensive perspective is limited. The development of the International Classification of Functioning, Disability and Health (ICF) on the one hand and recent developments in graphical modeling on the other hand might be combined and open the door to a more comprehensive understanding of human functioning. The objective of our paper therefore is to explore how graphical models can be used in the study of ICF data for a range of applications. Methods We show the applicability of graphical models on ICF data for different tasks: Visualization of the dependence structure of the data set, dimension reduction and comparison of subpopulations. Moreover, we further developed and applied recent findings in causal inference using graphical models to estimate bounds on intervention effects in an observational study with many variables and without knowing the underlying causal structure. Results In each field, graphical models could be applied giving results of high face-validity. In particular, graphical models could be used for visualization of functioning in patients with spinal cord injury. The resulting graph consisted of several connected components which can be used for dimension reduction. Moreover, we found that the differences in the dependence structures between subpopulations were relevant and could be systematically analyzed using graphical models. Finally, when estimating bounds on causal effects of ICF categories on general health perceptions among patients with chronic health conditions, we found that the five ICF categories that showed the strongest effect were plausible. Conclusions Graphical Models are a flexible tool and lend themselves for a wide range of applications. In particular, studies involving ICF data seem to be suited for analysis using graphical models. PMID:20149230

  19. Functional Error Models to Accelerate Nested Sampling

    NASA Astrophysics Data System (ADS)

    Josset, L.; Elsheikh, A. H.; Demyanov, V.; Lunati, I.

    2014-12-01

    The main challenge in groundwater problems is the reliance on large numbers of unknown parameters with wide rage of associated uncertainties. To translate this uncertainty to quantities of interest (for instance the concentration of pollutant in a drinking well), a large number of forward flow simulations is required. To make the problem computationally tractable, Josset et al. (2013, 2014) introduced the concept of functional error models. It consists in two elements: a proxy model that is cheaper to evaluate than the full physics flow solver and an error model to account for the missing physics. The coupling of the proxy model and the error models provides reliable predictions that approximate the full physics model's responses. The error model is tailored to the problem at hand by building it for the question of interest. It follows a typical approach in machine learning where both the full physics and proxy models are evaluated for a training set (subset of realizations) and the set of responses is used to construct the error model using functional data analysis. Once the error model is devised, a prediction of the full physics response for a new geostatistical realization can be obtained by computing the proxy response and applying the error model. We propose the use of functional error models in a Bayesian inference context by combining it to the Nested Sampling (Skilling 2006; El Sheikh et al. 2013, 2014). Nested Sampling offers a mean to compute the Bayesian Evidence by transforming the multidimensional integral into a 1D integral. The algorithm is simple: starting with an active set of samples, at each iteration, the sample with the lowest likelihood is kept aside and replaced by a sample of higher likelihood. The main challenge is to find this sample of higher likelihood. We suggest a new approach: first the active set is sampled, both proxy and full physics models are run and the functional error model is build. Then, at each iteration of the Nested

  20. Work Functions for Models of Scandate Surfaces

    NASA Technical Reports Server (NTRS)

    Mueller, Wolfgang

    1997-01-01

    The electronic structure, surface dipole properties, and work functions of scandate surfaces have been investigated using the fully relativistic scattered-wave cluster approach. Three different types of model surfaces are considered: (1) a monolayer of Ba-Sc-O on W(100), (2) Ba or BaO adsorbed on Sc2O3 + W, and (3) BaO on SC2O3 + WO3. Changes in the work function due to Ba or BaO adsorption on the different surfaces are calculated by employing the depolarization model of interacting surface dipoles. The largest work function change and the lowest work function of 1.54 eV are obtained for Ba adsorbed on the Sc-O monolayer on W(100). The adsorption of Ba on Sc2O3 + W does not lead to a low work function, but the adsorption of BaO results in a work function of about 1.6-1.9 eV. BaO adsorbed on Sc2O3 + WO3, or scandium tungstates, may also lead to low work functions.

  1. Measuring Psychometric Functions with the Diffusion Model

    PubMed Central

    Ratcliff, Roger

    2014-01-01

    The diffusion decision model (Ratcliff, 1978) was used to examine discrimination for a range of perceptual tasks: numerosity discrimination, number discrimination, brightness discrimination, motion discrimination, speed discrimination, and length discrimination. The model produces a measure of the quality of the information that drives decision processes, a measure termed “drift rate” in the model. As drift rate varies across experimental conditions that differ in difficulty, a psychometric function that plots drift rate against difficulty can be constructed. Psychometric functions for the tasks in this article usually plot accuracy against difficulty, but for some levels of difficulty, accuracy can be at ceiling. The diffusion model extends the range of difficulty that can be evaluated because drift rates depend on response times (RTs) as well as accuracy and when RTs decrease across conditions that are all at ceiling in accuracy, then drift rates will distinguish among the conditions. Signal detection theory assumes that the variable driving performance is the z-transform of the accuracy value and somewhat surprisingly, this closely matches drift rate extracted from the diffusion model when accuracy is not at ceiling, but not sometimes when accuracy is high. Even though the functions are similar in the middle of the range, the interpretations of the variability in the models (e.g., perceptual variability, decision process variability) are incompatible. PMID:24446719

  2. Transversity distribution functions in the valon model

    NASA Astrophysics Data System (ADS)

    Alizadeh Yazdi, Z.; Taghavi-Shahri, F.; Arash, F.; Zomorrodian, M. E.

    2014-05-01

    We use the valon model to calculate the transversity distribution functions inside the nucleon. Transversity distributions indicate the probability to find partons with spin aligned (antialigned) to the transversely polarized nucleon. The results are in good agreement with all available experimental data and also global fits.

  3. Functional genes of non-model arthropods

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Technology and bioinformatics facilitate studies of non-model organisms, including pest insects and insect biological control agents. A cDNA library prepared from a laboratory-reared colony of Lygus lineolaris male nymphs identified sequences that appeared to have known functions or close homologues...

  4. Mixture models for distance sampling detection functions.

    PubMed

    Miller, David L; Thomas, Len

    2015-01-01

    We present a new class of models for the detection function in distance sampling surveys of wildlife populations, based on finite mixtures of simple parametric key functions such as the half-normal. The models share many of the features of the widely-used "key function plus series adjustment" (K+A) formulation: they are flexible, produce plausible shapes with a small number of parameters, allow incorporation of covariates in addition to distance and can be fitted using maximum likelihood. One important advantage over the K+A approach is that the mixtures are automatically monotonic non-increasing and non-negative, so constrained optimization is not required to ensure distance sampling assumptions are honoured. We compare the mixture formulation to the K+A approach using simulations to evaluate its applicability in a wide set of challenging situations. We also re-analyze four previously problematic real-world case studies. We find mixtures outperform K+A methods in many cases, particularly spiked line transect data (i.e., where detectability drops rapidly at small distances) and larger sample sizes. We recommend that current standard model selection methods for distance sampling detection functions are extended to include mixture models in the candidate set. PMID:25793744

  5. A Functional Model of [Fe]-Hydrogenase.

    PubMed

    Xu, Tao; Yin, Chih-Juo Madeline; Wodrich, Matthew D; Mazza, Simona; Schultz, Katherine M; Scopelliti, Rosario; Hu, Xile

    2016-03-16

    [Fe]-Hydrogenase catalyzes the hydrogenation of a biological substrate via the heterolytic splitting of molecular hydrogen. While many synthetic models of [Fe]-hydrogenase have been prepared, none yet are capable of activating H2 on their own. Here, we report the first Fe-based functional mimic of the active site of [Fe]-hydrogenase, which was developed based on a mechanistic understanding. The activity of this iron model complex is enabled by its unique ligand environment, consisting of biomimetic pyridinylacyl and carbonyl ligands, as well as a bioinspired diphosphine ligand with a pendant amine moiety. The model complex activates H2 and mediates hydrogenation of an aldehyde. PMID:26926708

  6. Pattern Formation and Functionality in Swarm Models

    NASA Astrophysics Data System (ADS)

    Rauch, Erik; Millonas, Mark; Chialvo, Dante

    1996-03-01

    We explore a simplified class of models we call swarms, which are inspired by the collective behavior of social insects. We perform a mean-field type stability analysis and numerical simulations of the model. Several interesting types of functional behavior appear in the vicinity of a second order phase transition, including the formation of stable lines of traffic flow, memory consolidation, and bootstrapping. In addition to providing an understanding of certain classes of biological behavior, these models bear a generic resemblence to a number of pattern formation processes in the physical sciences.

  7. Maximum entropy models of ecosystem functioning

    SciTech Connect

    Bertram, Jason

    2014-12-05

    Using organism-level traits to deduce community-level relationships is a fundamental problem in theoretical ecology. This problem parallels the physical one of using particle properties to deduce macroscopic thermodynamic laws, which was successfully achieved with the development of statistical physics. Drawing on this parallel, theoretical ecologists from Lotka onwards have attempted to construct statistical mechanistic theories of ecosystem functioning. Jaynes’ broader interpretation of statistical mechanics, which hinges on the entropy maximisation algorithm (MaxEnt), is of central importance here because the classical foundations of statistical physics do not have clear ecological analogues (e.g. phase space, dynamical invariants). However, models based on the information theoretic interpretation of MaxEnt are difficult to interpret ecologically. Here I give a broad discussion of statistical mechanical models of ecosystem functioning and the application of MaxEnt in these models. Emphasising the sample frequency interpretation of MaxEnt, I show that MaxEnt can be used to construct models of ecosystem functioning which are statistical mechanical in the traditional sense using a savanna plant ecology model as an example.

  8. Maximum entropy models of ecosystem functioning

    NASA Astrophysics Data System (ADS)

    Bertram, Jason

    2014-12-01

    Using organism-level traits to deduce community-level relationships is a fundamental problem in theoretical ecology. This problem parallels the physical one of using particle properties to deduce macroscopic thermodynamic laws, which was successfully achieved with the development of statistical physics. Drawing on this parallel, theoretical ecologists from Lotka onwards have attempted to construct statistical mechanistic theories of ecosystem functioning. Jaynes' broader interpretation of statistical mechanics, which hinges on the entropy maximisation algorithm (MaxEnt), is of central importance here because the classical foundations of statistical physics do not have clear ecological analogues (e.g. phase space, dynamical invariants). However, models based on the information theoretic interpretation of MaxEnt are difficult to interpret ecologically. Here I give a broad discussion of statistical mechanical models of ecosystem functioning and the application of MaxEnt in these models. Emphasising the sample frequency interpretation of MaxEnt, I show that MaxEnt can be used to construct models of ecosystem functioning which are statistical mechanical in the traditional sense using a savanna plant ecology model as an example.

  9. Density Functional Theory Models for Radiation Damage

    NASA Astrophysics Data System (ADS)

    Dudarev, S. L.

    2013-07-01

    Density functional theory models developed over the past decade provide unique information about the structure of nanoscale defects produced by irradiation and about the nature of short-range interaction between radiation defects, clustering of defects, and their migration pathways. These ab initio models, involving no experimental input parameters, appear to be as quantitatively accurate and informative as the most advanced experimental techniques developed for the observation of radiation damage phenomena. Density functional theory models have effectively created a new paradigm for the scientific investigation and assessment of radiation damage effects, offering new insight into the origin of temperature- and dose-dependent response of materials to irradiation, a problem of pivotal significance for applications.

  10. Modelling functional effects of muscle geometry.

    PubMed

    van der Linden, B J; Koopman, H F; Grootenboer, H J; Huijing, P A

    1998-04-01

    Muscle architecture is an important aspect of muscle functioning. Hence, geometry and material properties of muscle have great influence on the force-length characteristics of muscle. We compared experimental results for the gastrocnemius medialis muscle (GM) of the rat to model results of simple geometric models such as a planimetric model and three-dimensional versions of this model. The capabilities of such models to adequately calculate muscle geometry and force-length characteristics were investigated. The planimetric model with elastic aponeurosis predicted GM muscle geometry well: maximal differences are 6, 1, 4 and 6% for fiber length, aponeurosis length, fiber angle and aponeurosis angle respectively. A slanted cylinder model with circular fiber cross-section did not predict muscle geometry as well as the planimetric model, whereas the geometry results of a second slanted cylinder model were identical to the planimetric model. It is concluded that the planimetric model is capable of adequately calculating the muscle geometry over the muscle length range studied. However, for modelling of force-length characteristics more complex models are needed, as none of the models yielded results sufficiently close to experimental data. Modelled force-length characteristics showed an overestimation of muscle optimum length by 2 mm with respect to experimental data, and the force at the ascending limb of the length force curve was underestimated. The models presented neglect important aspects such as non-linear geometry of muscle, certain passive material properties and mechanical interactions of fibers. These aspects may be responsible for short-comings in the modelling. It is argued that, considering the inability to adequately model muscle length-force characteristics for an isolated maximally activated (in situ) muscle, it is to be expected that prediction will fail for muscle properties in conditions of complex movement with many interacting factors. Therefore

  11. A Generic Modeling Process to Support Functional Fault Model Development

    NASA Technical Reports Server (NTRS)

    Maul, William A.; Hemminger, Joseph A.; Oostdyk, Rebecca; Bis, Rachael A.

    2016-01-01

    Functional fault models (FFMs) are qualitative representations of a system's failure space that are used to provide a diagnostic of the modeled system. An FFM simulates the failure effect propagation paths within a system between failure modes and observation points. These models contain a significant amount of information about the system including the design, operation and off nominal behavior. The development and verification of the models can be costly in both time and resources. In addition, models depicting similar components can be distinct, both in appearance and function, when created individually, because there are numerous ways of representing the failure space within each component. Generic application of FFMs has the advantages of software code reuse: reduction of time and resources in both development and verification, and a standard set of component models from which future system models can be generated with common appearance and diagnostic performance. This paper outlines the motivation to develop a generic modeling process for FFMs at the component level and the effort to implement that process through modeling conventions and a software tool. The implementation of this generic modeling process within a fault isolation demonstration for NASA's Advanced Ground System Maintenance (AGSM) Integrated Health Management (IHM) project is presented and the impact discussed.

  12. A Green's function quantum average atom model

    DOE PAGESBeta

    Starrett, Charles Edward

    2015-05-21

    A quantum average atom model is reformulated using Green's functions. This allows integrals along the real energy axis to be deformed into the complex plane. The advantage being that sharp features such as resonances and bound states are broadened by a Lorentzian with a half-width chosen for numerical convenience. An implementation of this method therefore avoids numerically challenging resonance tracking and the search for weakly bound states, without changing the physical content or results of the model. A straightforward implementation results in up to a factor of 5 speed-up relative to an optimized orbital based code.

  13. Mathematical Models of Cardiac Pacemaking Function

    NASA Astrophysics Data System (ADS)

    Li, Pan; Lines, Glenn T.; Maleckar, Mary M.; Tveito, Aslak

    2013-10-01

    Over the past half century, there has been intense and fruitful interaction between experimental and computational investigations of cardiac function. This interaction has, for example, led to deep understanding of cardiac excitation-contraction coupling; how it works, as well as how it fails. However, many lines of inquiry remain unresolved, among them the initiation of each heartbeat. The sinoatrial node, a cluster of specialized pacemaking cells in the right atrium of the heart, spontaneously generates an electro-chemical wave that spreads through the atria and through the cardiac conduction system to the ventricles, initiating the contraction of cardiac muscle essential for pumping blood to the body. Despite the fundamental importance of this primary pacemaker, this process is still not fully understood, and ionic mechanisms underlying cardiac pacemaking function are currently under heated debate. Several mathematical models of sinoatrial node cell membrane electrophysiology have been constructed as based on different experimental data sets and hypotheses. As could be expected, these differing models offer diverse predictions about cardiac pacemaking activities. This paper aims to present the current state of debate over the origins of the pacemaking function of the sinoatrial node. Here, we will specifically review the state-of-the-art of cardiac pacemaker modeling, with a special emphasis on current discrepancies, limitations, and future challenges.

  14. Functional derivatives for multi-scale modeling

    NASA Astrophysics Data System (ADS)

    Reeve, Samuel; Strachan, Alejandro

    2015-03-01

    As we look beyond petascale computing and towards the exascale, effectively utilizing computational resources by using multi-fidelity and multi-scale materials simulations becomes increasingly important. Determining when and where to run high-fidelity simulations in order to have the most effect on a given quantity of interest (QoI) is a difficult problem. This work utilizes functional uncertainty quantification (UQ) for this task. While most UQ focuses on uncertainty in output from uncertainty in input parameters, we focus on uncertainty from the function itself (e.g. from using a specific functional form for an interatomic potential or constitutive law). In the case of a multi-scale simulation with a given constitutive law, calculating the functional derivative of the QoI with respect to that constitutive law can determine where a fine-scale model evaluation will maximize the increase in accuracy of the predicted QoI. Additionally, for a given computational budget the optimal set of coarse and fine-scale simulations can be determined. Numerical calculation of the functional derivative has been developed and methods of including this work within existing multi-fidelity and multi-scale orchestrators are explored.

  15. The Pleiades mass function: Models versus observations

    NASA Astrophysics Data System (ADS)

    Moraux, E.; Kroupa, P.; Bouvier, J.

    2004-10-01

    Two stellar-dynamical models of binary-rich embedded proto-Orion-Nebula-type clusters that evolve to Pleiades-like clusters are studied with an emphasis on comparing the stellar mass function with observational constraints. By the age of the Pleiades (about 100 Myr) both models show a similar degree of mass segregation which also agrees with observational constraints. This thus indicates that the Pleiades is well relaxed and that it is suffering from severe amnesia. It is found that the initial mass function (IMF) must have been indistinguishable from the standard or Galactic-field IMF for stars with mass m ≲ 2 M⊙, provided the Pleiades precursor had a central density of about 104.8 stars/pc3. A denser model with 105.8 stars/pc3 also leads to reasonable agreement with observational constraints, but owing to the shorter relaxation time of the embedded cluster it evolves through energy equipartition to a mass-segregated condition just prior to residual-gas expulsion. This model consequently preferentially loses low-mass stars and brown dwarfs (BDs), but the effect is not very pronounced. The empirical data indicate that the Pleiades IMF may have been steeper than the Salpeter for stars with m⪆ 2 M⊙.

  16. A zonal model of cortical functions.

    PubMed

    Green, H S; Triffet, T

    1989-01-01

    A model of cortical functions is developed with the object of simulating the observed behavior of individual neurons organized in unit circuits and functional systems of the cerebellum, the cerebrum and the hippocampal formation. The neuronal model is capable of representing refractory and potentiated states, as well as the firing and lowest resting states. The unit circuits of each system consist of all common types of cells with known synaptic connections. In the cerebral system these unit circuits are interconnected to form columns as well as zones. A new discrete neural network equation, which takes account of interactions with the extracellular field, is proposed to simulate electrical activity in these circuits. A coherent theory of cortical activity and functions is derived that accounts for many of the observed phenomena, including those associated with the development of long-term potentiation and sequential memory. Three appendices are devoted to the theory of extracellular interactions, the derivation of non-linear network equations, and a computer program to simulate learning in the cortex. PMID:2779262

  17. Transfer function modeling of damping mechanisms in distributed parameter models

    NASA Technical Reports Server (NTRS)

    Slater, J. C.; Inman, D. J.

    1994-01-01

    This work formulates a method for the modeling of material damping characteristics in distributed parameter models which may be easily applied to models such as rod, plate, and beam equations. The general linear boundary value vibration equation is modified to incorporate hysteresis effects represented by complex stiffness using the transfer function approach proposed by Golla and Hughes. The governing characteristic equations are decoupled through separation of variables yielding solutions similar to those of undamped classical theory, allowing solution of the steady state as well as transient response. Example problems and solutions are provided demonstrating the similarity of the solutions to those of the classical theories and transient responses of nonviscous systems.

  18. Functionalized anatomical models for EM-neuron Interaction modeling.

    PubMed

    Neufeld, Esra; Cassará, Antonino Mario; Montanaro, Hazael; Kuster, Niels; Kainz, Wolfgang

    2016-06-21

    The understanding of interactions between electromagnetic (EM) fields and nerves are crucial in contexts ranging from therapeutic neurostimulation to low frequency EM exposure safety. To properly consider the impact of in vivo induced field inhomogeneity on non-linear neuronal dynamics, coupled EM-neuronal dynamics modeling is required. For that purpose, novel functionalized computable human phantoms have been developed. Their implementation and the systematic verification of the integrated anisotropic quasi-static EM solver and neuronal dynamics modeling functionality, based on the method of manufactured solutions and numerical reference data, is described. Electric and magnetic stimulation of the ulnar and sciatic nerve were modeled to help understanding a range of controversial issues related to the magnitude and optimal determination of strength-duration (SD) time constants. The results indicate the importance of considering the stimulation-specific inhomogeneous field distributions (especially at tissue interfaces), realistic models of non-linear neuronal dynamics, very short pulses, and suitable SD extrapolation models. These results and the functionalized computable phantom will influence and support the development of safe and effective neuroprosthetic devices and novel electroceuticals. Furthermore they will assist the evaluation of existing low frequency exposure standards for the entire population under all exposure conditions. PMID:27224508

  19. Functionalized anatomical models for EM-neuron Interaction modeling

    NASA Astrophysics Data System (ADS)

    Neufeld, Esra; Cassará, Antonino Mario; Montanaro, Hazael; Kuster, Niels; Kainz, Wolfgang

    2016-06-01

    The understanding of interactions between electromagnetic (EM) fields and nerves are crucial in contexts ranging from therapeutic neurostimulation to low frequency EM exposure safety. To properly consider the impact of in vivo induced field inhomogeneity on non-linear neuronal dynamics, coupled EM-neuronal dynamics modeling is required. For that purpose, novel functionalized computable human phantoms have been developed. Their implementation and the systematic verification of the integrated anisotropic quasi-static EM solver and neuronal dynamics modeling functionality, based on the method of manufactured solutions and numerical reference data, is described. Electric and magnetic stimulation of the ulnar and sciatic nerve were modeled to help understanding a range of controversial issues related to the magnitude and optimal determination of strength-duration (SD) time constants. The results indicate the importance of considering the stimulation-specific inhomogeneous field distributions (especially at tissue interfaces), realistic models of non-linear neuronal dynamics, very short pulses, and suitable SD extrapolation models. These results and the functionalized computable phantom will influence and support the development of safe and effective neuroprosthetic devices and novel electroceuticals. Furthermore they will assist the evaluation of existing low frequency exposure standards for the entire population under all exposure conditions.

  20. Inverse Modeling Via Linearized Functional Minimization

    NASA Astrophysics Data System (ADS)

    Barajas-Solano, D. A.; Wohlberg, B.; Vesselinov, V. V.; Tartakovsky, D. M.

    2014-12-01

    We present a novel parameter estimation methodology for transient models of geophysical systems with uncertain, spatially distributed, heterogeneous and piece-wise continuous parameters.The methodology employs a bayesian approach to propose an inverse modeling problem for the spatial configuration of the model parameters.The likelihood of the configuration is formulated using sparse measurements of both model parameters and transient states.We propose using total variation regularization (TV) as the prior reflecting the heterogeneous, piece-wise continuity assumption on the parameter distribution.The maximum a posteriori (MAP) estimator of the parameter configuration is then computed by minimizing the negative bayesian log-posterior using a linearized functional minimization approach. The computation of the MAP estimator is a large-dimensional nonlinear minimization problem with two sources of nonlinearity: (1) the TV operator, and (2) the nonlinear relation between states and parameters provided by the model's governing equations.We propose a a hybrid linearized functional minimization (LFM) algorithm in two stages to efficiently treat both sources of nonlinearity.The relation between states and parameters is linearized, resulting in a linear minimization sub-problem equipped with the TV operator; this sub-problem is then minimized using the Alternating Direction Method of Multipliers (ADMM). The methodology is illustrated with a transient saturated groundwater flow application in a synthetic domain, stimulated by external point-wise loadings representing aquifer pumping, together with an array of discrete measurements of hydraulic conductivity and transient measurements of hydraulic head.We show that our inversion strategy is able to recover the overall large-scale features of the parameter configuration, and that the reconstruction is improved by the addition of transient information of the state variable.

  1. Dynamic geometry, brain function modeling, and consciousness.

    PubMed

    Roy, Sisir; Llinás, Rodolfo

    2008-01-01

    Pellionisz and Llinás proposed, years ago, a geometric interpretation towards understanding brain function. This interpretation assumes that the relation between the brain and the external world is determined by the ability of the central nervous system (CNS) to construct an internal model of the external world using an interactive geometrical relationship between sensory and motor expression. This approach opened new vistas not only in brain research but also in understanding the foundations of geometry itself. The approach named tensor network theory is sufficiently rich to allow specific computational modeling and addressed the issue of prediction, based on Taylor series expansion properties of the system, at the neuronal level, as a basic property of brain function. It was actually proposed that the evolutionary realm is the backbone for the development of an internal functional space that, while being purely representational, can interact successfully with the totally different world of the so-called "external reality". Now if the internal space or functional space is endowed with stochastic metric tensor properties, then there will be a dynamic correspondence between events in the external world and their specification in the internal space. We shall call this dynamic geometry since the minimal time resolution of the brain (10-15 ms), associated with 40 Hz oscillations of neurons and their network dynamics, is considered to be responsible for recognizing external events and generating the concept of simultaneity. The stochastic metric tensor in dynamic geometry can be written as five-dimensional space-time where the fifth dimension is a probability space as well as a metric space. This extra dimension is considered an imbedded degree of freedom. It is worth noticing that the above-mentioned 40 Hz oscillation is present both in awake and dream states where the central difference is the inability of phase resetting in the latter. This framework of dynamic

  2. Catch bonds: physical models and biological functions.

    PubMed

    Zhu, Cheng; McEver, Rodger P

    2005-09-01

    Force can shorten the lifetimes of receptor-ligand bonds by accelerating their dissociation. Perhaps paradoxical at first glance, bond lifetimes can also be prolonged by force. This counterintuitive behavior was named catch bonds, which is in contrast to the ordinary slip bonds that describe the intuitive behavior of lifetimes being shortened by force. Fifteen years after their theoretical proposal, catch bonds have finally been observed. In this article we review recently published data that have demonstrated catch bonds in the selectin system and suggested catch bonds in other systems, the theoretical models for their explanations, and their function as a mechanism for flow-enhanced adhesion. PMID:16708472

  3. Linear functional minimization for inverse modeling

    NASA Astrophysics Data System (ADS)

    Barajas-Solano, D. A.; Wohlberg, B. E.; Vesselinov, V. V.; Tartakovsky, D. M.

    2015-06-01

    We present a novel inverse modeling strategy to estimate spatially distributed parameters of nonlinear models. The maximum a posteriori (MAP) estimators of these parameters are based on a likelihood functional, which contains spatially discrete measurements of the system parameters and spatiotemporally discrete measurements of the transient system states. The piecewise continuity prior for the parameters is expressed via Total Variation (TV) regularization. The MAP estimator is computed by minimizing a nonquadratic objective equipped with the TV operator. We apply this inversion algorithm to estimate hydraulic conductivity of a synthetic confined aquifer from measurements of conductivity and hydraulic head. The synthetic conductivity field is composed of a low-conductivity heterogeneous intrusion into a high-conductivity heterogeneous medium. Our algorithm accurately reconstructs the location, orientation, and extent of the intrusion from the steady-state data only. Addition of transient measurements of hydraulic head improves the parameter estimation, accurately reconstructing the conductivity field in the vicinity of observation locations.

  4. Linearized Functional Minimization for Inverse Modeling

    SciTech Connect

    Wohlberg, Brendt; Tartakovsky, Daniel M.; Dentz, Marco

    2012-06-21

    Heterogeneous aquifers typically consist of multiple lithofacies, whose spatial arrangement significantly affects flow and transport. The estimation of these lithofacies is complicated by the scarcity of data and by the lack of a clear correlation between identifiable geologic indicators and attributes. We introduce a new inverse-modeling approach to estimate both the spatial extent of hydrofacies and their properties from sparse measurements of hydraulic conductivity and hydraulic head. Our approach is to minimize a functional defined on the vectors of values of hydraulic conductivity and hydraulic head fields defined on regular grids at a user-determined resolution. This functional is constructed to (i) enforce the relationship between conductivity and heads provided by the groundwater flow equation, (ii) penalize deviations of the reconstructed fields from measurements where they are available, and (iii) penalize reconstructed fields that are not piece-wise smooth. We develop an iterative solver for this functional that exploits a local linearization of the mapping from conductivity to head. This approach provides a computationally efficient algorithm that rapidly converges to a solution. A series of numerical experiments demonstrates the robustness of our approach.

  5. Modeling the three-point correlation function

    SciTech Connect

    Marin, Felipe; Wechsler, Risa; Frieman, Joshua A.; Nichol, Robert; /Portsmouth U., ICG

    2007-04-01

    We present new theoretical predictions for the galaxy three-point correlation function (3PCF) using high-resolution dissipationless cosmological simulations of a flat {Lambda}CDM Universe which resolve galaxy-size halos and subhalos. We create realistic mock galaxy catalogs by assigning luminosities and colors to dark matter halos and subhalos, and we measure the reduced 3PCF as a function of luminosity and color in both real and redshift space. As galaxy luminosity and color are varied, we find small differences in the amplitude and shape dependence of the reduced 3PCF, at a level qualitatively consistent with recent measurements from the SDSS and 2dFGRS. We confirm that discrepancies between previous 3PCF measurements can be explained in part by differences in binning choices. We explore the degree to which a simple local bias model can fit the simulated 3PCF. The agreement between the model predictions and galaxy 3PCF measurements lends further credence to the straightforward association of galaxies with CDM halos and subhalos.

  6. A Prediction Model of the Capillary Pressure J-Function.

    PubMed

    Xu, W S; Luo, P Y; Sun, L; Lin, N

    2016-01-01

    The capillary pressure J-function is a dimensionless measure of the capillary pressure of a fluid in a porous medium. The function was derived based on a capillary bundle model. However, the dependence of the J-function on the saturation Sw is not well understood. A prediction model for it is presented based on capillary pressure model, and the J-function prediction model is a power function instead of an exponential or polynomial function. Relative permeability is calculated with the J-function prediction model, resulting in an easier calculation and results that are more representative. PMID:27603701

  7. Models of Protocellular Structure, Function and Evolution

    NASA Technical Reports Server (NTRS)

    New, Michael H.; Pohorille, Andrew; Szostak, Jack W.; Keefe, Tony; Lanyi, Janos K.; DeVincenzi, Donald L. (Technical Monitor)

    2001-01-01

    In the absence of any record of protocells, the most direct way to test our understanding, of the origin of cellular life is to construct laboratory models that capture important features of protocellular systems. Such efforts are currently underway in a collaborative project between NASA-Ames, Harvard Medical School and University of California. They are accompanied by computational studies aimed at explaining self-organization of simple molecules into ordered structures. The centerpiece of this project is a method for the in vitro evolution of protein enzymes toward arbitrary catalytic targets. A similar approach has already been developed for nucleic acids in which a small number of functional molecules are selected from a large, random population of candidates. The selected molecules are next vastly multiplied using the polymerase chain reaction.

  8. Scaling functions in the square Ising model

    NASA Astrophysics Data System (ADS)

    Hassani, S.; Maillard, J.-M.

    2015-03-01

    We show and give the linear differential operators Lqscal of order q={{n}2}/4+n+7/8+{{(-1)}n}/8, for the integrals {{I}n}(r) which appear in the two-point correlation scaling function of Ising model \\{{F}+/- }(r)={{lim }scaling}M+/- -2 \\lt {{σ }0,0} {{σ }M,N}\\gt ={{\\sum }n}{{I}n}(r). The integrals {{I}n}(r) are given in expansion around r=0 in the basis of the formal solutions of Lqscal with transcendental combination coefficients. We find that the expression {{r}1/4}exp ({{r}2}/8) is a solution of the Painlevé VI equation in the scaling limit. Combinations of the (analytic at r=0) solutions of Lqscal sum to exp ({{r}2}/8). We show that the expression {{r}1/4}exp ({{r}2}/8) is the scaling limit of the correlation function C(N,N) and C(N,N+1). The differential Galois groups of the factors occurring in the operators Lqscal are given.

  9. Models of protocellular structures, functions and evolution

    NASA Technical Reports Server (NTRS)

    Pohorille, Andrew; New, Michael H.; DeVincenzi, Donald L. (Technical Monitor)

    2000-01-01

    The central step in the origin of life was the emergence of organized structures from organic molecules available on the early earth. These predecessors to modern cells, called 'proto-cells,' were simple, membrane bounded structures able to maintain themselves, grow, divide, and evolve. Since there is no fossil record of these earliest of life forms, it is a scientific challenge to discover plausible mechanisms for how these entities formed and functioned. To meet this challenge, it is essential to create laboratory models of protocells that capture the main attributes associated with living systems, while remaining consistent with known, or inferred, protobiological conditions. This report provides an overview of a project which has focused on protocellular metabolism and the coupling of metabolism to energy transduction. We have assumed that the emergence of systems endowed with genomes and capable of Darwinian evolution was preceded by a pre-genomic phase, in which protocells functioned and evolved using mostly proteins, without self-replicating nucleic acids such as RNA.

  10. A reversible functional sensory neuropathy model.

    PubMed

    Danigo, Aurore; Magy, Laurent; Richard, Laurence; Sturtz, Franck; Funalot, Benoît; Demiot, Claire

    2014-06-13

    Small-fiber neuropathy was induced in young adult mice by intraperitoneal injection of resiniferatoxin (RTX), a TRPV1 agonist. At day 7, RTX induced significant thermal and mechanical hypoalgesia. At day 28, mechanical and thermal nociception were restored. No nerve degeneration in skin was observed and unmyelinated nerve fiber morphology and density in sciatic nerve were unchanged. At day 7, substance P (SP) was largely depleted in dorsal root ganglia (DRG) neurons, although calcitonin gene-related peptide (CGRP) was only moderately depleted. Three weeks after, SP and CGRP expression was restored in DRG neurons. At the same time, CGRP expression remained low in intraepidermal nerve fibers (IENFs) whereas SP expression had improved. In summary, RTX induced in our model a transient neuropeptide depletion in sensory neurons without nerve degeneration. We think this model is valuable as it brings the opportunity to study functional nerve changes in the very early phase of small fiber neuropathy. Moreover, it may represent a useful tool to study the mechanisms of action of therapeutic strategies to prevent sensory neuropathy of various origins. PMID:24792390

  11. Density functional calculations on model tyrosyl radicals.

    PubMed Central

    Himo, F; Gräslund, A; Eriksson, L A

    1997-01-01

    A gradient-corrected density functional theory approach (PWP86) has been applied, together with large basis sets (IGLO-III), to investigate the structure and hyperfine properties of model tyrosyl free radicals. In nature, these radicals are observed in, e.g., the charge transfer pathways in photosystem II (PSII) and in ribonucleotide reductases (RNRs). By comparing spin density distributions and proton hyperfine couplings with experimental data, it is confirmed that the tyrosyl radicals present in the proteins are neutral. It is shown that hydrogen bonding to the phenoxyl oxygen atom, when present, causes a reduction in spin density on O and a corresponding increase on C4. Calculated proton hyperfine coupling constants for the beta-protons show that the alpha-carbon is rotated 75-80 degrees out of the plane of the ring in PSII and Salmonella typhimurium RNR, but only 20-30 degrees in, e.g., Escherichia coli, mouse, herpes simplex, and bacteriophage T4-induced RNRs. Furthermore, based on the present calculations, we have revised the empirical parameters used in the experimental determination of the oxygen spin density in the tyrosyl radical in E. coli RNR and of the ring carbon spin densities, from measured hyperfine coupling constants. Images FIGURE 1 FIGURE 5 PMID:9083661

  12. Modeling Bamboo as a Functionally Graded Material

    SciTech Connect

    Silva, Emilio Carlos Nelli; Walters, Matthew C.; Paulino, Glaucio H.

    2008-02-15

    Natural fibers are promising for engineering applications due to their low cost. They are abundantly available in tropical and subtropical regions of the world, and they can be employed as construction materials. Among natural fibers, bamboo has been widely used for housing construction around the world. Bamboo is an optimized composite material which exploits the concept of Functionally Graded Material (FGM). Biological structures, such as bamboo, are composite materials that have complicated shapes and material distribution inside their domain, and thus the use of numerical methods such as the finite element method and multiscale methods such as homogenization, can help to further understanding of the mechanical behavior of these materials. The objective of this work is to explore techniques such as the finite element method and homogenization to investigate the structural behavior of bamboo. The finite element formulation uses graded finite elements to capture the varying material distribution through the bamboo wall. To observe bamboo behavior under applied loads, simulations are conducted considering a spatially-varying Young's modulus, an averaged Young's modulus, and orthotropic constitutive properties obtained from homogenization theory. The homogenization procedure uses effective, axisymmetric properties estimated from the spatially-varying bamboo composite. Three-dimensional models of bamboo cells were built and simulated under tension, torsion, and bending load cases.

  13. Models of Protocellular Structure, Function and Evolution

    NASA Technical Reports Server (NTRS)

    New, Michael H.; Pohorille, Andrew; Szostak, Jack W.; Keefe, Tony; Lanyi, Janos K.

    2001-01-01

    In the absence of any record of protocells, the most direct way to test our understanding of the origin of cellular life is to construct laboratory models that capture important features of protocellular systems. Such efforts are currently underway in a collaborative project between NASA-Ames, Harvard Medical School and University of California. They are accompanied by computational studies aimed at explaining self-organization of simple molecules into ordered structures. The centerpiece of this project is a method for the in vitro evolution of protein enzymes toward arbitrary catalytic targets. A similar approach has already been developed for nucleic acids in which a small number of functional molecules are selected from a large, random population of candidates. The selected molecules are next vastly multiplied using the polymerase chain reaction. A mutagenic approach, in which the sequences of selected molecules are randomly altered, can yield further improvements in performance or alterations of specificities. Unfortunately, the catalytic potential of nucleic acids is rather limited. Proteins are more catalytically capable but cannot be directly amplified. In the new technique, this problem is circumvented by covalently linking each protein of the initial, diverse, pool to the RNA sequence that codes for it. Then, selection is performed on the proteins, but the nucleic acids are replicated. Additional information is contained in the original extended abstract.

  14. School Teams up for SSP Functional Models

    NASA Astrophysics Data System (ADS)

    Pignolet, G.; Lallemand, R.; Celeste, A.; von Muldau, H.

    2002-01-01

    Space Solar Power systems appear increasingly as one of the major solutions to the upcoming global energy crisis, by collecting solar energy in space where this is most easy, and sending it by microwave beam to the surface of the planet, where the need for controlled energy is located. While fully operational systems are still decades away, the need for major development efforts is with us now. Yet, for many decision-makers and for most of the public, SSP often still sounds like science fiction. Six functional demonstration systems, based on the Japanese SPS-2000 concept, have been built as a result of a cooperation between France and Japan, and they are currently used extensively, in Japan, in Europe and in North America, for executive presentations as well as for public exhibitions. There is demand for more models, both for science museums and for use by energy dedicated groups, and a senior high school in La Reunion, France, has picked up the challenge to make the production of such models an integrated practical school project for pre-college students. In December 2001, the administration and the teachers of the school have evaluated the feasibility of the project and eventually taken the go decision for the school year 2002- 2003, when for education purposes a temporary "school business company" will be incorporated with the goal to study and manufacture a limited series of professional quality SSP demonstration models, and to sell them world- wide to institutions and advocacy groups concerned with energy problems and with the environment. The different sections of the school will act as the different services of an integrated business : based on the current existing models, the electronic section will redesign the energy management system and the microwave projector module, while the mechanical section of the school will adapt and re-conceive the whole packaging of the demonstrator. The French and foreign language sections will write up a technical manual for

  15. Predicting Transfer Performance: A Comparison of Competing Function Learning Models

    ERIC Educational Resources Information Center

    McDaniel, Mark A.; Dimperio, Eric; Griego, Jacqueline A.; Busemeyer, Jerome R.

    2009-01-01

    The population of linear experts (POLE) model suggests that function learning and transfer are mediated by activation of a set of prestored linear functions that together approximate the given function (Kalish, Lewandowsky, & Kruschke, 2004). In the extrapolation-association (EXAM) model, an exemplar-based architecture associates trained input…

  16. Functional state modelling approach validation for yeast and bacteria cultivations

    PubMed Central

    Roeva, Olympia; Pencheva, Tania

    2014-01-01

    In this paper, the functional state modelling approach is validated for modelling of the cultivation of two different microorganisms: yeast (Saccharomyces cerevisiae) and bacteria (Escherichia coli). Based on the available experimental data for these fed-batch cultivation processes, three different functional states are distinguished, namely primary product synthesis state, mixed oxidative state and secondary product synthesis state. Parameter identification procedures for different local models are performed using genetic algorithms. The simulation results show high degree of adequacy of the models describing these functional states for both S. cerevisiae and E. coli cultivations. Thus, the local models are validated for the cultivation of both microorganisms. This fact is a strong structure model verification of the functional state modelling theory not only for a set of yeast cultivations, but also for bacteria cultivation. As such, the obtained results demonstrate the efficiency and efficacy of the functional state modelling approach. PMID:26740778

  17. A Functional Test Platform for the Community Land Model

    SciTech Connect

    Xu, Yang; Thornton, Peter E; King, Anthony Wayne; Steed, Chad A; Gu, Lianhong; Schuchart, Joseph

    2014-01-01

    A functional test platform is presented to create direct linkages between site measurements and the process-based ecosystem model within the Community Earth System Models (CESM). The platform consists of three major parts: 1) interactive user interfaces, 2) functional test model and 3) observational datasets. It provides much needed integration interfaces for both field experimentalists and ecosystem modelers to improve the model s representation of ecosystem processes within the CESM framework without large software overhead.

  18. Parametric models for samples of random functions

    SciTech Connect

    Grigoriu, M.

    2015-09-15

    A new class of parametric models, referred to as sample parametric models, is developed for random elements that match sample rather than the first two moments and/or other global properties of these elements. The models can be used to characterize, e.g., material properties at small scale in which case their samples represent microstructures of material specimens selected at random from a population. The samples of the proposed models are elements of finite-dimensional vector spaces spanned by samples, eigenfunctions of Karhunen–Loève (KL) representations, or modes of singular value decompositions (SVDs). The implementation of sample parametric models requires knowledge of the probability laws of target random elements. Numerical examples including stochastic processes and random fields are used to demonstrate the construction of sample parametric models, assess their accuracy, and illustrate how these models can be used to solve efficiently stochastic equations.

  19. A Robot Model of Function Behavior in C/C++.

    ERIC Educational Resources Information Center

    Molluzzo, John C.

    2002-01-01

    Discussion of students' difficulties in C and C++ courses focuses on the function concept. Discusses function behavior through a model that uses a robot and its specially constructed environment, and distinguishes between the terms argument and parameter. (Author/LRW)

  20. On extended thermonuclear functions through pathway model

    NASA Astrophysics Data System (ADS)

    Kumar, Dilip

    when α → 1. The beauty of the result is that these different families of three different functional forms are covered through the pathway parameter α. In a physical set up if f (x) in (3) is the stable or limiting form, the Maxwell-Boltzmann approach to thermonuclear functions, then f (x) in (1) and (2) will contain a large variety of unstable or chaotic situations which will all tend to (3) in the limit. Thus we get a clear idea of all the stable and unstable situations around the Maxwell-Boltzmann approach. Thus the current theory is given a mathematical extension and physical interpretations can be found to situations in (1) and (2). Incidently Tsallis statistics is a special case of (1) for γ = 0, a = 1, δ = 1, η = 1. The Beck-Cohen superstatistics, discussed in current statistical mechanics literature is a special case of (2) for a = 1, η = 1, α > 1. The main purpose of the present paper is to investigate in some more detail, mathematically, the extended thermonuclear functions for Maxwell-Boltzmann statistics and in the cut-off case. The extended thermonuclear functions will be evaluated in closed form for all convenient values of the parameter by means of residue calculus. A comparison of the standard thermonuclear functions with the extended thermonuclear functions is also done. The results and derivations in this paper are new and these will be of interest to physicists, mathematicians, probabilists, and statisticians.

  1. Fourier functional analysis for unsteady aerodynamic modeling

    NASA Technical Reports Server (NTRS)

    Lan, C. Edward; Chin, Suei

    1991-01-01

    A method based on Fourier analysis is developed to analyze the force and moment data obtained in large amplitude forced oscillation tests at high angles of attack. The aerodynamic models for normal force, lift, drag, and pitching moment coefficients are built up from a set of aerodynamic responses to harmonic motions at different frequencies. Based on the aerodynamic models of harmonic data, the indicial responses are formed. The final expressions for the models involve time integrals of the indicial type advocated by Tobak and Schiff. Results from linear two- and three-dimensional unsteady aerodynamic theories as well as test data for a 70-degree delta wing are used to verify the models. It is shown that the present modeling method is accurate in producing the aerodynamic responses to harmonic motions and the ramp type motions. The model also produces correct trend for a 70-degree delta wing in harmonic motion with different mean angles-of-attack. However, the current model cannot be used to extrapolate data to higher angles-of-attack than that of the harmonic motions which form the aerodynamic model. For linear ramp motions, a special method is used to calculate the corresponding frequency and phase angle at a given time. The calculated results from modeling show a higher lift peak for linear ramp motion than for harmonic ramp motion. The current model also shows reasonably good results for the lift responses at different angles of attack.

  2. Modelling protein functional domains in signal transduction using Maude

    NASA Technical Reports Server (NTRS)

    Sriram, M. G.

    2003-01-01

    Modelling of protein-protein interactions in signal transduction is receiving increased attention in computational biology. This paper describes recent research in the application of Maude, a symbolic language founded on rewriting logic, to the modelling of functional domains within signalling proteins. Protein functional domains (PFDs) are a critical focus of modern signal transduction research. In general, Maude models can simulate biological signalling networks and produce specific testable hypotheses at various levels of abstraction. Developing symbolic models of signalling proteins containing functional domains is important because of the potential to generate analyses of complex signalling networks based on structure-function relationships.

  3. Latent Growth Modeling for Logistic Response Functions

    ERIC Educational Resources Information Center

    Choi, Jaehwa; Harring, Jeffrey R.; Hancock, Gregory R.

    2009-01-01

    Throughout much of the social and behavioral sciences, latent growth modeling (latent curve analysis) has become an important tool for understanding individuals' longitudinal change. Although nonlinear variations of latent growth models appear in the methodological and applied literature, a notable exclusion is the treatment of growth following…

  4. Dispersion analysis with inverse dielectric function modelling.

    PubMed

    Mayerhöfer, Thomas G; Ivanovski, Vladimir; Popp, Jürgen

    2016-11-01

    We investigate how dispersion analysis can profit from the use of a Lorentz-type description of the inverse dielectric function. In particular at higher angles of incidence, reflectance spectra using p-polarized light are dominated by bands from modes that have their transition moments perpendicular to the surface. Accordingly, the spectra increasingly resemble inverse dielectric functions. A corresponding description can therefore eliminate the complex dependencies of the dispersion parameters, allow their determination and facilitate a more accurate description of the optical properties of single crystals. PMID:27294550

  5. MODELING ENVIRONMENTAL TOBACCO SMOKE IN THE HOME USING TRANSFER FUNCTIONS

    EPA Science Inventory

    This paper presents the theoretical and practical development of a multi-compartment indoor air quality model designed for predicting pollutant concentrations from environmental tobacco smoke (ETS) in the home. he model is developed using transfer functions for each compartment, ...

  6. Hydroacoustic forcing function modeling using DNS database

    NASA Technical Reports Server (NTRS)

    Zawadzki, I.; Gershfield, J. L.; Na, Y.; Wang, M.

    1996-01-01

    A wall pressure frequency spectrum model (Blake 1971 ) has been evaluated using databases from Direct Numerical Simulations (DNS) of a turbulent boundary layer (Na & Moin 1996). Good agreement is found for moderate to strong adverse pressure gradient flows in the absence of separation. In the separated flow region, the model underpredicts the directly calculated spectra by an order of magnitude. The discrepancy is attributed to the violation of the model assumptions in that part of the flow domain. DNS computed coherence length scales and the normalized wall pressure cross-spectra are compared with experimental data. The DNS results are consistent with experimental observations.

  7. Using the canonical modelling approach to simplify the simulation of function in functional-structural plant models.

    PubMed

    Renton, Michael; Hanan, Jim; Burrage, Kevin

    2005-06-01

    Functional-structural plant models that include detailed mechanistic representation of underlying physiological processes can be expensive to construct and the resulting models can also be extremely complicated. On the other hand, purely empirical models are not able to simulate plant adaptability and response to different conditions. In this paper, we present an intermediate approach to modelling plant function that can simulate plant response without requiring detailed knowledge of underlying physiology. Plant function is modelled using a 'canonical' modelling approach, which uses compartment models with flux functions of a standard mathematical form, while plant structure is modelled using L-systems. Two modelling examples are used to demonstrate that canonical modelling can be used in conjunction with L-systems to create functional-structural plant models where function is represented either in an accurate and descriptive way, or in a more mechanistic and explanatory way. We conclude that canonical modelling provides a useful, flexible and relatively simple approach to modelling plant function at an intermediate level of abstraction. PMID:15869646

  8. Functional genomics of the chicken - a model organism

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The chicken has reached model organism status after genome sequencing and development of high-throughput tools for the exploration of functional elements of the genome. Functional genomics focuses on understanding the function and regulation of genes and gene products on a global or genome-wide scal...

  9. OAIS Functional Model Conformance Test: A Proposed Measurement

    ERIC Educational Resources Information Center

    Laughton, Paul

    2012-01-01

    Purpose: The purpose of this paper is to develop a test for data centres, repositories and archives to determine OAIS functional model conformance. The test developed was carried out among the World Data Centre (WDC) member data centres. The method used to develop the OAIS functional model conformance test is discussed, along with the test…

  10. Density Functional Model for Nondynamic and Strong Correlation.

    PubMed

    Kong, Jing; Proynov, Emil

    2016-01-12

    A single-term density functional model for the left-right nondynamic/strong electron correlation is presented based on single-determinant Kohn-Sham density functional theory. It is derived from modeling the adiabatic connection for kinetic correlation energy based on physical arguments, with the correlation potential energy based on the Becke'13 model ( Becke, A.D. J. Chem. Phys . 2013 , 138 , 074109 ). This functional satisfies some known scaling relationships for correlation functionals. The fractional spin error is further reduced substantially with a new density-functional correction. Preliminary tests with self-consistent-field implementation show that the model, with only three empirical parameters, recovers the majority of left-right nondynamic/strong correlation upon bond dissociation and performs reasonably well for atomization energies and singlet-triplet energy splittings. This study also demonstrates the feasibility of developing DFT functionals for nondynamic and strong correlation within the single-determinant KS scheme. PMID:26636190

  11. Multiscale Modeling of Form and Function

    PubMed Central

    Engler, Adam J.; Humbert, Patrick O.; Wehrle-Haller, Bernhard; Weaver, Valerie M.

    2015-01-01

    Topobiology posits that morphogenesis is driven by differential adhesive interactions among heterogeneous cell populations. This paradigm has been revised to include force-dependent molecular switches, cell and tissue tension, and reciprocal interactions with the microenvironment. It is now appreciated that tissue development is executed through conserved decision-making modules that operate on multiple length scales from the molecular and subcellular level through to the cell and tissue level and that these regulatory mechanisms specify cell and tissue fate by modifying the context of cellular signaling and gene expression. Here, we discuss the origin of these decision-making modules and illustrate how emergent properties of adhesion-directed multicellular structures sculpt the tissue, promote its functionality, and maintain its homeostasis through spatial segregation and organization of anchored proteins and secreted factors and through emergent properties of tissues, including tension fields and energy optimization. PMID:19359578

  12. Meson structure functions in the valon model

    NASA Astrophysics Data System (ADS)

    Arash, Firooz

    2004-03-01

    Parton distributions in a valon in the next-to-leading order are used to determine the parton distributions in a pion and kaon. The validity of the valon model is tested and it is shown that the partonic content of the valon is universal and independent of the valon type. We evaluate the valon distribution in the pion and kaon, and in particular it is shown that the results are in good agreement with the experimental data on the pion structure in a wide range of x=[10-4,1].

  13. Kaon fragmentation function from NJL-jet model

    SciTech Connect

    Matevosyan, Hrayr H.; Thomas, Anthony W.; Bentz, Wolfgang

    2010-07-27

    The NJL-jet model provides a sound framework for calculating the fragmentation functions in an effective chiral quark theory, where the momentum and isospin sum rules are satisfied without the introduction of ad hoc parameters [1]. Earlier studies of the pion fragmentation functions using the Nambu-Jona-Lasinio (NJL) model within this framework showed good qualitative agreement with the empirical parameterizations. Here we extend the NJL-jet model by including the strange quark. The corrections to the pion fragmentation function and corresponding kaon fragmentation functions are calculated using the elementary quark to quark-meson fragmentation functions from NJL. The results for the kaon fragmentation function exhibit a qualitative agreement with the empirical parameterizations, while the unfavored strange quark fragmentation to pions is shown to be of the same order of magnitude as the unfavored light quark's. The results of these studies are expected to provide important guidance for the analysis of a large variety of semi-inclusive data.

  14. Calibrating the ECCO ocean general circulation model using Green's functions

    NASA Technical Reports Server (NTRS)

    Menemenlis, D.; Fu, L. L.; Lee, T.; Fukumori, I.

    2002-01-01

    Green's functions provide a simple, yet effective, method to test and calibrate General-Circulation-Model(GCM) parameterizations, to study and quantify model and data errors, to correct model biases and trends, and to blend estimates from different solutions and data products.

  15. Tactile Teaching: Exploring Protein Structure/Function Using Physical Models

    ERIC Educational Resources Information Center

    Herman, Tim; Morris, Jennifer; Colton, Shannon; Batiza, Ann; Patrick, Michael; Franzen, Margaret; Goodsell, David S.

    2006-01-01

    The technology now exists to construct physical models of proteins based on atomic coordinates of solved structures. We review here our recent experiences in using physical models to teach concepts of protein structure and function at both the high school and the undergraduate levels. At the high school level, physical models are used in a…

  16. Recent History Functional Linear Models for Sparse Longitudinal Data

    PubMed Central

    Kim, Kion; Şentürk, Damla; Li, Runze

    2011-01-01

    We consider the recent history functional linear models, relating a longitudinal response to a longitudinal predictor where the predictor process only in a sliding window into the recent past has an effect on the response value at the current time. We propose an estimation procedure for recent history functional linear models that is geared towards sparse longitudinal data, where the observation times across subjects are irregular and total number of measurements per subject is small. The proposed estimation procedure builds upon recent developments in literature for estimation of functional linear models with sparse data and utilizes connections between the recent history functional linear models and varying coefficient models. We establish uniform consistency of the proposed estimators, propose prediction of the response trajectories and derive their asymptotic distribution leading to asymptotic point-wise confidence bands. We include a real data application and simulation studies to demonstrate the efficacy of the proposed methodology. PMID:21691421

  17. Distinguishing Differential Testlet Functioning from Differential Bundle Functioning Using the Multilevel Measurement Model

    ERIC Educational Resources Information Center

    Beretvas, S. Natasha; Walker, Cindy M.

    2012-01-01

    This study extends the multilevel measurement model to handle testlet-based dependencies. A flexible two-level testlet response model (the MMMT-2 model) for dichotomous items is introduced that permits assessment of differential testlet functioning (DTLF). A distinction is made between this study's conceptualization of DTLF and that of…

  18. Four-point function in the IOP matrix model

    NASA Astrophysics Data System (ADS)

    Michel, Ben; Polchinski, Joseph; Rosenhaus, Vladimir; Suh, S. Josephine

    2016-05-01

    The IOP model is a quantum mechanical system of a large- N matrix oscillator and a fundamental oscillator, coupled through a quartic interaction. It was introduced previously as a toy model of the gauge dual of an AdS black hole, and captures a key property that at infinite N the two-point function decays to zero on long time scales. Motivated by recent work on quantum chaos, we sum all planar Feynman diagrams contributing to the four-point function. We find that the IOP model does not satisfy the more refined criteria of exponential growth of the out-of-time-order four-point function.

  19. The Innovative Solution of Typical Engineering Based on Function Model

    NASA Astrophysics Data System (ADS)

    Shi, Dongyan; Shi, Xianjie; Zhao, Cunyou

    From the innovative perspective of the products, the function model of products and analysis are the basis of formulation of the innovative design. In order to solve this typical engineering problem, a function model of an actuator of shearer was constructed. Based on the foundation of function model analysis, the main problems of actuator of shearer productivity were clarified. An expression of contradictory conflict of helical drum was formulated using the creative technical method, i.e. the contradictory conflict theory. Furthermore, a creative design of helical drum was given to suggestion.

  20. Modeling Dynamic Functional Neuroimaging Data Using Structural Equation Modeling

    ERIC Educational Resources Information Center

    Price, Larry R.; Laird, Angela R.; Fox, Peter T.; Ingham, Roger J.

    2009-01-01

    The aims of this study were to present a method for developing a path analytic network model using data acquired from positron emission tomography. Regions of interest within the human brain were identified through quantitative activation likelihood estimation meta-analysis. Using this information, a "true" or population path model was then…

  1. BioModels: Content, Features, Functionality, and Use

    PubMed Central

    Juty, N; Ali, R; Glont, M; Keating, S; Rodriguez, N; Swat, MJ; Wimalaratne, SM; Hermjakob, H; Le Novère, N; Laibe, C; Chelliah, V

    2015-01-01

    BioModels is a reference repository hosting mathematical models that describe the dynamic interactions of biological components at various scales. The resource provides access to over 1,200 models described in literature and over 140,000 models automatically generated from pathway resources. Most model components are cross-linked with external resources to facilitate interoperability. A large proportion of models are manually curated to ensure reproducibility of simulation results. This tutorial presents BioModels' content, features, functionality, and usage. PMID:26225232

  2. A pairwise interaction model for multivariate functional and longitudinal data

    PubMed Central

    Chiou, Jeng-Min; Müller, Hans-Georg

    2016-01-01

    Functional data vectors consisting of samples of multivariate data where each component is a random function are encountered increasingly often but have not yet been comprehensively investigated. We introduce a simple pairwise interaction model that leads to an interpretable and straightforward decomposition of multivariate functional data and of their variation into component-specific processes and pairwise interaction processes. The latter quantify the degree of pairwise interactions between the components of the functional data vectors, while the component-specific processes reflect the functional variation of a particular functional vector component that cannot be explained by the other components. Thus the proposed model provides an extension of the usual notion of a covariance or correlation matrix for multivariate vector data to functional data vectors and generates an interpretable functional interaction map. The decomposition provided by the model can also serve as a basis for subsequent analysis, such as study of the network structure of functional data vectors. The decomposition of the total variance into componentwise and interaction contributions can be quantified by an \\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{upgreek} \\usepackage{mathrsfs} \\setlength{\\oddsidemargin}{-69pt} \\begin{document} }{}$R^2$\\end{document}-like decomposition. We provide consistency results for the proposed methods and illustrate the model by applying it to sparsely sampled longitudinal data from the Baltimore Longitudinal Study of Aging, examining the relationships between body mass index and blood fats. PMID:27279664

  3. Factorized domain wall partition functions in trigonometric vertex models

    NASA Astrophysics Data System (ADS)

    Foda, O.; Wheeler, M.; Zuparic, M.

    2007-10-01

    We obtain factorized domain wall partition functions for two sets of trigonometric vertex models: (1) the N-state Deguchi Akutsu models, for N \\in \\{2, 3, 4\\} (and conjecture the result for all N>=5), and (2) the sl(r+1|s+1) Perk Schultz models, for \\{r, s \\in \\mathbb {N}\\} , where (given the symmetries of these models) the result is independent of {r,s}.

  4. Probability density function modeling for sub-powered interconnects

    NASA Astrophysics Data System (ADS)

    Pater, Flavius; Amaricǎi, Alexandru

    2016-06-01

    This paper proposes three mathematical models for reliability probability density function modeling the interconnect supplied at sub-threshold voltages: spline curve approximations, Gaussian models,and sine interpolation. The proposed analysis aims at determining the most appropriate fitting for the switching delay - probability of correct switching for sub-powered interconnects. We compare the three mathematical models with the Monte-Carlo simulations of interconnects for 45 nm CMOS technology supplied at 0.25V.

  5. Functional models of power electronic components for system studies

    NASA Technical Reports Server (NTRS)

    Tam, Kwa-Sur; Yang, Lifeng; Dravid, Narayan

    1991-01-01

    A novel approach to model power electronic circuits has been developed to facilitate simulation studies of system-level issues. The underlying concept for this approach is to develop an equivalent circuit, the functional model, that performs the same functions as the actual circuit but whose operation can be simulated by using larger time step size and the reduction in model complexity, the computation time required by a functional model is significantly shorter than that required by alternative approaches. The authors present this novel modeling approach and discuss the functional models of two major power electronic components, the DC/DC converter unit and the load converter, that are being considered by NASA for use in the Space Station Freedom electric power system. The validity of these models is established by comparing the simulation results with available experimental data and other simulation results obtained by using a more established modeling approach. The usefulness of this approach is demonstrated by incorporating these models into a power system model and simulating the system responses and interactions between components under various conditions.

  6. The Interaction of Courseware Development and Implementation: Functions and Models

    ERIC Educational Resources Information Center

    Mahler, William A.

    1976-01-01

    A discussion of how the interaction of design and content of curricular materials determine their possible applications. A review of functions and models is presented for interactive curriculum development for computer based instructional systems. (HB)

  7. Accuracy of functional surfaces on comparatively modeled protein structures

    PubMed Central

    Zhao, Jieling; Dundas, Joe; Kachalo, Sema; Ouyang, Zheng; Liang, Jie

    2012-01-01

    Identification and characterization of protein functional surfaces are important for predicting protein function, understanding enzyme mechanism, and docking small compounds to proteins. As the rapid speed of accumulation of protein sequence information far exceeds that of structures, constructing accurate models of protein functional surfaces and identify their key elements become increasingly important. A promising approach is to build comparative models from sequences using known structural templates such as those obtained from structural genome projects. Here we assess how well this approach works in modeling binding surfaces. By systematically building three-dimensional comparative models of proteins using Modeller, we determine how well functional surfaces can be accurately reproduced. We use an alpha shape based pocket algorithm to compute all pockets on the modeled structures, and conduct a large-scale computation of similarity measurements (pocket RMSD and fraction of functional atoms captured) for 26,590 modeled enzyme protein structures. Overall, we find that when the sequence fragment of the binding surfaces has more than 45% identity to that of the tempalte protein, the modeled surfaces have on average an RMSD of 0.5 Å, and contain 48% or more of the binding surface atoms, with nearly all of the important atoms in the signatures of binding pockets captured. PMID:21541664

  8. Enhancements to the SSME transfer function modeling code

    NASA Technical Reports Server (NTRS)

    Irwin, R. Dennis; Mitchell, Jerrel R.; Bartholomew, David L.; Glenn, Russell D.

    1995-01-01

    This report details the results of a one year effort by Ohio University to apply the transfer function modeling and analysis tools developed under NASA Grant NAG8-167 (Irwin, 1992), (Bartholomew, 1992) to attempt the generation of Space Shuttle Main Engine High Pressure Turbopump transfer functions from time domain data. In addition, new enhancements to the transfer function modeling codes which enhance the code functionality are presented, along with some ideas for improved modeling methods and future work. Section 2 contains a review of the analytical background used to generate transfer functions with the SSME transfer function modeling software. Section 2.1 presents the 'ratio method' developed for obtaining models of systems that are subject to single unmeasured excitation sources and have two or more measured output signals. Since most of the models developed during the investigation use the Eigensystem Realization Algorithm (ERA) for model generation, Section 2.2 presents an introduction of ERA, and Section 2.3 describes how it can be used to model spectral quantities. Section 2.4 details the Residue Identification Algorithm (RID) including the use of Constrained Least Squares (CLS) and Total Least Squares (TLS). Most of this information can be found in the report (and is repeated for convenience). Section 3 chronicles the effort of applying the SSME transfer function modeling codes to the a51p394.dat and a51p1294.dat time data files to generate transfer functions from the unmeasured input to the 129.4 degree sensor output. Included are transfer function modeling attempts using five methods. The first method is a direct application of the SSME codes to the data files and the second method uses the underlying trends in the spectral density estimates to form transfer function models with less clustering of poles and zeros than the models obtained by the direct method. In the third approach, the time data is low pass filtered prior to the modeling process in an

  9. Spin Structure Functions in a Covariant Spectator Quark Model

    SciTech Connect

    G. Ramalho, Franz Gross and M. T. Peña

    2010-12-01

    We apply the covariant spectator quark–diquark model, already probed in the description of the nucleon elastic form factors, to the calculation of the deep inelastic scattering (DIS) spin-independent and spin-dependent structure functions of the nucleon. The nucleon wave function is given by a combination of quark–diquark orbital states, corresponding to S, D and P-waves. A simple form for the quark distribution function associated to the P and D waves is tested.

  10. a Nonextensive Statistical Model for the Nucleon Structure Function

    NASA Astrophysics Data System (ADS)

    Trevisan, Luis Augusto; Mirez, Carlos

    2013-07-01

    We studied an application of nonextensive thermodynamics to describe the structure function of nucleon, in a model where the usual Fermi-Dirac and Bose-Einstein energy distribution were replaced by the equivalent functions of the q-statistical. The parameters of the model are given by an effective temperature T, the q parameter (from Tsallis statistics), and two chemical potentials given by the corresponding up (u) and down (d) quark normalizations in the nucleon.

  11. A no extensive statistical model for the nucleon structure function

    NASA Astrophysics Data System (ADS)

    Trevisan, Luis A.; Mirez, Carlos

    2013-03-01

    We studied an application of nonextensive thermodynamics to describe the structure function of nucleon, in a model where the usual Fermi-Dirac and Bose-Einstein energy distribution were replaced by the equivalent functions of the q-statistical. The parameters of the model are given by an effective temperature T, the q parameter (from Tsallis statistics), and two chemical potentials given by the corresponding up (u) and down (d) quark normalization in the nucleon.

  12. Functional linear models for association analysis of quantitative traits.

    PubMed

    Fan, Ruzong; Wang, Yifan; Mills, James L; Wilson, Alexander F; Bailey-Wilson, Joan E; Xiong, Momiao

    2013-11-01

    Functional linear models are developed in this paper for testing associations between quantitative traits and genetic variants, which can be rare variants or common variants or the combination of the two. By treating multiple genetic variants of an individual in a human population as a realization of a stochastic process, the genome of an individual in a chromosome region is a continuum of sequence data rather than discrete observations. The genome of an individual is viewed as a stochastic function that contains both linkage and linkage disequilibrium (LD) information of the genetic markers. By using techniques of functional data analysis, both fixed and mixed effect functional linear models are built to test the association between quantitative traits and genetic variants adjusting for covariates. After extensive simulation analysis, it is shown that the F-distributed tests of the proposed fixed effect functional linear models have higher power than that of sequence kernel association test (SKAT) and its optimal unified test (SKAT-O) for three scenarios in most cases: (1) the causal variants are all rare, (2) the causal variants are both rare and common, and (3) the causal variants are common. The superior performance of the fixed effect functional linear models is most likely due to its optimal utilization of both genetic linkage and LD information of multiple genetic variants in a genome and similarity among different individuals, while SKAT and SKAT-O only model the similarities and pairwise LD but do not model linkage and higher order LD information sufficiently. In addition, the proposed fixed effect models generate accurate type I error rates in simulation studies. We also show that the functional kernel score tests of the proposed mixed effect functional linear models are preferable in candidate gene analysis and small sample problems. The methods are applied to analyze three biochemical traits in data from the Trinity Students Study. PMID:24130119

  13. A no extensive statistical model for the nucleon structure function

    SciTech Connect

    Trevisan, Luis A.; Mirez, Carlos

    2013-03-25

    We studied an application of nonextensive thermodynamics to describe the structure function of nucleon, in a model where the usual Fermi-Dirac and Bose-Einstein energy distribution were replaced by the equivalent functions of the q-statistical. The parameters of the model are given by an effective temperature T, the q parameter (from Tsallis statistics), and two chemical potentials given by the corresponding up (u) and down (d) quark normalization in the nucleon.

  14. Career Exploration Program: A Composite Systematic Functional Objective Model.

    ERIC Educational Resources Information Center

    Mohamed, Othman

    The composite systematic functional objective career exploration program model integrates various career development theoretical approaches. These approaches emphasize self-concept, life values, personality, the environment, and academic achievement and training as separate functions in explaining career development. Current social development in…

  15. Green's functions for a CPn - 1 model with massless fermions

    NASA Astrophysics Data System (ADS)

    Schaposnik, F. A.

    1983-07-01

    We study the CPn - 1 model with massless fermions making a chiral change in the fermionic variables. We construct the generating functional and discuss relevant features of the theory. The factorization of a pure fermionic part shows a power law correction to the free fermion Green's function. The dynamical gauge field becomes massive and a screening phenomenon occurs. Member of CIC, Buenos Aires, Argentina

  16. ILNCSIM: improved lncRNA functional similarity calculation model.

    PubMed

    Huang, Yu-An; Chen, Xing; You, Zhu-Hong; Huang, De-Shuang; Chan, Keith C C

    2016-05-01

    Increasing observations have indicated that lncRNAs play a significant role in various critical biological processes and the development and progression of various human diseases. Constructing lncRNA functional similarity networks could benefit the development of computational models for inferring lncRNA functions and identifying lncRNA-disease associations. However, little effort has been devoted to quantifying lncRNA functional similarity. In this study, we developed an Improved LNCRNA functional SIMilarity calculation model (ILNCSIM) based on the assumption that lncRNAs with similar biological functions tend to be involved in similar diseases. The main improvement comes from the combination of the concept of information content and the hierarchical structure of disease directed acyclic graphs for disease similarity calculation. ILNCSIM was combined with the previously proposed model of Laplacian Regularized Least Squares for lncRNA-Disease Association to further evaluate its performance. As a result, new model obtained reliable performance in the leave-one-out cross validation (AUCs of 0.9316 and 0.9074 based on MNDR and Lnc2cancer databases, respectively), and 5-fold cross validation (AUCs of 0.9221 and 0.9033 for MNDR and Lnc2cancer databases), which significantly improved the prediction performance of previous models. It is anticipated that ILNCSIM could serve as an effective lncRNA function prediction model for future biomedical researches. PMID:27028993

  17. Computational models of basal-ganglia pathway functions: focus on functional neuroanatomy

    PubMed Central

    Schroll, Henning; Hamker, Fred H.

    2013-01-01

    Over the past 15 years, computational models have had a considerable impact on basal-ganglia research. Most of these models implement multiple distinct basal-ganglia pathways and assume them to fulfill different functions. As there is now a multitude of different models, it has become complex to keep track of their various, sometimes just marginally different assumptions on pathway functions. Moreover, it has become a challenge to oversee to what extent individual assumptions are corroborated or challenged by empirical data. Focusing on computational, but also considering non-computational models, we review influential concepts of pathway functions and show to what extent they are compatible with or contradict each other. Moreover, we outline how empirical evidence favors or challenges specific model assumptions and propose experiments that allow testing assumptions against each other. PMID:24416002

  18. Ab initio derivation of model energy density functionals

    NASA Astrophysics Data System (ADS)

    Dobaczewski, Jacek

    2016-08-01

    I propose a simple and manageable method that allows for deriving coupling constants of model energy density functionals (EDFs) directly from ab initio calculations performed for finite fermion systems. A proof-of-principle application allows for linking properties of finite nuclei, determined by using the nuclear nonlocal Gogny functional, to the coupling constants of the quasilocal Skyrme functional. The method does not rely on properties of infinite fermion systems but on the ab initio calculations in finite systems. It also allows for quantifying merits of different model EDFs in describing the ab initio results.

  19. Ensemble modeling with pedotransfer functions in the hydropedological context

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Uncertainty of soil water content and/or soil water flux estimates with soil water models has recently become of a particular interest in various applications. This work provides examples of using pedotransfer functions (PTFs) to build ensembles of models to characterize the uncertainty of simulatio...

  20. A Functional Model of Cortical Gyri and Sulci

    PubMed Central

    Deng, Fan; Jiang, Xi; Zhu, Dajiang; Zhang, Tuo; Li, Kaiming; Guo, Lei; Liu, Tianming

    2013-01-01

    Diffusion tensor imaging (DTI) and high angular resolution diffusion imaging (HARDI) have been broadly used in the neuroimaging field to investigate the macro-scale fiber connection patterns in the cerebral cortex. Our recent analyses of DTI and HARDI data demonstrated that gyri are connected by much denser streamline fibers than sulci. Inspired by this finding and motivated by the fact that DTI-derived fibers provide the structural substrates for functional connectivity, we hypothesize that gyri are global functional connection centers and sulci are local functional units. To test this functional model of gyri and sulci, we examined the structural and functional connectivity among the landmarks on the selected gyral/sulcal areas in the frontal/parietal lobe and in the whole cerebral cortex via multimodal DTI and resting state fMRI (R-fMRI) datasets. Our results demonstrate that functional connectivity is strong among gyri, weak among sulci, and moderate between gyri and sulci. These results suggest that gyri are functional connection centers that exchange information among remote structurally-connected gyri and neighboring sulci, while sulci communicate directly with their neighboring gyri and indirectly with other cortical regions through gyri. This functional model of gyri and sulci has been supported by a series of experiments, and provides novel perspectives on the functional architecture of the cerebral cortex. PMID:23689502

  1. Analyzing Unfavored Fragmentation Functions Using NJL-Jet Model

    SciTech Connect

    Matevosyan, Hrayr H.; Thomas, Anthony W.; Bentz, Wolfgang

    2011-10-24

    The Nambu-Jona-Lasinio (NJL)-jet model provides a sound framework for calculating the fragmentation functions in an effective chiral quark theory, where the momentum and isospin sum rules are satisfied without the introduction of ad hoc parameters. The most recent version of the model includes the fragmentation of the light and strange quarks to pions, kaons, nucleons, and antinucleons; where the effects of the production of secondary pions and kaons from the vector mesons {rho}, K* and {phi} are also calculated. The results for the model fragmentation function exhibit a qualitative agreement with the empirical parameterizations. The results also allow to test, within the model assumptions, several assumption in parametrizations of the unfavored fragmentation functions used in empirical fits to the experimental data.

  2. Phillips' Lambda function: Data summary and physical model

    NASA Astrophysics Data System (ADS)

    Irisov, V.; Plant, W.

    2016-03-01

    Measurements of Phillips' Lambda function describing the average length of breakers on the ocean per unit area at speed cb are summarized. An expression is developed that fits these data within reasonable bounds. A physical model for the Lambda function is derived based on the assumption that breaking occurs when the surface steepness exceeds a threshold value. The energy contained in the breaking region is related to the fifth power of the breaker speed, as Phillips showed, and from this the probability of finding a breaker with a speed cb may be determined from a simulation of the long-wave surface based on a linear superposition of Fourier components. This probability is directly related to the Lambda function so that a form for this function can be determined. The Lambda function so determined agrees in both shape and intensity with the fit to the measured Lambda functions.

  3. Modeling uncertainty in reservoir loss functions using fuzzy sets

    NASA Astrophysics Data System (ADS)

    Teegavarapu, Ramesh S. V.; Simonovic, Slobodan P.

    1999-09-01

    Imprecision involved in the definition of reservoir loss functions is addressed using fuzzy set theory concepts. A reservoir operation problem is solved using the concepts of fuzzy mathematical programming. Membership functions from fuzzy set theory are used to represent the decision maker's preferences in the definition of shape of loss curves. These functions are assumed to be known and are used to model the uncertainties. Linear and nonlinear optimization models are developed under fuzzy environment. A new approach is presented that involves development of compromise reservoir operating policies based on the rules from the traditional optimization models and their fuzzy equivalents while considering the preferences of the decision maker. The imprecision associated with the definition of penalty and storage zones and uncertainty in the penalty coefficients are the main issues addressed through this study. The models developed are applied to the Green Reservoir, Kentucky. Simulations are performed to evaluate the operating rules generated by the models considering the uncertainties in the loss functions. Results indicate that the reservoir operating policies are sensitive to change in the shapes of loss functions.

  4. Using computational models to relate structural and functional brain connectivity

    PubMed Central

    Hlinka, Jaroslav; Coombes, Stephen

    2012-01-01

    Modern imaging methods allow a non-invasive assessment of both structural and functional brain connectivity. This has lead to the identification of disease-related alterations affecting functional connectivity. The mechanism of how such alterations in functional connectivity arise in a structured network of interacting neural populations is as yet poorly understood. Here we use a modeling approach to explore the way in which this can arise and to highlight the important role that local population dynamics can have in shaping emergent spatial functional connectivity patterns. The local dynamics for a neural population is taken to be of the Wilson–Cowan type, whilst the structural connectivity patterns used, describing long-range anatomical connections, cover both realistic scenarios (from the CoComac database) and idealized ones that allow for more detailed theoretical study. We have calculated graph–theoretic measures of functional network topology from numerical simulations of model networks. The effect of the form of local dynamics on the observed network state is quantified by examining the correlation between structural and functional connectivity. We document a profound and systematic dependence of the simulated functional connectivity patterns on the parameters controlling the dynamics. Importantly, we show that a weakly coupled oscillator theory explaining these correlations and their variation across parameter space can be developed. This theoretical development provides a novel way to characterize the mechanisms for the breakdown of functional connectivity in diseases through changes in local dynamics. PMID:22805059

  5. Quark fragmentation functions in NJL-jet model

    NASA Astrophysics Data System (ADS)

    Bentz, Wolfgang; Matevosyan, Hrayr; Thomas, Anthony

    2014-09-01

    We report on our studies of quark fragmentation functions in the Nambu-Jona-Lasinio (NJL) - jet model. The results of Monte-Carlo simulations for the fragmentation functions to mesons and nucleons, as well as to pion and kaon pairs (dihadron fragmentation functions) are presented. The important role of intermediate vector meson resonances for those semi-inclusive deep inelastic production processes is emphasized. Our studies are very relevant for the extraction of transverse momentum dependent quark distribution functions from measured scattering cross sections. We report on our studies of quark fragmentation functions in the Nambu-Jona-Lasinio (NJL) - jet model. The results of Monte-Carlo simulations for the fragmentation functions to mesons and nucleons, as well as to pion and kaon pairs (dihadron fragmentation functions) are presented. The important role of intermediate vector meson resonances for those semi-inclusive deep inelastic production processes is emphasized. Our studies are very relevant for the extraction of transverse momentum dependent quark distribution functions from measured scattering cross sections. Supported by Grant in Aid for Scientific Research, Japanese Ministry of Education, Culture, Sports, Science and Technology, Project No. 20168769.

  6. Image-based modeling of lung structure and function

    PubMed Central

    Tawhai, Merryn H.; Lin, Ching-Long

    2010-01-01

    Current state-of-the-art in image-based modeling allows derivation of patient-specific models of the lung, lobes, airways, and pulmonary vascular trees. The application of traditional engineering analyses of fluid and structural mechanics to image-based subject-specific models has the potential to provide new insight into structure-function relationships in the individual via functional interpretation that complements imaging and experimental studies. Three major issues that are encountered in studies of air flow through the bronchial airways are the representation of airway geometry, the imposition of physiological boundary conditions, and the treatment of turbulence. Here we review some efforts to resolve each of these issues, with particular focus on image-based models that have been developed to simulate air flow from the mouth to the terminal bronchiole, and subjected to physiologically meaningful boundary conditions via image registration and soft tissue mechanics models. PMID:21105146

  7. Gravity modeling: the Jacobian function and its approximation

    NASA Astrophysics Data System (ADS)

    Strykowski, G.; Lauritsen, N. L. B.

    2012-04-01

    In mathematics, the elements of a Jacobian matrix are the first-order partial derivatives of a scalar function or a vector function with respect to another vector. In inversion theory of geophysics the elements of a Jacobian matrix are a measure of the change of the output signal caused by a local perturbation of a parameter of a given (Earth) model. The elements of a Jacobian matrix can be determined from the general Jacobian function. In gravity modeling this function consists of the "geometrical part" (related to the relative location in 3D of a field point with respect to the source element) and the "source-strength part" (related to the change of mass density of the source element). The explicit (functional) expressions for the Jacobian function can be quite complicated and depend both on the coordinates used (Cartesian, spherical, ellipsoidal) and on the mathematical parametrization of the source (e.g. the homogenous rectangular prism). In practice, and irrespective of the exact expression for the Jacobian function, its value on a computer will always be rounded to a finite number of digits. In fact, in using the exact formulas such finite representation may cause numerical instabilities. If the Jacobian function is smooth enough, it is an advantage to approximate it by a simpler function, e.g. a piecewise-polynomial, which numerically is more robust than the exact formulas and which is more suitable for the subsequent integration. In our contribution we include a whole family of the Jacobian functions which are associated with all the partial derivatives of the gravitational potential of order 0 to 2, i.e. including all the elements of the gravity gradient tensor. The quality of the support points for the subsequent polynomial approximation of the Jacobian function is ensured by using the exact prism formulas in quadruple precision. We will show some first results. Also, we will discuss how such approximated Jacobian functions can be used for large scale

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

    NASA Astrophysics Data System (ADS)

    Bolia, Pratiksh; Weiskircher, Thomas; Müller, Steffen

    2014-05-01

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

  9. REVIEW: Zebrafish: A Renewed Model System For Functional Genomics

    NASA Astrophysics Data System (ADS)

    Wen, Xiao-Yan

    2008-01-01

    In the post genome era, a major goal in molecular biology is to determine the function of the many thousands of genes present in the vertebrate genome. The zebrafish (Danio rerio) provides an almost ideal genetic model to identify the biological roles of these novel genes, in part because their embryos are transparent and develop rapidly. The zebrafish has many advantages over mouse for genome-wide mutagenesis studies, allowing for easier, cheaper and faster functional characterization of novel genes in the vertebrate genome. Many molecular research tools such as chemical mutagenesis, transgenesis, gene trapping, gene knockdown, TILLING, gene targeting, RNAi and chemical genetic screen are now available in zebrafish. Combining all the forward, reverse, and chemical genetic tools, it is expected that zebrafish will make invaluable contribution to vertebrate functional genomics in functional annotation of the genes, modeling human diseases and drug discoveries.

  10. Mining functional modules in genetic networks with decomposable graphical models.

    PubMed

    Dejori, Mathäus; Schwaighofer, Anton; Tresp, Volker; Stetter, Martin

    2004-01-01

    In recent years, graphical models have become an increasingly important tool for the structural analysis of genome-wide expression profiles at the systems level. Here we present a new graphical modelling technique, which is based on decomposable graphical models, and apply it to a set of gene expression profiles from acute lymphoblastic leukemia (ALL). The new method explains probabilistic dependencies of expression levels in terms of the concerted action of underlying genetic functional modules, which are represented as so-called "cliques" in the graph. In addition, the method uses continuous-valued (instead of discretized) expression levels, and makes no particular assumption about their probability distribution. We show that the method successfully groups members of known functional modules to cliques. Our method allows the evaluation of the importance of genes for global cellular functions based on both link count and the clique membership count. PMID:15268775

  11. Bread dough rheology: Computing with a damage function model

    NASA Astrophysics Data System (ADS)

    Tanner, Roger I.; Qi, Fuzhong; Dai, Shaocong

    2015-01-01

    We describe an improved damage function model for bread dough rheology. The model has relatively few parameters, all of which can easily be found from simple experiments. Small deformations in the linear region are described by a gel-like power-law memory function. A set of large non-reversing deformations - stress relaxation after a step of shear, steady shearing and elongation beginning from rest, and biaxial stretching, is used to test the model. With the introduction of a revised strain measure which includes a Mooney-Rivlin term, all of these motions can be well described by the damage function described in previous papers. For reversing step strains, larger amplitude oscillatory shearing and recoil reasonable predictions have been found. The numerical methods used are discussed and we give some examples.

  12. Using Lambert W function and error function to model phase change on microfluidics

    NASA Astrophysics Data System (ADS)

    Bermudez Garcia, Anderson

    2014-05-01

    Solidification and melting modeling on microfluidics are solved using Lambert W's function and error's functions. Models are formulated using the heat's diffusion equation. The generic posed case is the melting of a slab with time dependent surface temperature, having a micro or nano-fluid liquid phase. At the beginning the solid slab is at melting temperature. A slab's face is put and maintained at temperature greater than the melting limit and varying in time. Lambert W function and error function are applied via Maple to obtain the analytic solution evolution of the front of microfluidic-solid interface, it is analytically computed and slab's corresponding melting time is determined. It is expected to have analytical results to be useful for food engineering, cooking engineering, pharmaceutical engineering, nano-engineering and bio-medical engineering.

  13. Transverse momentum dependent distribution functions in the bag model

    SciTech Connect

    Harut A. Avakian; Efremov, A. V.; Schweitzer, P.; Yuan, F.

    2010-04-01

    Leading and subleading twist transverse momentum dependent parton distribution functions (TMDs) are studied in a quark model framework provided by the bag model. A complete set of relations among different TMDs is derived, and the question is discussed how model-(in)dependent such relations are. A connection of the pretzelosity distribution and quark orbital angular momentum is derived. Numerical results are presented, and applications for phenomenology discussed. In particular, it is shown that in the valence-x region the bag model supports a Gaussian Ansatz for the transverse momentum dependence of TMDs.

  14. Transverse momentum dependent distribution functions in the bag model

    SciTech Connect

    Avakian, H.; Efremov, A. V.; Schweitzer, P.; Yuan, F.

    2010-04-01

    Leading and subleading-twist transverse momentum dependent parton distribution functions (TMDs) are studied in a quark-model framework provided by the bag model. A complete set of relations among different TMDs is derived, and the question is discussed how model (in)dependent such relations are. A connection of the pretzelosity distribution and quark orbital angular momentum is derived. Numerical results are presented, and applications for phenomenology are discussed. In particular, it is shown that in the valence-x region the bag model supports a Gaussian Ansatz for the transverse momentum dependence of TMDs.

  15. The transverse momentum dependent distribution functions in the bag model

    SciTech Connect

    Avakian, Harut; Efremov, Anatoly; Schweitzer, Peter; Yuan, Feng

    2010-01-29

    Leading and subleading twist transverse momentum dependent parton distribution functions (TMDs) are studied in a quark model framework provided by the bag model. A complete set of relations among different TMDs is derived, and the question is discussed how model-(in)dependent such relations are. A connection of the pretzelosity distribution and quark orbital angular momentum is derived. Numerical results are presented, and applications for phenomenology discussed. In particular, it is shown that in the valence-x region the bag model supports a Gaussian Ansatz for the transverse momentum dependence of TMDs.

  16. A New Mixed Model Based on the Velocity Structure Function

    NASA Astrophysics Data System (ADS)

    Brun, Christophe; Friedrich, Rainer; Da Silva, Carlos B.; Métais, Olivier

    We propose a new mixed model for Large Eddy-Simulation based on the 3D spatial velocity increment. This approach blends the non-linear properties of the Increment model (Brun & Friedrich (2001)) with the eddy viscosity characteristics of the Structure Function model (Métais & Lesieur (1992)). The behaviour of this subgrid scale model is studied both via a priori tests of a plane jet at ReH=3000 and Large Eddy-Simulation of a round jet at ReD=25000. This approach allows to describe both forward and backward energy transfer encountered in transitional shear flows.

  17. Using special functions to model the propagation of airborne diseases

    NASA Astrophysics Data System (ADS)

    Bolaños, Daniela

    2014-06-01

    Some special functions of the mathematical physics are using to obtain a mathematical model of the propagation of airborne diseases. In particular we study the propagation of tuberculosis in closed rooms and we model the propagation using the error function and the Bessel function. In the model, infected individual emit pathogens to the environment and this infect others individuals who absorb it. The evolution in time of the concentration of pathogens in the environment is computed in terms of error functions. The evolution in time of the number of susceptible individuals is expressed by a differential equation that contains the error function and it is solved numerically for different parametric simulations. The evolution in time of the number of infected individuals is plotted for each numerical simulation. On the other hand, the spatial distribution of the pathogen around the source of infection is represented by the Bessel function K0. The spatial and temporal distribution of the number of infected individuals is computed and plotted for some numerical simulations. All computations were made using software Computer algebra, specifically Maple. It is expected that the analytical results that we obtained allow the design of treatment rooms and ventilation systems that reduce the risk of spread of tuberculosis.

  18. Dissecting the two models of TCR structure-function relationships.

    PubMed

    Cohn, Melvin

    2016-08-01

    There are only two comprehensive models attempting to account for the TCR structure-function relationships, referred to as the Standard or Centric model (Model I) and the Tritope model (Model II). This essay is written to analyze comparatively the two formulations of restrictive reactivity, stressing in particular the logic of each. Model I is essentially built on an analogy between the TCR and the BCR. Given a TCR with only one combining site (paratope), restrictive recognition requires that its ligand be viewed as a composite structure between the peptide and restricting element. It is this relationship that entrains a set of correlates that makes Model I untenable. Model II is predicated on the postulate that the recognition of the allele-specific determinants expressed by MHC-encoded restricting elements (R) is germline encoded and selected, whereas the recognition of peptide (P) is somatically encoded and selected. These selective pressures must operate on definable structures and this, in turn, necessitates a multiply recognitive T cell antigen receptor (TCR) with independent anti-R and anti-P paratopes that function coherently to signal restrictive reactivity. The consequences of this "two repertoire" postulate give us a concept of TCR structure quite distinct from that at present generally accepted, as well as a surprising relationship between numbers of functional TCR V gene segments and allele-specific determinants in the species. In the end, both models must deal with the relationship between the epitope-paratope interaction(s) and the signals to the T cell necessary for its differentiation and function. PMID:27114367

  19. Exact Solutions for Confined Model Systems Using Kummer Functions

    NASA Astrophysics Data System (ADS)

    Burrows, B. L.; Cohen, M.

    We treat model systems where an electron is confined in a region of space. The particular models considered have solutions which may be expressed in terms of the Kummer functions. Both standard and non-standard Kummer functions are used in these models and a comprehensive summary of the usual and exceptional Kummer functions is given. The definition of confinement is widened to treat radial confinement in any spherical shell, including the asymptotic region and cases where the electron is confined to a lower dimension. Initially we consider the theory in K dimensional space and then give particular examples in 1, 2, and 3 dimensions. A commonly treated model is the radially confined hydrogen atom in 3 dimensions with an infinite barrier on a confining sphere so that the wavefunction is identically zero on this sphere. We have extended this model to treat a more general model of spherical confinement where the derivative of the charge density is zero on the confining sphere. It is shown that the analogous models for the radial harmonic oscillator and radial constant potentials may be treated using a generic technique.

  20. Semiparametric Stochastic Modeling of the Rate Function in Longitudinal Studies

    PubMed Central

    Zhu, Bin; Taylor, Jeremy M.G.; Song, Peter X.-K.

    2011-01-01

    In longitudinal biomedical studies, there is often interest in the rate functions, which describe the functional rates of change of biomarker profiles. This paper proposes a semiparametric approach to model these functions as the realizations of stochastic processes defined by stochastic differential equations. These processes are dependent on the covariates of interest and vary around a specified parametric function. An efficient Markov chain Monte Carlo algorithm is developed for inference. The proposed method is compared with several existing methods in terms of goodness-of-fit and more importantly the ability to forecast future functional data in a simulation study. The proposed methodology is applied to prostate-specific antigen profiles for illustration. Supplementary materials for this paper are available online. PMID:22423170

  1. The Thirring-Wess model revisited: a functional integral approach

    SciTech Connect

    Belvedere, L.V. . E-mail: armflavio@if.uff.br

    2005-06-01

    We consider the Wess-Zumino-Witten theory to obtain the functional integral bosonization of the Thirring-Wess model with an arbitrary regularization parameter. Proceeding a systematic of decomposing the Bose field algebra into gauge-invariant- and gauge-non-invariant field subalgebras, we obtain the local decoupled quantum action. The generalized operator solutions for the equations of motion are reconstructed from the functional integral formalism. The isomorphism between the QED {sub 2} (QCD {sub 2}) with broken gauge symmetry by a regularization prescription and the Abelian (non-Abelian) Thirring-Wess model with a fixed bare mass for the meson field is established.

  2. Functional error modeling for uncertainty quantification in hydrogeology

    NASA Astrophysics Data System (ADS)

    Josset, L.; Ginsbourger, D.; Lunati, I.

    2015-02-01

    Approximate models (proxies) can be employed to reduce the computational costs of estimating uncertainty. The price to pay is that the approximations introduced by the proxy model can lead to a biased estimation. To avoid this problem and ensure a reliable uncertainty quantification, we propose to combine functional data analysis and machine learning to build error models that allow us to obtain an accurate prediction of the exact response without solving the exact model for all realizations. We build the relationship between proxy and exact model on a learning set of geostatistical realizations for which both exact and approximate solvers are run. Functional principal components analysis (FPCA) is used to investigate the variability in the two sets of curves and reduce the dimensionality of the problem while maximizing the retained information. Once obtained, the error model can be used to predict the exact response of any realization on the basis of the sole proxy response. This methodology is purpose-oriented as the error model is constructed directly for the quantity of interest, rather than for the state of the system. Also, the dimensionality reduction performed by FPCA allows a diagnostic of the quality of the error model to assess the informativeness of the learning set and the fidelity of the proxy to the exact model. The possibility of obtaining a prediction of the exact response for any newly generated realization suggests that the methodology can be effectively used beyond the context of uncertainty quantification, in particular for Bayesian inference and optimization.

  3. Cohesive fracture model for functionally graded fiber reinforced concrete

    SciTech Connect

    Park, Kyoungsoo; Paulino, Glaucio H.; Roesler, Jeffery

    2010-06-15

    A simple, effective, and practical constitutive model for cohesive fracture of fiber reinforced concrete is proposed by differentiating the aggregate bridging zone and the fiber bridging zone. The aggregate bridging zone is related to the total fracture energy of plain concrete, while the fiber bridging zone is associated with the difference between the total fracture energy of fiber reinforced concrete and the total fracture energy of plain concrete. The cohesive fracture model is defined by experimental fracture parameters, which are obtained through three-point bending and split tensile tests. As expected, the model describes fracture behavior of plain concrete beams. In addition, it predicts the fracture behavior of either fiber reinforced concrete beams or a combination of plain and fiber reinforced concrete functionally layered in a single beam specimen. The validated model is also applied to investigate continuously, functionally graded fiber reinforced concrete composites.

  4. Structural model updating using incomplete transfer function of strain data

    NASA Astrophysics Data System (ADS)

    Esfandiari, A.

    2014-08-01

    In this paper a model updating algorithm is presented to estimate structural parameters at the element level utilizing frequency domain representation of the strain data. Sensitivity equations for mass and stiffness parameters estimation are derived using decomposed form of the strain-based transfer functions. The rate of changes of eigenvectors and a subset of measured natural frequencies are used to assemble the sensitivity equation of the strain-based transfer function. Solution of the derived sensitivity equations through the least square method resulted in a robust parameters estimation method. Numerical examples using simulated noise polluted data of 2D truss and frame models confirm that the proposed method is able to successfully update structural models even in the presence of mass modeling errors.

  5. Cox Regression Models with Functional Covariates for Survival Data

    PubMed Central

    Gellar, Jonathan E.; Colantuoni, Elizabeth; Needham, Dale M.; Crainiceanu, Ciprian M.

    2015-01-01

    We extend the Cox proportional hazards model to cases when the exposure is a densely sampled functional process, measured at baseline. The fundamental idea is to combine penalized signal regression with methods developed for mixed effects proportional hazards models. The model is fit by maximizing the penalized partial likelihood, with smoothing parameters estimated by a likelihood-based criterion such as AIC or EPIC. The model may be extended to allow for multiple functional predictors, time varying coefficients, and missing or unequally-spaced data. Methods were inspired by and applied to a study of the association between time to death after hospital discharge and daily measures of disease severity collected in the intensive care unit, among survivors of acute respiratory distress syndrome. PMID:26441487

  6. Predicting plants -modeling traits as a function of environment

    NASA Astrophysics Data System (ADS)

    Franklin, Oskar

    2016-04-01

    A central problem in understanding and modeling vegetation dynamics is how to represent the variation in plant properties and function across different environments. Addressing this problem there is a strong trend towards trait-based approaches, where vegetation properties are functions of the distributions of functional traits rather than of species. Recently there has been enormous progress in in quantifying trait variability and its drivers and effects (Van Bodegom et al. 2012; Adier et al. 2014; Kunstler et al. 2015) based on wide ranging datasets on a small number of easily measured traits, such as specific leaf area (SLA), wood density and maximum plant height. However, plant function depends on many other traits and while the commonly measured trait data are valuable, they are not sufficient for driving predictive and mechanistic models of vegetation dynamics -especially under novel climate or management conditions. For this purpose we need a model to predict functional traits, also those not easily measured, and how they depend on the plants' environment. Here I present such a mechanistic model based on fitness concepts and focused on traits related to water and light limitation of trees, including: wood density, drought response, allocation to defense, and leaf traits. The model is able to predict observed patterns of variability in these traits in relation to growth and mortality, and their responses to a gradient of water limitation. The results demonstrate that it is possible to mechanistically predict plant traits as a function of the environment based on an eco-physiological model of plant fitness. References Adier, P.B., Salguero-Gómez, R., Compagnoni, A., Hsu, J.S., Ray-Mukherjee, J., Mbeau-Ache, C. et al. (2014). Functional traits explain variation in plant lifehistory strategies. Proc. Natl. Acad. Sci. U. S. A., 111, 740-745. Kunstler, G., Falster, D., Coomes, D.A., Hui, F., Kooyman, R.M., Laughlin, D.C. et al. (2015). Plant functional traits

  7. Model Adequacy and the Macroevolution of Angiosperm Functional Traits.

    PubMed

    Pennell, Matthew W; FitzJohn, Richard G; Cornwell, William K; Harmon, Luke J

    2015-08-01

    Making meaningful inferences from phylogenetic comparative data requires a meaningful model of trait evolution. It is thus important to determine whether the model is appropriate for the data and the question being addressed. One way to assess this is to ask whether the model provides a good statistical explanation for the variation in the data. To date, researchers have focused primarily on the explanatory power of a model relative to alternative models. Methods have been developed to assess the adequacy, or absolute explanatory power, of phylogenetic trait models, but these have been restricted to specific models or questions. Here we present a general statistical framework for assessing the adequacy of phylogenetic trait models. We use our approach to evaluate the statistical performance of commonly used trait models on 337 comparative data sets covering three key angiosperm functional traits. In general, the models we tested often provided poor statistical explanations for the evolution of these traits. This was true for many different groups and at many different scales. Whether such statistical inadequacy will qualitatively alter inferences drawn from comparative data sets will depend on the context. Regardless, assessing model adequacy can provide interesting biological insights-how and why a model fails to describe variation in a data set give us clues about what evolutionary processes may have driven trait evolution across time. PMID:26655160

  8. An integral representation of functions in gas-kinetic models

    NASA Astrophysics Data System (ADS)

    Perepelitsa, Misha

    2016-08-01

    Motivated by the theory of kinetic models in gas dynamics, we obtain an integral representation of lower semicontinuous functions on {{{R}}^d,} {d≥1}. We use the representation to study the problem of compactness of a family of the solutions of the discrete time BGK model for the compressible Euler equations. We determine sufficient conditions for strong compactness of moments of kinetic densities, in terms of the measures from their integral representations.

  9. Functional and stochastic models estimation for GNSS coordinates time series

    NASA Astrophysics Data System (ADS)

    Galera Monico, J. F.; Silva, H. A.; Marques, H. A.

    2014-12-01

    GNSS has been largely used in Geodesy and correlated areas for positioning. The position and velocity of terrestrial stations have been estimated using GNSS data based on daily solutions. So, currently it is possible to analyse the GNSS coordinates time series aiming to improve the functional and stochastic models what can help to understand geodynamic phenomena. Several sources of errors are mathematically modelled or estimated in the GNSS data processing to obtain precise coordinates what in general is carried out by using scientific software. However, due to impossibility to model all errors some kind of noises can remain contaminating the coordinate time series, especially those related with seasonal effects. The noise affecting GNSS coordinate time series can be composed by white and coloured noises what can be characterized from Variance Component Estimation technique through Least Square Method. The methodology to characterize noise in GNSS coordinates time series will be presented in this paper so that the estimated variance can be used to reconstruct stochastic and functional models of the times series providing a more realistic and reliable modeling of time series. Experiments were carried out by using GNSS time series for few Brazilian stations considering almost ten years of daily solutions. The noises components were characterized as white, flicker and random walk noise and applied to estimate the times series functional model considering semiannual and annual effects. The results show that the adoption of an adequate stochastic model considering the noises variances of time series can produce more realistic and reliable functional model for GNSS coordinate time series. Such results may be applied in the context of the realization of the Brazilian Geodetic System.

  10. Bifurcations in a discrete time model composed of Beverton-Holt function and Ricker function.

    PubMed

    Shang, Jin; Li, Bingtuan; Barnard, Michael R

    2015-05-01

    We provide rigorous analysis for a discrete-time model composed of the Ricker function and Beverton-Holt function. This model was proposed by Lewis and Li [Bull. Math. Biol. 74 (2012) 2383-2402] in the study of a population in which reproduction occurs at a discrete instant of time whereas death and competition take place continuously during the season. We show analytically that there exists a period-doubling bifurcation curve in the model. The bifurcation curve divides the parameter space into the region of stability and the region of instability. We demonstrate through numerical bifurcation diagrams that the regions of periodic cycles are intermixed with the regions of chaos. We also study the global stability of the model. PMID:25765885

  11. Quasirelativistic quasilocal finite wave-function collapse model

    SciTech Connect

    Pearle, Philip

    2005-03-01

    A Markovian wave-function collapse model is presented where the collapse-inducing operator, constructed from quantum fields, is a manifestly covariant generalization of the mass-density operator utilized in the nonrelativistic continuous spontaneous localization (CSL) wave-function collapse model. However, the model is not Lorentz invariant because two such operators do not commute at spacelike separation, i.e., the time-ordering operation in one Lorentz frame, the 'preferred' frame, is not the time-ordering operation in another frame. However, the characteristic spacelike distance over which the commutator decays is the particle's Compton wavelength so, since the commutator rapidly gets quite small, the model is 'almost' relativistic. This quasirelativistic CSL (QRCSL) model is completely finite: unlike previous, relativistic, models, it has no (infinite) energy production from the vacuum state. QRCSL calculations are given of the collapse rate for a single free particle in a superposition of spatially separated packets, and of the energy production rate for any number of free particles: these reduce to the CSL rates if the particle's Compton wavelength is small compared to the model's distance parameter. One motivation for QRCSL is the realization that previous relativistic models entail excitation of nuclear states which exceeds that of experiment, whereas QRCSL does not; an example is given involving quadrupole excitation of the {sup 74}Ge nucleus.

  12. The functional neuroanatomy of bipolar disorder: a consensus model

    PubMed Central

    Strakowski, Stephen M; Adler, Caleb M; Almeida, Jorge; Altshuler, Lori L; Blumberg, Hilary P; Chang, Kiki D; DelBello, Melissa P; Frangou, Sophia; McIntosh, Andrew; Phillips, Mary L; Sussman, Jessika E; Townsend, Jennifer D

    2013-01-01

    Objectives Functional neuroimaging methods have proliferated in recent years, such that functional magnetic resonance imaging, in particular, is now widely used to study bipolar disorder. However, discrepant findings are common. A workgroup was organized by the Department of Psychiatry, University of Cincinnati (Cincinnati, OH, USA) to develop a consensus functional neuroanatomic model of bipolar I disorder based upon the participants’ work as well as that of others. Methods Representatives from several leading bipolar disorder neuroimaging groups were organized to present an overview of their areas of expertise as well as focused reviews of existing data. The workgroup then developed a consensus model of the functional neuroanatomy of bipolar disorder based upon these data. Results Among the participants, a general consensus emerged that bipolar I disorder arises from abnormalities in the structure and function of key emotional control networks in the human brain. Namely, disruption in early development (e.g., white matter connectivity, prefrontal pruning) within brain networks that modulate emotional behavior leads to decreased connectivity among ventral prefrontal networks and limbic brain regions, especially amygdala. This developmental failure to establish healthy ventral prefrontal–limbic modulation underlies the onset of mania and ultimately, with progressive changes throughout these networks over time and with affective episodes, a bipolar course of illness. Conclusions This model provides a potential substrate to guide future investigations and areas needing additional focus are identified. PMID:22631617

  13. A new tropospheric mapping function based on ECMWF models

    NASA Astrophysics Data System (ADS)

    Biancale, Richard; Dupuy, Stephanie; Soudarin, Laurent

    The tropospheric propagation delay of Earth-satellite tracking data (from electromagnetic or optical signals) is generally corrected in two steps: 1) computing the zenithal dry and wet delays at the station, 2) applying a mapping function to pull them down at the elevation needed. Considering that zenithal delays can be well computed from ground pressure, temperature and humidity data through hydrostatic theory, or can be integrated from ECMWF multiple layer models (for instance), or at least can be adjusted in orbit processing, we turned our attention more specifically to the validity of the mapping function. Starting on one hand from a few maps of the ECMWF meteorological model of pressure, temperature and humidity available each 6h in 91 isobaric layers we reconstructed first the dry and wet tropospheric delays at each grid point for several azimuth and elevation angles. On the other hand we computed the same delays from a Marini-type mapping function based on the integrated zenithal delays computed themselves from the same ECMWF models. An adequacy was searched between both approaches which led us to adjust all coefficients of the dry and wet mapping functions. We propose here to describe our approach and to present the dry and wet mapping functions obtained with some tests with real data.

  14. Laguerre-Gauss basis functions in observer models

    NASA Astrophysics Data System (ADS)

    Burgess, Arthur E.

    2003-05-01

    Observer models based on linear classifiers with basis functions (channels) are useful for evaluation of detection performance with medical images. They allow spatial domain calculations with a covariance matrix of tractable size. The term "channelized Fisher-Hotelling observer" will be used here. It is also called the "channelized Hotelling observer" model. There are an infinite number of basis function (channel ) sets that could be employed. Examples of channel sets that have been used include: difference of Gaussian (DOG) filters, difference of Mesa (DOM) filters and Laguerre-Gauss (LG) basis functions. Another option, sums of LG functions (LGS), will also be presented here. This set has the advantage of having no DC response. The effect of the number of images used to estimate model observer performance will be described, for both filtered 1/f3 noise and GE digital mammogram backgrounds. Finite sample image sets introduce both bias and variance to the estimate. The results presented here agree with previous work on linear classifiers. The LGS basis set gives a small but statistically significant reduction in bias. However, this may not be of much practical benefit. Finally, the effect of varying the number of basis functions included in the set will be addressed. It was found that four LG bases or three LGS bases are adequate.

  15. Adding ecosystem function to agent-based land use models

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objective of this paper is to examine issues in the inclusion of simulations of ecosystem functions in agent-based models of land use decision-making. The reasons for incorporating these simulations include local interests in land fertility and global interests in carbon sequestration. Biogeoche...

  16. Subgrid spatial variability of soil hydraulic functions for hydrological modelling

    NASA Astrophysics Data System (ADS)

    Kreye, Phillip; Meon, Günter

    2016-07-01

    State-of-the-art hydrological applications require a process-based, spatially distributed hydrological model. Runoff characteristics are demanded to be well reproduced by the model. Despite that, the model should be able to describe the processes at a subcatchment scale in a physically credible way. The objective of this study is to present a robust procedure to generate various sets of parameterisations of soil hydraulic functions for the description of soil heterogeneity on a subgrid scale. Relations between Rosetta-generated values of saturated hydraulic conductivity (Ks) and van Genuchten's parameters of soil hydraulic functions were statistically analysed. An universal function that is valid for the complete bandwidth of Ks values could not be found. After concentrating on natural texture classes, strong correlations were identified for all parameters. The obtained regression results were used to parameterise sets of hydraulic functions for each soil class. The methodology presented in this study is applicable on a wide range of spatial scales and does not need input data from field studies. The developments were implemented into a hydrological modelling system.

  17. Verbal Neuropsychological Functions in Aphasia: An Integrative Model

    ERIC Educational Resources Information Center

    Vigliecca, Nora Silvana; Báez, Sandra

    2015-01-01

    A theoretical framework which considers the verbal functions of the brain under a multivariate and comprehensive cognitive model was statistically analyzed. A confirmatory factor analysis was performed to verify whether some recognized aphasia constructs can be hierarchically integrated as latent factors from a homogenously verbal test. The Brief…

  18. The fundamental structure function of oscillator noise models

    NASA Technical Reports Server (NTRS)

    Greenhall, C. A.

    1983-01-01

    Continuous-time models of oscillator phase noise x(t) usually have stationary nth differences, for some n. The covariance structure of such a model can be characterized in the time domain by the structure function: D sub n (t;gamma sub 1, gamma sub 2) = E delta (n) sub gamma sub 1 x(s+t) delta(n) sub gamma sub 2 x (s). Although formulas for the special case D sub 2 (0;gamma,gamma) (the Allan variance times 2 gamma(2)) exist for power-law spectral models, certain estimation problems require a more complete knowledge of (0). Exhibited is a much simpler function of one time variable, D(t), from which (0) can easily be obtained from the spectral density by uncomplicated integrations. Believing that D(t) is the simplest function of time that holds the same information as (0), D(t) is called the fundamental structure function. D(t) is computed for several power-law spectral models. Two examples are D(t) = K/t/(3) for random walk FM, D(t) = Kt(2) 1n/t/ for flicker FM. Then, to demonstrate its use, a BASIC program is given that computes means and variances of two Allan variance estimators, one of which incorporates a method of frequency drift estimation and removal.

  19. An Analytic Function of Lunar Surface Temperature for Exospheric Modeling

    NASA Technical Reports Server (NTRS)

    Hurley, Dana M.; Sarantos, Menelaos; Grava, Cesare; Williams, Jean-Pierre; Retherford, Kurt D.; Siegler, Matthew; Greenhagen, Benjamin; Paige, David

    2014-01-01

    We present an analytic expression to represent the lunar surface temperature as a function of Sun-state latitude and local time. The approximation represents neither topographical features nor compositional effects and therefore does not change as a function of selenographic latitude and longitude. The function reproduces the surface temperature measured by Diviner to within +/-10 K at 72% of grid points for dayside solar zenith angles of less than 80, and at 98% of grid points for nightside solar zenith angles greater than 100. The analytic function is least accurate at the terminator, where there is a strong gradient in the temperature, and the polar regions. Topographic features have a larger effect on the actual temperature near the terminator than at other solar zenith angles. For exospheric modeling the effects of topography on the thermal model can be approximated by using an effective longitude for determining the temperature. This effective longitude is randomly redistributed with 1 sigma of 4.5deg. The resulting ''roughened'' analytical model well represents the statistical dispersion in the Diviner data and is expected to be generally useful for future models of lunar surface temperature, especially those implemented within exospheric simulations that address questions of volatile transport.

  20. A Multi-Level Model of Moral Functioning Revisited

    ERIC Educational Resources Information Center

    Reed, Don Collins

    2009-01-01

    The model of moral functioning scaffolded in the 2008 "JME" Special Issue is here revisited in response to three papers criticising that volume. As guest editor of that Special Issue I have formulated the main body of this response, concerning the dynamic systems approach to moral development, the problem of moral relativism and the role of…

  1. An Adaptive Complex Network Model for Brain Functional Networks

    PubMed Central

    Gomez Portillo, Ignacio J.; Gleiser, Pablo M.

    2009-01-01

    Brain functional networks are graph representations of activity in the brain, where the vertices represent anatomical regions and the edges their functional connectivity. These networks present a robust small world topological structure, characterized by highly integrated modules connected sparsely by long range links. Recent studies showed that other topological properties such as the degree distribution and the presence (or absence) of a hierarchical structure are not robust, and show different intriguing behaviors. In order to understand the basic ingredients necessary for the emergence of these complex network structures we present an adaptive complex network model for human brain functional networks. The microscopic units of the model are dynamical nodes that represent active regions of the brain, whose interaction gives rise to complex network structures. The links between the nodes are chosen following an adaptive algorithm that establishes connections between dynamical elements with similar internal states. We show that the model is able to describe topological characteristics of human brain networks obtained from functional magnetic resonance imaging studies. In particular, when the dynamical rules of the model allow for integrated processing over the entire network scale-free non-hierarchical networks with well defined communities emerge. On the other hand, when the dynamical rules restrict the information to a local neighborhood, communities cluster together into larger ones, giving rise to a hierarchical structure, with a truncated power law degree distribution. PMID:19738902

  2. Functional Nonlinear Mixed Effects Models For Longitudinal Image Data

    PubMed Central

    Luo, Xinchao; Zhu, Lixing; Kong, Linglong; Zhu, Hongtu

    2015-01-01

    Motivated by studying large-scale longitudinal image data, we propose a novel functional nonlinear mixed effects modeling (FN-MEM) framework to model the nonlinear spatial-temporal growth patterns of brain structure and function and their association with covariates of interest (e.g., time or diagnostic status). Our FNMEM explicitly quantifies a random nonlinear association map of individual trajectories. We develop an efficient estimation method to estimate the nonlinear growth function and the covariance operator of the spatial-temporal process. We propose a global test and a simultaneous confidence band for some specific growth patterns. We conduct Monte Carlo simulation to examine the finite-sample performance of the proposed procedures. We apply FNMEM to investigate the spatial-temporal dynamics of white-matter fiber skeletons in a national database for autism research. Our FNMEM may provide a valuable tool for charting the developmental trajectories of various neuropsychiatric and neurodegenerative disorders. PMID:26213453

  3. OFMTutor: An operator function model intelligent tutoring system

    NASA Technical Reports Server (NTRS)

    Jones, Patricia M.

    1989-01-01

    The design, implementation, and evaluation of an Operator Function Model intelligent tutoring system (OFMTutor) is presented. OFMTutor is intended to provide intelligent tutoring in the context of complex dynamic systems for which an operator function model (OFM) can be constructed. The human operator's role in such complex, dynamic, and highly automated systems is that of a supervisory controller whose primary responsibilities are routine monitoring and fine-tuning of system parameters and occasional compensation for system abnormalities. The automated systems must support the human operator. One potentially useful form of support is the use of intelligent tutoring systems to teach the operator about the system and how to function within that system. Previous research on intelligent tutoring systems (ITS) is considered. The proposed design for OFMTutor is presented, and an experimental evaluation is described.

  4. Systemic Modeling of Biological Functions in Consideration of Physiome Project

    NASA Astrophysics Data System (ADS)

    Minamitani, Haruyuki

    Emerging of the physiome project provides various influences on the medical, biological and pharmaceutical development. In this paper, as an example of physiome research, neural network model analysis providing the conduction mechanisms of pain and tactile sensations was presented, and the functional relations between neural activities of the network cells and stimulus intensity applied on the peripheral receptive fields were described. The modeling presented here is based on the various assumptions made by the results of physiological and anatomical studies reported in the literature. The functional activities of spinothalamic and thalamocortical cells show a good agreement with the physiological and psychophysical functions of somatosensory system that are very instructive for covering the gap between physiologically and psychophysically aspects of pain and tactile sensation.

  5. Development on electromagnetic impedance function modeling and its estimation

    SciTech Connect

    Sutarno, D.

    2015-09-30

    Today the Electromagnetic methods such as magnetotellurics (MT) and controlled sources audio MT (CSAMT) is used in a broad variety of applications. Its usefulness in poor seismic areas and its negligible environmental impact are integral parts of effective exploration at minimum cost. As exploration was forced into more difficult areas, the importance of MT and CSAMT, in conjunction with other techniques, has tended to grow continuously. However, there are obviously important and difficult problems remaining to be solved concerning our ability to collect process and interpret MT as well as CSAMT in complex 3D structural environments. This talk aim at reviewing and discussing the recent development on MT as well as CSAMT impedance functions modeling, and also some improvements on estimation procedures for the corresponding impedance functions. In MT impedance modeling, research efforts focus on developing numerical method for computing the impedance functions of three dimensionally (3-D) earth resistivity models. On that reason, 3-D finite elements numerical modeling for the impedances is developed based on edge element method. Whereas, in the CSAMT case, the efforts were focused to accomplish the non-plane wave problem in the corresponding impedance functions. Concerning estimation of MT and CSAMT impedance functions, researches were focused on improving quality of the estimates. On that objective, non-linear regression approach based on the robust M-estimators and the Hilbert transform operating on the causal transfer functions, were used to dealing with outliers (abnormal data) which are frequently superimposed on a normal ambient MT as well as CSAMT noise fields. As validated, the proposed MT impedance modeling method gives acceptable results for standard three dimensional resistivity models. Whilst, the full solution based modeling that accommodate the non-plane wave effect for CSAMT impedances is applied for all measurement zones, including near-, transition

  6. Development on electromagnetic impedance function modeling and its estimation

    NASA Astrophysics Data System (ADS)

    Sutarno, D.

    2015-09-01

    Today the Electromagnetic methods such as magnetotellurics (MT) and controlled sources audio MT (CSAMT) is used in a broad variety of applications. Its usefulness in poor seismic areas and its negligible environmental impact are integral parts of effective exploration at minimum cost. As exploration was forced into more difficult areas, the importance of MT and CSAMT, in conjunction with other techniques, has tended to grow continuously. However, there are obviously important and difficult problems remaining to be solved concerning our ability to collect process and interpret MT as well as CSAMT in complex 3D structural environments. This talk aim at reviewing and discussing the recent development on MT as well as CSAMT impedance functions modeling, and also some improvements on estimation procedures for the corresponding impedance functions. In MT impedance modeling, research efforts focus on developing numerical method for computing the impedance functions of three dimensionally (3-D) earth resistivity models. On that reason, 3-D finite elements numerical modeling for the impedances is developed based on edge element method. Whereas, in the CSAMT case, the efforts were focused to accomplish the non-plane wave problem in the corresponding impedance functions. Concerning estimation of MT and CSAMT impedance functions, researches were focused on improving quality of the estimates. On that objective, non-linear regression approach based on the robust M-estimators and the Hilbert transform operating on the causal transfer functions, were used to dealing with outliers (abnormal data) which are frequently superimposed on a normal ambient MT as well as CSAMT noise fields. As validated, the proposed MT impedance modeling method gives acceptable results for standard three dimensional resistivity models. Whilst, the full solution based modeling that accommodate the non-plane wave effect for CSAMT impedances is applied for all measurement zones, including near-, transition

  7. Developing a Causal Model from Liver Function Test Data

    NASA Astrophysics Data System (ADS)

    Inada, Masanori; Terano, Takao

    As Active Mining is a new concept among data mining and/or knowledge discovery in databases communities, in order to validate the effectiveness, it is important to carry out empirical studies using practical data. Based on the concept of Active User Reaction, this paper develops a causal model from liver function test data in a medical domain. To develop the model, we have set a problem to predict the values of ICG (indocyanine green) test from given observation data and experts' background knowledge. We therefore employ a framework of meta-learning and structural equation modeling. In this paper meta-learning means learning about mined results from multiple data-mining techniques. Structural equation modeling enables us to describe flexible models from background knowledge. The construction of the causal model contains two phases: meta-learning and the model building. The meta-learning phase utilizes both the linear regression and the neural network as data mining techniques, then examines the predictability on the given data set. Mining models are n-folded learned from the training data set. Each of the prediction accuracy of the mining models is compared using with the testing data. On the model building phase, we use structural equation modeling to develop a causal model based on results of meta-learning and background knowledge. We again compare the accuracy of the causal model with each of the mining models. Consequently we have developed the causal model, which is comprehensible and have good predictive performance, via the meta-learning phase. Through the empirical study, we have got the conclusion that the framework of meta-learning is effective in data mining in a difficult medical domain.

  8. Optimal hemodynamic response model for functional near-infrared spectroscopy

    PubMed Central

    Kamran, Muhammad A.; Jeong, Myung Yung; Mannan, Malik M. N.

    2015-01-01

    Functional near-infrared spectroscopy (fNIRS) is an emerging non-invasive brain imaging technique and measures brain activities by means of near-infrared light of 650–950 nm wavelengths. The cortical hemodynamic response (HR) differs in attributes at different brain regions and on repetition of trials, even if the experimental paradigm is kept exactly the same. Therefore, an HR model that can estimate such variations in the response is the objective of this research. The canonical hemodynamic response function (cHRF) is modeled by two Gamma functions with six unknown parameters (four of them to model the shape and other two to scale and baseline respectively). The HRF model is supposed to be a linear combination of HRF, baseline, and physiological noises (amplitudes and frequencies of physiological noises are supposed to be unknown). An objective function is developed as a square of the residuals with constraints on 12 free parameters. The formulated problem is solved by using an iterative optimization algorithm to estimate the unknown parameters in the model. Inter-subject variations in HRF and physiological noises have been estimated for better cortical functional maps. The accuracy of the algorithm has been verified using 10 real and 15 simulated data sets. Ten healthy subjects participated in the experiment and their HRF for finger-tapping tasks have been estimated and analyzed. The statistical significance of the estimated activity strength parameters has been verified by employing statistical analysis (i.e., t-value > tcritical and p-value < 0.05). PMID:26136668

  9. Analytical Model for Thermal Elastoplastic Stresses of Functionally Graded Materials

    SciTech Connect

    Zhai, P. C.; Chen, G.; Liu, L. S.; Fang, C.; Zhang, Q. J.

    2008-02-15

    A modification analytical model is presented for the thermal elastoplastic stresses of functionally graded materials subjected to thermal loading. The presented model follows the analytical scheme presented by Y. L. Shen and S. Suresh [6]. In the present model, the functionally graded materials are considered as multilayered materials. Each layer consists of metal and ceramic with different volume fraction. The ceramic layer and the FGM interlayers are considered as elastic brittle materials. The metal layer is considered as elastic-perfectly plastic ductile materials. Closed-form solutions for different characteristic temperature for thermal loading are presented as a function of the structure geometries and the thermomechanical properties of the materials. A main advance of the present model is that the possibility of the initial and spread of plasticity from the two sides of the ductile layers taken into account. Comparing the analytical results with the results from the finite element analysis, the thermal stresses and deformation from the present model are in good agreement with the numerical ones.

  10. A Comparison of Functional Models for Use in the Function-Failure Design Method

    NASA Technical Reports Server (NTRS)

    Stock, Michael E.; Stone, Robert B.; Tumer, Irem Y.

    2006-01-01

    When failure analysis and prevention, guided by historical design knowledge, are coupled with product design at its conception, shorter design cycles are possible. By decreasing the design time of a product in this manner, design costs are reduced and the product will better suit the customer s needs. Prior work indicates that similar failure modes occur with products (or components) with similar functionality. To capitalize on this finding, a knowledge base of historical failure information linked to functionality is assembled for use by designers. One possible use for this knowledge base is within the Elemental Function-Failure Design Method (EFDM). This design methodology and failure analysis tool begins at conceptual design and keeps the designer cognizant of failures that are likely to occur based on the product s functionality. The EFDM offers potential improvement over current failure analysis methods, such as FMEA, FMECA, and Fault Tree Analysis, because it can be implemented hand in hand with other conceptual design steps and carried throughout a product s design cycle. These other failure analysis methods can only truly be effective after a physical design has been completed. The EFDM however is only as good as the knowledge base that it draws from, and therefore it is of utmost importance to develop a knowledge base that will be suitable for use across a wide spectrum of products. One fundamental question that arises in using the EFDM is: At what level of detail should functional descriptions of components be encoded? This paper explores two approaches to populating a knowledge base with actual failure occurrence information from Bell 206 helicopters. Functional models expressed at various levels of detail are investigated to determine the necessary detail for an applicable knowledge base that can be used by designers in both new designs as well as redesigns. High level and more detailed functional descriptions are derived for each failed component based

  11. Identifying Model-Based Reconfiguration Goals through Functional Deficiencies

    NASA Technical Reports Server (NTRS)

    Benazera, Emmanuel; Trave-Massuyes, Louise

    2004-01-01

    Model-based diagnosis is now advanced to the point autonomous systems face some uncertain and faulty situations with success. The next step toward more autonomy is to have the system recovering itself after faults occur, a process known as model-based reconfiguration. After faults occur, given a prediction of the nominal behavior of the system and the result of the diagnosis operation, this paper details how to automatically determine the functional deficiencies of the system. These deficiencies are characterized in the case of uncertain state estimates. A methodology is then presented to determine the reconfiguration goals based on the deficiencies. Finally, a recovery process interleaves planning and model predictive control to restore the functionalities in prioritized order.

  12. A Method of EC Model Implementation Using Web Service Functions

    NASA Astrophysics Data System (ADS)

    Kurihara, Jun; Koizumi, Hisao; Ishikawa, Toshiyuki; Dasai, Takashi

    In recent years, advances in computer and communication technology and the associated rapid increase in the number of Internet users are encouraging advances in Electronic Commerce (EC). Business models of EC are being actively developed by many different enterprises and engineers, and implemented in many kinds of fields. Meanwhile Web services that reuse remote components over the Internet are drawing attention. Web services are based on SOAP/WSDL/UDDI and are given an important position as the infrastructure of the EC systems. The article analyzes the functions and structures of various business models, establishing the patterns of their distinctive and common features, and proposes a method of determining the implementation specifications of business models utilizing these patterns and Web service functions. This method has been applied to a parts purchasing system, which is a typical pattern of the B to B (Business to Business) EC applications. The article also discusses the results of evaluating this prototype system.

  13. Future of Plant Functional Types in Terrestrial Biosphere Models

    NASA Astrophysics Data System (ADS)

    Wullschleger, S. D.; Euskirchen, E. S.; Iversen, C. M.; Rogers, A.; Serbin, S.

    2015-12-01

    Earth system models describe the physical, chemical, and biological processes that govern our global climate. While it is difficult to single out one component as being more important than another in these sophisticated models, terrestrial vegetation is a critical player in the biogeochemical and biophysical dynamics of the Earth system. There is much debate, however, as to how plant diversity and function should be represented in these models. Plant functional types (PFTs) have been adopted by modelers to represent broad groupings of plant species that share similar characteristics (e.g. growth form) and roles (e.g. photosynthetic pathway) in ecosystem function. In this review the PFT concept is traced from its origin in the early 1800s to its current use in regional and global dynamic vegetation models (DVMs). Special attention is given to the representation and parameterization of PFTs and to validation and benchmarking of predicted patterns of vegetation distribution in high-latitude ecosystems. These ecosystems are sensitive to changing climate and thus provide a useful test case for model-based simulations of past, current, and future distribution of vegetation. Models that incorporate the PFT concept predict many of the emerging patterns of vegetation change in tundra and boreal forests, given known processes of tree mortality, treeline migration, and shrub expansion. However, representation of above- and especially belowground traits for specific PFTs continues to be problematic. Potential solutions include developing trait databases and replacing fixed parameters for PFTs with formulations based on trait co-variance and empirical trait-environment relationships. Surprisingly, despite being important to land-atmosphere interactions of carbon, water, and energy, PFTs such as moss and lichen are largely absent from DVMs. Close collaboration among those involved in modelling with the disciplines of taxonomy, biogeography, ecology, and remote sensing will be

  14. Linking geophysics and soil function modelling - two examples

    NASA Astrophysics Data System (ADS)

    Krüger, J.; Franko, U.; Werban, U.; Dietrich, P.; Behrens, T.; Schmidt, K.; Fank, J.; Kroulik, M.

    2011-12-01

    iSOIL - "Interactions between soil related sciences - Linking geophysics, soil science and digital soil mapping" is a Collaborative Project (Grant Agreement number 211386) co-funded by the Research DG of the European Commission within the RTD activities of the FP7 Thematic Priority Environment. The iSOIL project aims at reliable mapping of soil properties and soil functions with various methods including geophysical, spectroscopic and monitoring techniques. The general procedure contains three steps (i) geophysical monitoring, (ii) generation of soil property maps and (iii) process modelling. The objective of this work is to demonstrate the methodological procedure on two different examples. Example A focuses on the turnover conditions for soil organic matter (SOM) since many soil functions in a direct or indirect way depend on SOM and SOM depletion is amongst the worst soil threats. Example B deals with the dynamics of soil water and the direct influence on crop biomass production. The applied CANDY model (Franko et al. 1995) was developed to describe dynamics of soil organic matter and mineral nitrogen as well as soil water and temperature. The new module PLUS extends CANDY to simulate crop biomass production based on environmental influences (Krüger et al. 2011). The methodological procedure of example A illustrates a model application for a field site in the Czech Republic using generated soil maps from combined geophysical data. Modelling requires a complete set of soil parameters. Combining measured soil properties and data of geophysical measurements (electrical conductivity and gamma spectrometry) is the basis for digital soil mapping which provided data about clay, silt and sand as well as SOC content. With these data pedotransfer functions produce detailed soil input data (e.g. bulk and particle density, field capacity, wilting point, saturated conductivity) for the rooted soil profile. CANDY calculated different indicators for SOM and gave hints about

  15. Model updating using correlation analysis of strain frequency response function

    NASA Astrophysics Data System (ADS)

    Guo, Ning; Yang, Zhichun; Jia, You; Wang, Le

    2016-03-01

    A method is proposed to modify the structural parameters of a dynamic finite element (FE) model by using the correlation analysis for strain frequency response function (SFRF). Sensitivity analysis of correlation coefficients is used to establish the linear algebraic equations for model updating. In order to improve the accuracy of updated model, the regularization technique is used to solve the ill-posed problem in model updating procedure. Finally, a numerical study and a model updating experiment are performed to verify the feasibility and robustness of the proposed method. The results show that the updated SFRFs and experimental SFRFs agree well, especially in resonance regions. Meanwhile, the proposed method has good robustness to noise ability and remains good feasibility even the number of measurement locations reduced significantly.

  16. Improving nonlinear modeling capabilities of functional link adaptive filters.

    PubMed

    Comminiello, Danilo; Scarpiniti, Michele; Scardapane, Simone; Parisi, Raffaele; Uncini, Aurelio

    2015-09-01

    The functional link adaptive filter (FLAF) represents an effective solution for online nonlinear modeling problems. In this paper, we take into account a FLAF-based architecture, which separates the adaptation of linear and nonlinear elements, and we focus on the nonlinear branch to improve the modeling performance. In particular, we propose a new model that involves an adaptive combination of filters downstream of the nonlinear expansion. Such combination leads to a cooperative behavior of the whole architecture, thus yielding a performance improvement, particularly in the presence of strong nonlinearities. An advanced architecture is also proposed involving the adaptive combination of multiple filters on the nonlinear branch. The proposed models are assessed in different nonlinear modeling problems, in which their effectiveness and capabilities are shown. PMID:26057613

  17. Radial Basis Function Neural Network-based PID model for functional electrical stimulation system control.

    PubMed

    Cheng, Longlong; Zhang, Guangju; Wan, Baikun; Hao, Linlin; Qi, Hongzhi; Ming, Dong

    2009-01-01

    Functional electrical stimulation (FES) has been widely used in the area of neural engineering. It utilizes electrical current to activate nerves innervating extremities affected by paralysis. An effective combination of a traditional PID controller and a neural network, being capable of nonlinear expression and adaptive learning property, supply a more reliable approach to construct FES controller that help the paraplegia complete the action they want. A FES system tuned by Radial Basis Function (RBF) Neural Network-based Proportional-Integral-Derivative (PID) model was designed to control the knee joint according to the desired trajectory through stimulation of lower limbs muscles in this paper. Experiment result shows that the FES system with RBF Neural Network-based PID model get a better performance when tracking the preset trajectory of knee angle comparing with the system adjusted by Ziegler- Nichols tuning PID model. PMID:19964991

  18. Reducing equifinality of hydrological models by integrating Functional Streamflow Disaggregation

    NASA Astrophysics Data System (ADS)

    Lüdtke, Stefan; Apel, Heiko; Nied, Manuela; Carl, Peter; Merz, Bruno

    2014-05-01

    A universal problem of the calibration of hydrological models is the equifinality of different parameter sets derived from the calibration of models against total runoff values. This is an intrinsic problem stemming from the quality of the calibration data and the simplified process representation by the model. However, discharge data contains additional information which can be extracted by signal processing methods. An analysis specifically developed for the disaggregation of runoff time series into flow components is the Functional Streamflow Disaggregation (FSD; Carl & Behrendt, 2008). This method is used in the calibration of an implementation of the hydrological model SWIM in a medium sized watershed in Thailand. FSD is applied to disaggregate the discharge time series into three flow components which are interpreted as base flow, inter-flow and surface runoff. In addition to total runoff, the model is calibrated against these three components in a modified GLUE analysis, with the aim to identify structural model deficiencies, assess the internal process representation and to tackle equifinality. We developed a model dependent (MDA) approach calibrating the model runoff components against the FSD components, and a model independent (MIA) approach comparing the FSD of the model results and the FSD of calibration data. The results indicate, that the decomposition provides valuable information for the calibration. Particularly MDA highlights and discards a number of standard GLUE behavioural models underestimating the contribution of soil water to river discharge. Both, MDA and MIA yield to a reduction of the parameter ranges by a factor up to 3 in comparison to standard GLUE. Based on these results, we conclude that the developed calibration approach is able to reduce the equifinality of hydrological model parameterizations. The effect on the uncertainty of the model predictions is strongest by applying MDA and shows only minor reductions for MIA. Besides

  19. Functional requirements of a mathematical model of the heart.

    PubMed

    Palladino, Joseph L; Noordergraaf, Abraham

    2009-01-01

    Functional descriptions of the heart, especially the left ventricle, are often based on the measured variables pressure and ventricular outflow, embodied as a time-varying elastance. The fundamental difficulty of describing the mechanical properties of the heart with a time-varying elastance function that is set a priori is described. As an alternative, a new functional model of the heart is presented, which characterizes the ventricle's contractile state with parameters, rather than variables. Each chamber is treated as a pressure generator that is time and volume dependent. The heart's complex dynamics develop from a single equation based on the formation and relaxation of crossbridge bonds. This equation permits the calculation of ventricular elastance via E(v) = partial differentialp(v)/ partial differentialV(v). This heart model is defined independently from load properties, and ventricular elastance is dynamic and reflects changing numbers of crossbridge bonds. In this paper, the functionality of this new heart model is presented via computed work loops that demonstrate the Frank-Starling mechanism and the effects of preload, the effects of afterload, inotropic changes, and varied heart rate, as well as the interdependence of these effects. Results suggest the origin of the equivalent of Hill's force-velocity relation in the ventricle. PMID:19964370

  20. Trends in stratospheric ozone profiles using functional mixed models

    NASA Astrophysics Data System (ADS)

    Park, A. Y.; Guillas, S.; Petropavlovskikh, I.

    2013-05-01

    This paper is devoted to the modeling of altitude-dependent patterns of ozone variations over time. Umkher ozone profiles (quarter of Umkehr layer) from 1978 to 2011 are investigated at two locations: Boulder (USA) and Arosa (Switzerland). The study consists of two statistical stages. First we approximate ozone profiles employing an appropriate basis. To capture primary modes of ozone variations without losing essential information, a functional principal component analysis is performed as it penalizes roughness of the function and smooths excessive variations in the shape of the ozone profiles. As a result, data driven basis functions are obtained. Secondly we estimate the effects of covariates - month, year (trend), quasi biennial oscillation, the Solar cycle, arctic oscillation and the El Niño/Southern Oscillation cycle - on the principal component scores of ozone profiles over time using generalized additive models. The effects are smooth functions of the covariates, and are represented by knot-based regression cubic splines. Finally we employ generalized additive mixed effects models incorporating a more complex error structure that reflects the observed seasonality in the data. The analysis provides more accurate estimates of influences and trends, together with enhanced uncertainty quantification. We are able to capture fine variations in the time evolution of the profiles such as the semi-annual oscillation. We conclude by showing the trends by altitude over Boulder. The strongly declining trends over 2003-2011 for altitudes of 32-64 hPa show that stratospheric ozone is not yet fully recovering.

  1. Prostaglandin signaling suppresses beneficial microglial function in Alzheimer's disease models.

    PubMed

    Johansson, Jenny U; Woodling, Nathaniel S; Wang, Qian; Panchal, Maharshi; Liang, Xibin; Trueba-Saiz, Angel; Brown, Holden D; Mhatre, Siddhita D; Loui, Taylor; Andreasson, Katrin I

    2015-01-01

    Microglia, the innate immune cells of the CNS, perform critical inflammatory and noninflammatory functions that maintain normal neural function. For example, microglia clear misfolded proteins, elaborate trophic factors, and regulate and terminate toxic inflammation. In Alzheimer's disease (AD), however, beneficial microglial functions become impaired, accelerating synaptic and neuronal loss. Better understanding of the molecular mechanisms that contribute to microglial dysfunction is an important objective for identifying potential strategies to delay progression to AD. The inflammatory cyclooxygenase/prostaglandin E2 (COX/PGE2) pathway has been implicated in preclinical AD development, both in human epidemiology studies and in transgenic rodent models of AD. Here, we evaluated murine models that recapitulate microglial responses to Aβ peptides and determined that microglia-specific deletion of the gene encoding the PGE2 receptor EP2 restores microglial chemotaxis and Aβ clearance, suppresses toxic inflammation, increases cytoprotective insulin-like growth factor 1 (IGF1) signaling, and prevents synaptic injury and memory deficits. Our findings indicate that EP2 signaling suppresses beneficial microglia functions that falter during AD development and suggest that inhibition of the COX/PGE2/EP2 immune pathway has potential as a strategy to restore healthy microglial function and prevent progression to AD. PMID:25485684

  2. Zebrafish models for the functional genomics of neurogenetic disorders.

    PubMed

    Kabashi, Edor; Brustein, Edna; Champagne, Nathalie; Drapeau, Pierre

    2011-03-01

    In this review, we consider recent work using zebrafish to validate and study the functional consequences of mutations of human genes implicated in a broad range of degenerative and developmental disorders of the brain and spinal cord. Also we present technical considerations for those wishing to study their own genes of interest by taking advantage of this easily manipulated and clinically relevant model organism. Zebrafish permit mutational analyses of genetic function (gain or loss of function) and the rapid validation of human variants as pathological mutations. In particular, neural degeneration can be characterized at genetic, cellular, functional, and behavioral levels. Zebrafish have been used to knock down or express mutations in zebrafish homologs of human genes and to directly express human genes bearing mutations related to neurodegenerative disorders such as spinal muscular atrophy, ataxia, hereditary spastic paraplegia, amyotrophic lateral sclerosis (ALS), epilepsy, Huntington's disease, Parkinson's disease, fronto-temporal dementia, and Alzheimer's disease. More recently, we have been using zebrafish to validate mutations of synaptic genes discovered by large-scale genomic approaches in developmental disorders such as autism, schizophrenia, and non-syndromic mental retardation. Advances in zebrafish genetics such as multigenic analyses and chemical genetics now offer a unique potential for disease research. Thus, zebrafish hold much promise for advancing the functional genomics of human diseases, the understanding of the genetics and cell biology of degenerative and developmental disorders, and the discovery of therapeutics. This article is part of a Special Issue entitled Zebrafish Models of Neurological Diseases. PMID:20887784

  3. System identification and model reduction using modulating function techniques

    NASA Technical Reports Server (NTRS)

    Shen, Yan

    1993-01-01

    Weighted least squares (WLS) and adaptive weighted least squares (AWLS) algorithms are initiated for continuous-time system identification using Fourier type modulating function techniques. Two stochastic signal models are examined using the mean square properties of the stochastic calculus: an equation error signal model with white noise residuals, and a more realistic white measurement noise signal model. The covariance matrices in each model are shown to be banded and sparse, and a joint likelihood cost function is developed which links the real and imaginary parts of the modulated quantities. The superior performance of above algorithms is demonstrated by comparing them with the LS/MFT and popular predicting error method (PEM) through 200 Monte Carlo simulations. A model reduction problem is formulated with the AWLS/MFT algorithm, and comparisons are made via six examples with a variety of model reduction techniques, including the well-known balanced realization method. Here the AWLS/MFT algorithm manifests higher accuracy in almost all cases, and exhibits its unique flexibility and versatility. Armed with this model reduction, the AWLS/MFT algorithm is extended into MIMO transfer function system identification problems. The impact due to the discrepancy in bandwidths and gains among subsystem is explored through five examples. Finally, as a comprehensive application, the stability derivatives of the longitudinal and lateral dynamics of an F-18 aircraft are identified using physical flight data provided by NASA. A pole-constrained SIMO and MIMO AWLS/MFT algorithm is devised and analyzed. Monte Carlo simulations illustrate its high-noise rejecting properties. Utilizing the flight data, comparisons among different MFT algorithms are tabulated and the AWLS is found to be strongly favored in almost all facets.

  4. Regional TEC dynamic modeling based on Slepian functions

    NASA Astrophysics Data System (ADS)

    Sharifi, Mohammad Ali; Farzaneh, Saeed

    2015-09-01

    In this work, the three-dimensional state of the ionosphere has been estimated by integrating the spherical Slepian harmonic function and Kalman filter. The spherical Slepian harmonic functions have been used to establish the observation equations because of their properties in local modeling. Spherical harmonics are poor choices to represent or analyze geophysical processes without perfect global coverage but the Slepian functions afford spatial and spectral selectivity. The Kalman filter has been utilized to perform the parameter estimation due to its suitable properties in processing the GPS measurements in the real-time mode. The proposed model has been applied to the real data obtained from the ground-based GPS observations across some portion of the IGS network in Europe. Results have been compared with the estimated TECs by the CODE, ESA, IGS centers and IRI-2012 model. The results indicated that the proposed model which takes advantage of the Slepian basis and Kalman filter is efficient and allows for the generation of the near-real-time regional TEC map.

  5. A Review of Modeling Pedagogies: Pedagogical Functions, Discursive Acts, and Technology in Modeling Instruction

    ERIC Educational Resources Information Center

    Campbell, Todd; Oh, Phil Seok; Maughn, Milo; Kiriazis, Nick; Zuwallack, Rebecca

    2015-01-01

    The current review examined modeling literature in top science education journals to better understand the pedagogical functions of modeling instruction reported over the last decade. Additionally, the review sought to understand the extent to which different modeling pedagogies were employed, the discursive acts that were identified as important,…

  6. Generation of saturation functions for simulation models of carbonate reservoirs

    NASA Astrophysics Data System (ADS)

    Huang, Qingfeng

    A rock type is the unit of rock deposited under similar conditions, which went through similar diagenetic processes, producing analogous rock fabric, with distinct set of pore types, and pore throat size distribution, having specific range of porosity and permeability. Rock typing can generally be used as a guide to assign petrophysical characteristics to different zones for detailed reservoir characterization, modeling and simulation, which provide valid frames for reservoir development. It is often assumed that conventional rock types are capable of assigning multiphase flow characteristics, such as capillary pressure and relative permeability to the cells of dynamic simulation models. However, these conventional rock types, or static reservoir rock types (SRRT) fail to capture the actual variability of capillary pressure and relative permeability, due to lack of representation of wettability difference at different elevation above the free water level (FWL) in carbonate reservoirs, especially in the highly heterogeneous reservoirs. This should be resolved through dynamic reservoir rock types (DRRT), in which wettability effect is imposed on the SRRTs to generate saturation functions for simulation models. This research studies Ghedan's comprehensive DRRT model7, and proposes a modified Ghedan's model. First, the defined static rock types are sub-divided into sub-static rock types based on porosity frequency. Second, three curve-fitting programs are coded to generate the related saturation-height functions. These are the modified Ghedan-Okuyiga equation, Cuddy function and Power Law function. Developed from Ghedan-Okuyiga function113, the recommended modified Ghedan-Okuyiga function has been proposed with saturation and implicit porosity as a function of height above FWL in the transition zone. Third, each sub-static rock type is divided into a number of DRRTs by determining the capillary pressure and relative permeability curves in the oil zone from gas

  7. Photonic encryption : modeling and functional analysis of all optical logic.

    SciTech Connect

    Tang, Jason D.; Schroeppel, Richard Crabtree; Robertson, Perry J.

    2004-10-01

    With the build-out of large transport networks utilizing optical technologies, more and more capacity is being made available. Innovations in Dense Wave Division Multiplexing (DWDM) and the elimination of optical-electrical-optical conversions have brought on advances in communication speeds as we move into 10 Gigabit Ethernet and above. Of course, there is a need to encrypt data on these optical links as the data traverses public and private network backbones. Unfortunately, as the communications infrastructure becomes increasingly optical, advances in encryption (done electronically) have failed to keep up. This project examines the use of optical logic for implementing encryption in the photonic domain to achieve the requisite encryption rates. This paper documents the innovations and advances of work first detailed in 'Photonic Encryption using All Optical Logic,' [1]. A discussion of underlying concepts can be found in SAND2003-4474. In order to realize photonic encryption designs, technology developed for electrical logic circuits must be translated to the photonic regime. This paper examines S-SEED devices and how discrete logic elements can be interconnected and cascaded to form an optical circuit. Because there is no known software that can model these devices at a circuit level, the functionality of S-SEED devices in an optical circuit was modeled in PSpice. PSpice allows modeling of the macro characteristics of the devices in context of a logic element as opposed to device level computational modeling. By representing light intensity as voltage, 'black box' models are generated that accurately represent the intensity response and logic levels in both technologies. By modeling the behavior at the systems level, one can incorporate systems design tools and a simulation environment to aid in the overall functional design. Each black box model takes certain parameters (reflectance, intensity, input response), and models the optical ripple and time delay

  8. Four-point Green functions in the Schwinger model

    NASA Astrophysics Data System (ADS)

    Radożycki, Tomasz; Namysłowski, Józef M.

    1999-03-01

    The evaluation of the four-point Green functions in the 1+1 Schwinger model is presented both in momentum and coordinate space representations. The crucial role in our calculations is played by two Ward identities: (i) the standard one and (ii) the chiral one. We demonstrate how the infinite set of Dyson-Schwinger equations is simplified, and is so reduced that a given n-point Green function is expressed only through itself and lower ones. For the four-point Green function, with two bosonic and two fermionic external ``legs,'' a compact solution is given both in momentum and coordinate space representations. For the four-fermion Green function a self-consistent equation is written down in the momentum representation and a concrete solution is given in the coordinate space. This exact solution is further analyzed and we show that it contains a pole corresponding to the Schwinger boson. All detailed considerations given for various four-point Green functions are easily generizable to higher functions.

  9. Coupled vibro-acoustic model updating using frequency response functions

    NASA Astrophysics Data System (ADS)

    Nehete, D. V.; Modak, S. V.; Gupta, K.

    2016-03-01

    Interior noise in cavities of motorized vehicles is of increasing significance due to the lightweight design of these structures. Accurate coupled vibro-acoustic FE models of such cavities are required so as to allow a reliable design and analysis. It is, however, experienced that the vibro-acoustic predictions using these models do not often correlate acceptably well with the experimental measurements and hence require model updating. Both the structural and the acoustic parameters addressing the stiffness as well as the damping modeling inaccuracies need to be considered simultaneously in the model updating framework in order to obtain an accurate estimate of these parameters. It is also noted that the acoustic absorption properties are generally frequency dependent. This makes use of modal data based methods for updating vibro-acoustic FE models difficult. In view of this, the present paper proposes a method based on vibro-acoustic frequency response functions that allow updating of a coupled FE model by considering simultaneously the parameters associated with both the structural as well as the acoustic model of the cavity. The effectiveness of the proposed method is demonstrated through numerical studies on a 3D rectangular box cavity with a flexible plate. Updating parameters related to the material property, stiffness of joints between the plate and the rectangular cavity and the properties of absorbing surfaces of the acoustic cavity are considered. The robustness of the method under presence of noise is also studied.

  10. Hubbard operator density functional theory for Fermionic lattice models

    NASA Astrophysics Data System (ADS)

    Cheng, Zhengqian; Marianetti, Chris

    We formulate an effective action as a functional of Hubbard operator densities whose stationary point delivers all local static information of the interacting lattice model. Using the variational principle, we get a self-consistent equation for Hubbard operator densities. The computational cost of our approach is set by diagonalizing the local Fock space. We apply our method to the one and two band Hubbard model (including crystal field and on-site exchange) in infinite dimensions where the exact solution is known. Excellent agreement is obtained for the one-band model. In the two-band model, good agreement is obtained in the metallic region of the phase diagram in addition to the metal-insulator transition. While our approach does not address frequency dependent observables, it has a negligible computational cost as compared to dynamical mean field theory and could be highly applicable in the context total energies of strongly correlated materials and molecules.

  11. Computation of Schenberg response function by using finite element modelling

    NASA Astrophysics Data System (ADS)

    Frajuca, C.; Bortoli, F. S.; Magalhaes, N. S.

    2016-05-01

    Schenberg is a detector of gravitational waves resonant mass type, with a central frequency of operation of 3200 Hz. Transducers located on the surface of the resonating sphere, according to a distribution half-dodecahedron, are used to monitor a strain amplitude. The development of mechanical impedance matchers that act by increasing the coupling of the transducers with the sphere is a major challenge because of the high frequency and small in size. The objective of this work is to study the Schenberg response function obtained by finite element modeling (FEM). Finnaly, the result is compared with the result of the simplified model for mass spring type system modeling verifying if that is suitable for the determination of sensitivity detector, as the conclusion the both modeling give the same results.

  12. Adding ecosystem function to agent-based land use models

    PubMed Central

    Yadav, V.; Del Grosso, S.J.; Parton, W.J.; Malanson, G.P.

    2015-01-01

    The objective of this paper is to examine issues in the inclusion of simulations of ecosystem functions in agent-based models of land use decision-making. The reasons for incorporating these simulations include local interests in land fertility and global interests in carbon sequestration. Biogeochemical models are needed in order to calculate such fluxes. The Century model is described with particular attention to the land use choices that it can encompass. When Century is applied to a land use problem the combinatorial choices lead to a potentially unmanageable number of simulation runs. Century is also parameter-intensive. Three ways of including Century output in agent-based models, ranging from separately calculated look-up tables to agents running Century within the simulation, are presented. The latter may be most efficient, but it moves the computing costs to where they are most problematic. Concern for computing costs should not be a roadblock. PMID:26191077

  13. Pelagic functional group modeling: Progress, challenges and prospects

    NASA Astrophysics Data System (ADS)

    Hood, Raleigh R.; Laws, Edward A.; Armstrong, Robert A.; Bates, Nicholas R.; Brown, Christopher W.; Carlson, Craig A.; Chai, Fei; Doney, Scott C.; Falkowski, Paul G.; Feely, Richard A.; Friedrichs, Marjorie A. M.; Landry, Michael R.; Keith Moore, J.; Nelson, David M.; Richardson, Tammi L.; Salihoglu, Baris; Schartau, Markus; Toole, Dierdre A.; Wiggert, Jerry D.

    2006-03-01

    In this paper, we review the state of the art and major challenges in current efforts to incorporate biogeochemical functional groups into models that can be applied on basin-wide and global scales, with an emphasis on models that might ultimately be used to predict how biogeochemical cycles in the ocean will respond to global warming. We define the term "biogeochemical functional group" to refer to groups of organisms that mediate specific chemical reactions in the ocean. Thus, according to this definition, "functional groups" have no phylogenetic meaning—these are composed of many different species with common biogeochemical functions. Substantial progress has been made in the last decade toward quantifying the rates of these various functions and understanding the factors that control them. For some of these groups, we have developed fairly sophisticated models that incorporate this understanding, e.g. for diazotrophs (e.g. Trichodesmium), silica producers (diatoms) and calcifiers (e.g. coccolithophorids and specifically Emiliania huxleyi). However, current representations of nitrogen fixation and calcification are incomplete, i.e., based primarily upon models of Trichodesmium and E. huxleyi, respectively, and many important functional groups have not yet been considered in open-ocean biogeochemical models. Progress has been made over the last decade in efforts to simulate dimethylsulfide (DMS) production and cycling (i.e., by dinoflagellates and prymnesiophytes) and denitrification, but these efforts are still in their infancy, and many significant problems remain. One obvious gap is that virtually all functional group modeling efforts have focused on autotrophic microbes, while higher trophic levels have been completely ignored. It appears that in some cases (e.g., calcification), incorporating higher trophic levels may be essential not only for representing a particular biogeochemical reaction, but also for modeling export. Another serious problem is our

  14. Functional genomics of Plasmodium falciparum using metabolic modelling and analysis

    PubMed Central

    Oppenheim, Rebecca D.; Soldati-Favre, Dominique; Hatzimanikatis, Vassily

    2013-01-01

    Plasmodium falciparum is an obligate intracellular parasite and the leading cause of severe malaria responsible for tremendous morbidity and mortality particularly in sub-Saharan Africa. Successful completion of the P. falciparum genome sequencing project in 2002 provided a comprehensive foundation for functional genomic studies on this pathogen in the following decade. Over this period, a large spectrum of experimental approaches has been deployed to improve and expand the scope of functionally annotated genes. Meanwhile, rapidly evolving methods of systems biology have also begun to contribute to a more global understanding of various aspects of the biology and pathogenesis of malaria. Herein we provide an overview on metabolic modelling, which has the capability to integrate information from functional genomics studies in P. falciparum and guide future malaria research efforts towards the identification of novel candidate drug targets. PMID:23793264

  15. Quark-jet model for transverse momentum dependent fragmentation functions

    NASA Astrophysics Data System (ADS)

    Bentz, W.; Kotzinian, A.; Matevosyan, H. H.; Ninomiya, Y.; Thomas, A. W.; Yazaki, K.

    2016-08-01

    In order to describe the hadronization of polarized quarks, we discuss an extension of the quark-jet model to transverse momentum dependent fragmentation functions. The description is based on a product ansatz, where each factor in the product represents one of the transverse momentum dependent splitting functions, which can be calculated by using effective quark theories. The resulting integral equations and sum rules are discussed in detail for the case of inclusive pion production. In particular, we demonstrate that the three-dimensional momentum sum rules are satisfied naturally in this transverse momentum dependent quark-jet model. Our results are well suited for numerical calculations in effective quark theories and can be implemented in Monte Carlo simulations of polarized quark hadronization processes.

  16. Rationalisation of distribution functions for models of nanoparticle magnetism

    NASA Astrophysics Data System (ADS)

    El-Hilo, M.; Chantrell, R. W.

    2012-08-01

    A formalism is presented which reconciles the use of different distribution functions of particle diameter in analytical models of the magnetic properties of nanoparticle systems. For the lognormal distribution a transformation is derived which shows that a distribution of volume fraction transforms into a lognormal distribution of particle number albeit with a modified median diameter. This transformation resolves an apparent discrepancy reported in Tournus and Tamion [Journal of Magnetism and Magnetic Materials 323 (2011) 1118].

  17. Quark and gluon decay functions in QCD and recombination model

    SciTech Connect

    Change, V.; Hwa, R.C.

    1980-04-01

    Inclusive longitudinal-momentum distributions of pions in jets initiated by quarks and gluons are determined in perturbative QCD and recombination model. The quark and antiquark joint distributions in jets are first calculated in the leading-order approximation at high Q/sup 2/. Gluons in the jets are completely converted to quark pairs. From the overall distribution q anti q pairs with definite quantum numbers then recombine to form pions. The recombination function for the process is well determined in the valon model. No adjustable parameters are involved in these calculations, and no data at low Q/sup 2/ are used as phenomenological input. The result for the quark decay functions can be compared with data on e/sup +/e/sup -/ annihilation, and the agreement is very good in both shape and normalization. Predictions for the gluon decay functions are presented, but they cannot yet be checked by experiments. The x and Q/sup 2/ dependences of both types of decay functions have been parametrized in simple form suitable for use in theoretical and experimental applications. 17 figures, 1 table.

  18. Calibration of two complex ecosystem models with different likelihood functions

    NASA Astrophysics Data System (ADS)

    Hidy, Dóra; Haszpra, László; Pintér, Krisztina; Nagy, Zoltán; Barcza, Zoltán

    2014-05-01

    The biosphere is a sensitive carbon reservoir. Terrestrial ecosystems were approximately carbon neutral during the past centuries, but they became net carbon sinks due to climate change induced environmental change and associated CO2 fertilization effect of the atmosphere. Model studies and measurements indicate that the biospheric carbon sink can saturate in the future due to ongoing climate change which can act as a positive feedback. Robustness of carbon cycle models is a key issue when trying to choose the appropriate model for decision support. The input parameters of the process-based models are decisive regarding the model output. At the same time there are several input parameters for which accurate values are hard to obtain directly from experiments or no local measurements are available. Due to the uncertainty associated with the unknown model parameters significant bias can be experienced if the model is used to simulate the carbon and nitrogen cycle components of different ecosystems. In order to improve model performance the unknown model parameters has to be estimated. We developed a multi-objective, two-step calibration method based on Bayesian approach in order to estimate the unknown parameters of PaSim and Biome-BGC models. Biome-BGC and PaSim are a widely used biogeochemical models that simulate the storage and flux of water, carbon, and nitrogen between the ecosystem and the atmosphere, and within the components of the terrestrial ecosystems (in this research the developed version of Biome-BGC is used which is referred as BBGC MuSo). Both models were calibrated regardless the simulated processes and type of model parameters. The calibration procedure is based on the comparison of measured data with simulated results via calculating a likelihood function (degree of goodness-of-fit between simulated and measured data). In our research different likelihood function formulations were used in order to examine the effect of the different model

  19. Simple and complex models for studying muscle function in walking.

    PubMed

    Pandy, Marcus G

    2003-09-29

    While simple models can be helpful in identifying basic features of muscle function, more complex models are needed to discern the functional roles of specific muscles in movement. In this paper, two very different models of walking, one simple and one complex, are used to study how muscle forces, gravitational forces and centrifugal forces (i.e. forces arising from motion of the joints) combine to produce the pattern of force exerted on the ground. Both the simple model and the complex one predict that muscles contribute significantly to the ground force pattern generated in walking; indeed, both models show that muscle action is responsible for the appearance of the two peaks in the vertical force. The simple model, an inverted double pendulum, suggests further that the first and second peaks are due to net extensor muscle moments exerted about the knee and ankle, respectively. Analyses based on a much more complex, muscle-actuated simulation of walking are in general agreement with these results; however, the more detailed model also reveals that both the hip extensor and hip abductor muscles contribute significantly to vertical motion of the centre of mass, and therefore to the appearance of the first peak in the vertical ground force, in early single-leg stance. This discrepancy in the model predictions is most probably explained by the difference in model complexity. First, movements of the upper body in the sagittal plane are not represented properly in the double-pendulum model, which may explain the anomalous result obtained for the contribution of a hip-extensor torque to the vertical ground force. Second, the double-pendulum model incorporates only three of the six major elements of walking, whereas the complex model is fully 3D and incorporates all six gait determinants. In particular, pelvic list occurs primarily in the frontal plane, so there is the potential for this mechanism to contribute significantly to the vertical ground force, especially

  20. Optimizing experimental design for comparing models of brain function.

    PubMed

    Daunizeau, Jean; Preuschoff, Kerstin; Friston, Karl; Stephan, Klaas

    2011-11-01

    This article presents the first attempt to formalize the optimization of experimental design with the aim of comparing models of brain function based on neuroimaging data. We demonstrate our approach in the context of Dynamic Causal Modelling (DCM), which relates experimental manipulations to observed network dynamics (via hidden neuronal states) and provides an inference framework for selecting among candidate models. Here, we show how to optimize the sensitivity of model selection by choosing among experimental designs according to their respective model selection accuracy. Using Bayesian decision theory, we (i) derive the Laplace-Chernoff risk for model selection, (ii) disclose its relationship with classical design optimality criteria and (iii) assess its sensitivity to basic modelling assumptions. We then evaluate the approach when identifying brain networks using DCM. Monte-Carlo simulations and empirical analyses of fMRI data from a simple bimanual motor task in humans serve to demonstrate the relationship between network identification and the optimal experimental design. For example, we show that deciding whether there is a feedback connection requires shorter epoch durations, relative to asking whether there is experimentally induced change in a connection that is known to be present. Finally, we discuss limitations and potential extensions of this work. PMID:22125485

  1. Linking geophysics and soil function modelling - biomass production

    NASA Astrophysics Data System (ADS)

    Krüger, J.; Franko, U.; Werban, U.; Fank, J.

    2012-04-01

    The iSOIL project aims at reliable mapping of soil properties and soil functions with various methods including geophysical, spectroscopic and monitoring techniques. The general procedure contains three steps (i) geophysical monitoring, (ii) generation of soil property maps and (iii) process modelling. The objective of this work is to demonstrate the mentioned procedure with a focus on process modelling. It deals with the dynamics of soil water and the direct influence on crop biomass production. The new module PLUS extends CANDY to simulate crop biomass production based on environmental influences. A soil function modelling with an adapted model parameterisation based on data of ground penetration radar (GPR) and conductivity (EM38) was realized. This study shows an approach to handle heterogeneity of soil properties with geophysical data used for biomass production modelling. The Austrian field site Wagna is characterised by highly heterogenic soil with fluvioglacial gravel sediments. The variation of thickness of topsoil above a sandy subsoil with gravels strongly influences the soil water balance. EM38, mounted on a mobile platform, enables to rapidly scan large areas whereas GPR requires a greater logistical effort. However, GPR can detect exact soil horizon depth between topsoil and subsoil, the combination of both results in a detailed large scale soil map. The combined plot-specific GPR and field site EM38 measurements extends the soil input data and improves the model performance of CANDY PLUS for plant biomass production (Krüger et al. 2011). The example demonstrates how geophysics provides a surplus of data for agroecosystem modelling which identifies and contributes alternative options for agricultural management decisions. iSOIL - "Interactions between soil related sciences - Linking geophysics, soil science and digital soil mapping" is a Collaborative Project (Grant Agreement number 211386) co-funded by the Research DG of the European Commission

  2. Modeling phytoplankton community in reservoirs. A comparison between taxonomic and functional groups-based models.

    PubMed

    Di Maggio, Jimena; Fernández, Carolina; Parodi, Elisa R; Diaz, M Soledad; Estrada, Vanina

    2016-01-01

    In this paper we address the formulation of two mechanistic water quality models that differ in the way the phytoplankton community is described. We carry out parameter estimation subject to differential-algebraic constraints and validation for each model and comparison between models performance. The first approach aggregates phytoplankton species based on their phylogenetic characteristics (Taxonomic group model) and the second one, on their morpho-functional properties following Reynolds' classification (Functional group model). The latter approach takes into account tolerance and sensitivity to environmental conditions. The constrained parameter estimation problems are formulated within an equation oriented framework, with a maximum likelihood objective function. The study site is Paso de las Piedras Reservoir (Argentina), which supplies water for consumption for 450,000 population. Numerical results show that phytoplankton morpho-functional groups more closely represent each species growth requirements within the group. Each model performance is quantitatively assessed by three diagnostic measures. Parameter estimation results for seasonal dynamics of the phytoplankton community and main biogeochemical variables for a one-year time horizon are presented and compared for both models, showing the functional group model enhanced performance. Finally, we explore increasing nutrient loading scenarios and predict their effect on phytoplankton dynamics throughout a one-year time horizon. PMID:26406877

  3. Electrophysiological Modeling of Cardiac Ventricular Function: From Cell to Organ

    PubMed Central

    Winslow, R. L.; Scollan, D. F.; Holmes, A.; Yung, C. K.; Zhang, J.; Jafri, M. S.

    2005-01-01

    Three topics of importance to modeling the integrative function of the heart are reviewed. The first is modeling of the ventricular myocyte. Emphasis is placed on excitation-contraction coupling and intracellular Ca2+ handling, and the interpretation of experimental data regarding interval-force relationships. Second, data on use of diffusion tensor magnetic resonance (DTMR) imaging for measuring the anatomical structure of the cardiac ventricles are presented. A method for the semi-automated reconstruction of the ventricles using a combination of gradient recalled acquisition in the steady state (GRASS) and DTMR images is described. Third, we describe how these anatomically and biophysically based models of the cardiac ventricles can be implemented on parallel computers. PMID:11701509

  4. Eigen model with general fitness functions and degradation rates

    NASA Astrophysics Data System (ADS)

    Hu, Chin-Kun; Saakian, David B.

    2006-03-01

    We present an exact solution of Eigen's quasispecies model with a general degradation rate and fitness functions, including a square root decrease of fitness with increasing Hamming distance from the wild type. The found behavior of the model with a degradation rate is analogous to a viral quasi-species under attack by the immune system of the host. Our exact solutions also revise the known results of neutral networks in quasispecies theory. To explain the existence of mutants with large Hamming distances from the wild type, we propose three different modifications of the Eigen model: mutation landscape, multiple adjacent mutations, and frequency-dependent fitness in which the steady state solution shows a multi-center behavior.

  5. Mouse Models for the Evaluation of Osteocyte Functions

    PubMed Central

    2014-01-01

    Osteocytes establish an extensive intracellular and extracellular communication system via gap junction-coupled cell processes and canaliculi, through which cell processes pass throughout bone, and the communication system is extended to osteoblasts on the bone surface. To examine the osteocyte function, several mouse models were established. To ablate osteocytes, osteocytes death was induced by diphtheria toxin. However, any types of osteocyte death result in necrosis, because dying osteocytes are not phagocytosed by scavengers. After the rupture of cytoplasmic membrane, immunostimulatory molecules are released from lacunae to bone surface through canaliculi, and stimulate macrophages. The stimulated macrophages produce interleukin (IL)-1, IL-6, and tumor necrosis factor-alpha (TNF-α), which are the most important proinflammatory cytokines triggering inflammatory bone loss. Therefore, the osteocyte ablation results in necrosis-induced severe osteoporosis. In conditional knockout mice of gap junction protein alpha-1 (GJA1), which encodes connexin 43 in Gap junction, using dentin matrix protein 1 (DMP1) Cre transgenic mice, osteocyte apoptosis and enhanced bone resorption occur, because extracellular communication is intact. Overexpression of Bcl-2 in osteoblasts using 2.3 kb collagen type I alpha1 (COL1A1) promoter causes osteocyte apoptosis due to the severe reduction in the number of osteocyte processes, resulting in the disruption of both intracellular and extracellular communication systems. This mouse model unraveled osteocyte functions. Osteocytes negatively regulate bone mass by stimulating osteoclastogenesis and inhibiting osteoblast function in physiological condition. Osteocytes are responsible for bone loss in unloaded condition, and osteocytes augment their functions by further stimulating osteoclastogenesis and further inhibiting osteoblast function, at least partly, through the upregulation of receptor activator of nuclear factor-kappa B ligand

  6. Functional GI disorders: from animal models to drug development

    PubMed Central

    Mayer, E A; Bradesi, S; Chang, L; Spiegel, B M R; Bueller, J A; Naliboff, B D

    2014-01-01

    Despite considerable efforts by academic researchers and by the pharmaceutical industry, the development of novel pharmacological treatments for irritable bowel syndrome (IBS) and other functional gastrointestinal (GI) disorders has been slow and disappointing. The traditional approach to identifying and evaluating novel drugs for these symptom-based syndromes has relied on a fairly standard algorithm using animal models, experimental medicine models and clinical trials. In the current article, the empirical basis for this process is reviewed, focusing on the utility of the assessment of visceral hypersensitivity and GI transit, in both animals and humans, as well as the predictive validity of preclinical and clinical models of IBS for identifying successful treatments for IBS symptoms and IBS-related quality of life impairment. A review of published evidence suggests that abdominal pain, defecation-related symptoms (urgency, straining) and psychological factors all contribute to overall symptom severity and to health-related quality of life. Correlations between readouts obtained in preclinical and clinical models and respective symptoms are small, and the ability to predict drug effectiveness for specific as well as for global IBS symptoms is limited. One possible drug development algorithm is proposed which focuses on pharmacological imaging approaches in both preclinical and clinical models, with decreased emphasis on evaluating compounds in symptom-related animal models, and more rapid screening of promising candidate compounds in man. PMID:17965064

  7. On point spread function modelling: towards optimal interpolation

    NASA Astrophysics Data System (ADS)

    Bergé, Joel; Price, Sedona; Amara, Adam; Rhodes, Jason

    2012-01-01

    Point spread function (PSF) modelling is a central part of any astronomy data analysis relying on measuring the shapes of objects. It is especially crucial for weak gravitational lensing, in order to beat down systematics and allow one to reach the full potential of weak lensing in measuring dark energy. A PSF modelling pipeline is made of two main steps: the first one is to assess its shape on stars, and the second is to interpolate it at any desired position (usually galaxies). We focus on the second part, and compare different interpolation schemes, including polynomial interpolation, radial basis functions, Delaunay triangulation and Kriging. For that purpose, we develop simulations of PSF fields, in which stars are built from a set of basis functions defined from a principal components analysis of a real ground-based image. We find that Kriging gives the most reliable interpolation, significantly better than the traditionally used polynomial interpolation. We also note that although a Kriging interpolation on individual images is enough to control systematics at the level necessary for current weak lensing surveys, more elaborate techniques will have to be developed to reach future ambitious surveys' requirements.

  8. Holonomy spin foam models: asymptotic geometry of the partition function

    NASA Astrophysics Data System (ADS)

    Hellmann, Frank; Kaminski, Wojciech

    2013-10-01

    We study the asymptotic geometry of the spin foam partition function for a large class of models, including the models of Barrett and Crane, Engle, Pereira, Rovelli and Livine, and, Freidel and Krasnov. The asymptotics is taken with respect to the boundary spins only, no assumption of large spins is made in the interior. We give a sufficient criterion for the existence of the partition function. We find that geometric boundary data is suppressed unless its interior continuation satisfies certain accidental curvature constraints. This means in particular that most Regge manifolds are suppressed in the asymptotic regime. We discuss this explicitly for the case of the configurations arising in the 3-3 Pachner move. We identify the origin of these accidental curvature constraints as an incorrect twisting of the face amplitude upon introduction of the Immirzi parameter and propose a way to resolve this problem, albeit at the price of losing the connection to the SU(2) boundary Hilbert space. The key methodological innovation that enables these results is the introduction of the notion of wave front sets, and the adaptation of tools for their study from micro local analysis to the case of spin foam partition functions.

  9. Modeling individual differences in ferret external ear transfer functions

    NASA Astrophysics Data System (ADS)

    Schnupp, Jan W. H.; Booth, John; King, Andrew J.

    2003-04-01

    Individual variations in head and outer ear size, as well as growth of these structures during development, can markedly alter the values of the binaural and monaural cues which form the basis for auditory localization. This study investigated individual differences in the directional component of the head-related transfer function of both adult and juvenile ferrets. In line with previous studies in humans and cats, intersubject spectral differences were found to be reduced by scaling one of the directional transfer functions on a log-frequency axis. The optimal scale factor correlated most highly with pinna cavity height. Optimal frequency scaling reduced interear spectral difference equally well for adult-juvenile comparisons as for comparisons between pairs of adult ears. This illustrates that the developmental changes in localization cue values should be at least partly predictable on the basis of the expected growth rate of the outer ear structures. Predictions of interaural time differences (ITDs) were also derived from the physical dimensions of the head. ITDs were found to be poorly fitted by the spherical head model, while much better predictions could be derived from a model based on von Mises spherical basis functions. Together, these findings show how more accurate estimates of spatial cue values can be made from knowledge of the dimensions of the head and outer ears, and may facilitate the generation of virtual acoustic space stimuli in the absence of acoustical measurements from individual subjects.

  10. Assessing functional performance in the mdx mouse model.

    PubMed

    Aartsma-Rus, Annemieke; van Putten, Maaike

    2014-01-01

    Duchenne muscular dystrophy (DMD) is a severe and progressive muscle wasting disorder for which no cure is available. Nevertheless, several potential pharmaceutical compounds and gene therapy approaches have progressed into clinical trials. With improvement in muscle function being the most important end point in these trials, a lot of emphasis has been placed on setting up reliable, reproducible, and easy to perform functional tests to pre clinically assess muscle function, strength, condition, and coordination in the mdx mouse model for DMD. Both invasive and noninvasive tests are available. Tests that do not exacerbate the disease can be used to determine the natural history of the disease and the effects of therapeutic interventions (e.g. forelimb grip strength test, two different hanging tests using either a wire or a grid and rotarod running). Alternatively, forced treadmill running can be used to enhance disease progression and/or assess protective effects of therapeutic interventions on disease pathology. We here describe how to perform these most commonly used functional tests in a reliable and reproducible manner. Using these protocols based on standard operating procedures enables comparison of data between different laboratories. PMID:24747372

  11. Functional Regression Models for Epistasis Analysis of Multiple Quantitative Traits

    PubMed Central

    Xie, Dan; Liang, Meimei; Xiong, Momiao

    2016-01-01

    To date, most genetic analyses of phenotypes have focused on analyzing single traits or analyzing each phenotype independently. However, joint epistasis analysis of multiple complementary traits will increase statistical power and improve our understanding of the complicated genetic structure of the complex diseases. Despite their importance in uncovering the genetic structure of complex traits, the statistical methods for identifying epistasis in multiple phenotypes remains fundamentally unexplored. To fill this gap, we formulate a test for interaction between two genes in multiple quantitative trait analysis as a multiple functional regression (MFRG) in which the genotype functions (genetic variant profiles) are defined as a function of the genomic position of the genetic variants. We use large-scale simulations to calculate Type I error rates for testing interaction between two genes with multiple phenotypes and to compare the power with multivariate pairwise interaction analysis and single trait interaction analysis by a single variate functional regression model. To further evaluate performance, the MFRG for epistasis analysis is applied to five phenotypes of exome sequence data from the NHLBI’s Exome Sequencing Project (ESP) to detect pleiotropic epistasis. A total of 267 pairs of genes that formed a genetic interaction network showed significant evidence of epistasis influencing five traits. The results demonstrate that the joint interaction analysis of multiple phenotypes has a much higher power to detect interaction than the interaction analysis of a single trait and may open a new direction to fully uncovering the genetic structure of multiple phenotypes. PMID:27104857

  12. Assessing Functional Performance in the Mdx Mouse Model

    PubMed Central

    Aartsma-Rus, Annemieke; van Putten, Maaike

    2014-01-01

    Duchenne muscular dystrophy (DMD) is a severe and progressive muscle wasting disorder for which no cure is available. Nevertheless, several potential pharmaceutical compounds and gene therapy approaches have progressed into clinical trials. With improvement in muscle function being the most important end point in these trials, a lot of emphasis has been placed on setting up reliable, reproducible, and easy to perform functional tests to pre clinically assess muscle function, strength, condition, and coordination in the mdx mouse model for DMD. Both invasive and noninvasive tests are available. Tests that do not exacerbate the disease can be used to determine the natural history of the disease and the effects of therapeutic interventions (e.g. forelimb grip strength test, two different hanging tests using either a wire or a grid and rotarod running). Alternatively, forced treadmill running can be used to enhance disease progression and/or assess protective effects of therapeutic interventions on disease pathology. We here describe how to perform these most commonly used functional tests in a reliable and reproducible manner. Using these protocols based on standard operating procedures enables comparison of data between different laboratories. PMID:24747372

  13. AgBase: supporting functional modeling in agricultural organisms.

    PubMed

    McCarthy, Fiona M; Gresham, Cathy R; Buza, Teresia J; Chouvarine, Philippe; Pillai, Lakshmi R; Kumar, Ranjit; Ozkan, Seval; Wang, Hui; Manda, Prashanti; Arick, Tony; Bridges, Susan M; Burgess, Shane C

    2011-01-01

    AgBase (http://www.agbase.msstate.edu/) provides resources to facilitate modeling of functional genomics data and structural and functional annotation of agriculturally important animal, plant, microbe and parasite genomes. The website is redesigned to improve accessibility and ease of use, including improved search capabilities. Expanded capabilities include new dedicated pages for horse, cat, dog, cotton, rice and soybean. We currently provide 590 240 Gene Ontology (GO) annotations to 105 454 gene products in 64 different species, including GO annotations linked to transcripts represented on agricultural microarrays. For many of these arrays, this provides the only functional annotation available. GO annotations are available for download and we provide comprehensive, species-specific GO annotation files for 18 different organisms. The tools available at AgBase have been expanded and several existing tools improved based upon user feedback. One of seven new tools available at AgBase, GOModeler, supports hypothesis testing from functional genomics data. We host several associated databases and provide genome browsers for three agricultural pathogens. Moreover, we provide comprehensive training resources (including worked examples and tutorials) via links to Educational Resources at the AgBase website. PMID:21075795

  14. AgBase: supporting functional modeling in agricultural organisms

    PubMed Central

    McCarthy, Fiona M.; Gresham, Cathy R.; Buza, Teresia J.; Chouvarine, Philippe; Pillai, Lakshmi R.; Kumar, Ranjit; Ozkan, Seval; Wang, Hui; Manda, Prashanti; Arick, Tony; Bridges, Susan M.; Burgess, Shane C.

    2011-01-01

    AgBase (http://www.agbase.msstate.edu/) provides resources to facilitate modeling of functional genomics data and structural and functional annotation of agriculturally important animal, plant, microbe and parasite genomes. The website is redesigned to improve accessibility and ease of use, including improved search capabilities. Expanded capabilities include new dedicated pages for horse, cat, dog, cotton, rice and soybean. We currently provide 590 240 Gene Ontology (GO) annotations to 105 454 gene products in 64 different species, including GO annotations linked to transcripts represented on agricultural microarrays. For many of these arrays, this provides the only functional annotation available. GO annotations are available for download and we provide comprehensive, species-specific GO annotation files for 18 different organisms. The tools available at AgBase have been expanded and several existing tools improved based upon user feedback. One of seven new tools available at AgBase, GOModeler, supports hypothesis testing from functional genomics data. We host several associated databases and provide genome browsers for three agricultural pathogens. Moreover, we provide comprehensive training resources (including worked examples and tutorials) via links to Educational Resources at the AgBase website. PMID:21075795

  15. Resonating valence bond wave functions and classical interacting dimer models.

    PubMed

    Damle, Kedar; Dhar, Deepak; Ramola, Kabir

    2012-06-15

    We relate properties of nearest-neighbor resonating valence-bond (NNRVB) wave functions for SU(g) spin systems on two-dimensional bipartite lattices to those of fully packed interacting classical dimer models on the same lattice. The interaction energy can be expressed as a sum of n-body potentials V(n), which are recursively determined from the NNRVB wave function on finite subgraphs of the original lattice. The magnitude of the n-body interaction V(n) (n>1) is of order O(g(-(n-1))) for small g(-1). The leading term is a two-body nearest-neighbor interaction V2(g) favoring two parallel dimers on elementary plaquettes. For SU(2) spins, using our calculated value of V2(g=2), we find that the long-distance behavior of the bond-energy correlation function is dominated by an oscillatory term that decays as 1/|r|α with α≈1.22. This result is in remarkable quantitative agreement with earlier direct numerical studies of the corresponding wave function, which give α≈1.20. PMID:23004328

  16. Functional Regression Models for Epistasis Analysis of Multiple Quantitative Traits.

    PubMed

    Zhang, Futao; Xie, Dan; Liang, Meimei; Xiong, Momiao

    2016-04-01

    To date, most genetic analyses of phenotypes have focused on analyzing single traits or analyzing each phenotype independently. However, joint epistasis analysis of multiple complementary traits will increase statistical power and improve our understanding of the complicated genetic structure of the complex diseases. Despite their importance in uncovering the genetic structure of complex traits, the statistical methods for identifying epistasis in multiple phenotypes remains fundamentally unexplored. To fill this gap, we formulate a test for interaction between two genes in multiple quantitative trait analysis as a multiple functional regression (MFRG) in which the genotype functions (genetic variant profiles) are defined as a function of the genomic position of the genetic variants. We use large-scale simulations to calculate Type I error rates for testing interaction between two genes with multiple phenotypes and to compare the power with multivariate pairwise interaction analysis and single trait interaction analysis by a single variate functional regression model. To further evaluate performance, the MFRG for epistasis analysis is applied to five phenotypes of exome sequence data from the NHLBI's Exome Sequencing Project (ESP) to detect pleiotropic epistasis. A total of 267 pairs of genes that formed a genetic interaction network showed significant evidence of epistasis influencing five traits. The results demonstrate that the joint interaction analysis of multiple phenotypes has a much higher power to detect interaction than the interaction analysis of a single trait and may open a new direction to fully uncovering the genetic structure of multiple phenotypes. PMID:27104857

  17. Modeling halo mass functions in chameleon f(R) gravity

    NASA Astrophysics Data System (ADS)

    Lombriser, Lucas; Li, Baojiu; Koyama, Kazuya; Zhao, Gong-Bo

    2013-06-01

    On cosmological scales, observations of the cluster abundance currently place the strongest constraints on f(R) gravity. These constraints lie in the large-field limit, where the modifications of general relativity can correctly be modeled by setting the Compton wavelength of the scalar field to its background value. These bounds are, however, at the verge of penetrating into a regime where the modifications become nonlinearly suppressed due to the chameleon mechanism and cannot be described by this linearized approximation. For future constraints based on observations subjected to cluster abundance, it is therefore essential to consistently model the chameleon effect. We analyze descriptions of the halo mass function in chameleon f(R) gravity using a mass- and environment-dependent spherical collapse model in combination with excursion set theory and phenomenological fits to N-body simulations in the ΛCDM and f(R) gravity scenarios. Our halo mass functions consistently incorporate the chameleon suppression and cosmological parameter dependencies, improving upon previous formalisms and providing an important extension to N-body simulations for the application in consistent tests of gravity with observables sensitive to the abundance of clusters.

  18. Genetic Models for the Study of Luteinizing Hormone Receptor Function

    PubMed Central

    Narayan, Prema

    2015-01-01

    The luteinizing hormone/chorionic gonadotropin receptor (LHCGR) is essential for fertility in men and women. LHCGR binds luteinizing hormone (LH) as well as the highly homologous chorionic gonadotropin. Signaling from LHCGR is required for steroidogenesis and gametogenesis in males and females and for sexual differentiation in the male. The importance of LHCGR in reproductive physiology is underscored by the large number of naturally occurring inactivating and activating mutations in the receptor that result in reproductive disorders. Consequently, several genetically modified mouse models have been developed for the study of LHCGR function. They include targeted deletion of LH and LHCGR that mimic inactivating mutations in hormone and receptor, expression of a constitutively active mutant in LHCGR that mimics activating mutations associated with familial male-limited precocious puberty and transgenic models of LH and hCG overexpression. This review summarizes the salient findings from these models and their utility in understanding the physiological and pathological consequences of loss and gain of function in LHCGR signaling. PMID:26483755

  19. Dynamic causal modelling for functional near-infrared spectroscopy

    PubMed Central

    Tak, S.; Kempny, A.M.; Friston, K.J.; Leff, A.P.; Penny, W.D.

    2015-01-01

    Functional near-infrared spectroscopy (fNIRS) is an emerging technique for measuring changes in cerebral hemoglobin concentration via optical absorption changes. Although there is great interest in using fNIRS to study brain connectivity, current methods are unable to infer the directionality of neuronal connections. In this paper, we apply Dynamic Causal Modelling (DCM) to fNIRS data. Specifically, we present a generative model of how observed fNIRS data are caused by interactions among hidden neuronal states. Inversion of this generative model, using an established Bayesian framework (variational Laplace), then enables inference about changes in directed connectivity at the neuronal level. Using experimental data acquired during motor imagery and motor execution tasks, we show that directed (i.e., effective) connectivity from the supplementary motor area to the primary motor cortex is negatively modulated by motor imagery, and this suppressive influence causes reduced activity in the primary motor cortex during motor imagery. These results are consistent with findings of previous functional magnetic resonance imaging (fMRI) studies, suggesting that the proposed method enables one to infer directed interactions in the brain mediated by neuronal dynamics from measurements of optical density changes. PMID:25724757

  20. Experimental assessment of presumed filtered density function models

    NASA Astrophysics Data System (ADS)

    Stetsyuk, V.; Soulopoulos, N.; Hardalupas, Y.; Taylor, A. M. K. P.

    2015-06-01

    Measured filtered density functions (FDFs) as well as assumed beta distribution model of mixture fraction and "subgrid" scale (SGS) scalar variance z '' 2 ¯ , used typically in large eddy simulations, were studied by analysing experimental data, obtained from two-dimensional planar, laser induced fluorescence measurements in isothermal swirling turbulent flows at a constant Reynolds number of 29 000 for different swirl numbers (0.3, 0.58, and 1.07). Two-dimensional spatial filtering, by using a box filter, was performed in order to obtain the filtered variables, namely, resolved mean and "subgrid" scale scalar variance. These were used as inputs for assumed beta distribution of mixture fraction and top-hat FDF shape estimates. The presumed beta distribution model, top-hat FDF, and the measured filtered density functions were used to integrate a laminar flamelet solution in order to calculate the corresponding resolved temperature. The experimentally measured FDFs varied with the flow swirl number and both axial and radial positions in the flow. The FDFs were unimodal at flow regions with low SGS scalar variance, z '' 2 ¯ < 0.01, and bimodal at regions with high SGS variance, z '' 2 ¯ > 0.02. Bimodal FDF could be observed for a filter size of approximately 1.5-2 times the Batchelor scale. Unimodal FDF could be observed for a filter size as large as four times the Batchelor scale under well-mixed conditions. In addition, two common computational models (a gradient assumption and a scale similarity model) for the SGS scalar variance were used with the aim to evaluate their validity through comparison with the experimental data. It was found that the gradient assumption model performed generally better than the scale similarity one.

  1. Teleseismic receiver functions modeling of the eastern Indian craton

    NASA Astrophysics Data System (ADS)

    Mandal, Prantik; Biswas, Koushik

    2016-09-01

    We estimate receiver functions (RFs) through the time-domain deconvolution using three-component broadband data of 100 teleseismic events (30° ⩽ ∧ ⩽ 90°) from 15 seismographs in the eastern Indian craton. Estimated radial RFs show a positive phase at 4.6-5.8 s delay time corresponding to the crustal thicknesses of 37-46 km. Through the differential evolution (DE) waveform inversion modeling of radial receiver functions, we delineate the crustal structure at 15 broadband stations. On an average, the Archean Singhbhum Odisha Craton (SOC) is characterized by a thick crust of 43 ± 3 km in comparison to a relatively thin crust of 41 ± 1 km underlying the Proterozoic Chotanagpur Granite Gneissic terrain (CGGT). While, a thin crust of 38 ± 1 km characterizes the younger Eastern Ghats Mobile Belt (EGMB). The main results of our modeling reveal a 46 km thick Archean crust underlying the Singhbhum granite (SG) of 3.6 Ga, which is characterized by a 3 km crustal thickening probably resulted from the Archean subduction process. Our modeling also detects a 2-3 km crustal thinning with the thinnest crust of 37 km below the region near South Singhbhum Shear Zone, which could be attributed to the 1.6 Ga plume activity associated with Dalma volcanic. Our modeling also led to the delineation of a crustal thinning of 2-3 km underlying the region in EGMB, which was influenced by a much younger (∼117 Ma) Rajmahal magmatism associated with the Gondwana break-up episode. However, our study could not detect any age-dependent variation of crustal thicknesses in the eastern Indian craton. The main result of our modeling suggests a two-phase crustal evolution process for the SOC viz. older E-W crustal thickening due to E-W plate compression and later crustal thinning episodes associated with the Dalma volcanism in the north and the Rajmahal volcanism in the South.

  2. AMFESYS: Modelling and diagnosis functions for operations support

    NASA Technical Reports Server (NTRS)

    Wheadon, J.

    1993-01-01

    Packetized telemetry, combined with low station coverage for close-earth satellites, may introduce new problems in presenting to the operator a clear picture of what the spacecraft is doing. A recent ESOC study has gone some way to show, by means of a practical demonstration, how the use of subsystem models combined with artificial intelligence techniques, within a real-time spacecraft control system (SCS), can help to overcome these problems. A spin-off from using these techniques can be an improvement in the reliability of the telemetry (TM) limit-checking function, as well as the telecommand verification function, of the Spacecraft Control systems (SCS). The problem and how it was addressed, including an overview of the 'AMF Expert System' prototype are described, and proposes further work which needs to be done to prove the concept. The Automatic Mirror Furnace is part of the payload of the European Retrievable Carrier (EURECA) spacecraft, which was launched in July 1992.

  3. Models, Regulations, and Functions of Microtubule Severing by Katanin

    PubMed Central

    Ghosh, Debasish Kumar; Dasgupta, Debdeep; Guha, Abhishek

    2012-01-01

    Regulation of microtubule dynamics depends on stochastic balance between polymerization and severing process which lead to differential spatiotemporal abundance and distribution of microtubules during cell development, differentiation, and morphogenesis. Microtubule severing by a conserved AAA family protein Katanin has emerged as an important microtubule architecture modulating process in cellular functions like division, migration, shaping and so on. Regulated by several factors, Katanin manifests connective crosstalks in network motifs in regulation of anisotropic severing pattern of microtubule protofilaments in cell type and stage dependent way. Mechanisms of structural disintegration of microtubules by Katanin involve heterogeneous mechanochemical processes and sensitivity of microtubules to Katanin plays significant roles in mitosis/meiosis, neurogenesis, cilia/flagella formation, cell wall development and so on. Deregulated and uncoordinated expression of Katanin has been shown to have implications in pathophysiological conditions. In this paper, we highlight mechanistic models and regulations of microtubule severing by Katanin in context of structure and various functions of Katanin in different organisms.

  4. Droplet model for autocorrelation functions in an Ising ferromagnet

    NASA Technical Reports Server (NTRS)

    Tang, Chao; Nakanishi, Hiizu; Langer, J. S.

    1989-01-01

    The autocorrelation function of Ising spins in an ordered phase is studied via a droplet model. Only noninteracting spherical droplets are considered. The Langevin equation which describes fluctuations in the radius of a single droplet is studied in detail. A general description of the transformation to a Fokker-Planck equations and the ways in which a spectral analysis of that equation can be used to compute the autocorrelation function is given. It is shown that the eigenvalues of the Fokker-Planck operator form (1) a continuous spectrum of relaxation rates starting from zero for d = 2, (2) a continuous spectrum with a finite gap for d = 3, and (3) a discrete spectrum for d greater than 4, where d is the spatial dimensionality. Detailed solutions for various cases are presented.

  5. Effects of exercise on brain functions in diabetic animal models

    PubMed Central

    Yi, Sun Shin

    2015-01-01

    Human life span has dramatically increased over several decades, and the quality of life has been considered to be equally important. However, diabetes mellitus (DM) characterized by problems related to insulin secretion and recognition has become a serious health problem in recent years that threatens human health by causing decline in brain functions and finally leading to neurodegenerative diseases. Exercise is recognized as an effective therapy for DM without medication administration. Exercise studies using experimental animals are a suitable option to overcome this drawback, and animal studies have improved continuously according to the needs of the experimenters. Since brain health is the most significant factor in human life, it is very important to assess brain functions according to the different exercise conditions using experimental animal models. Generally, there are two types of DM; insulin-dependent type 1 DM and an insulin-independent type 2 DM (T2DM); however, the author will mostly discuss brain functions in T2DM animal models in this review. Additionally, many physiopathologic alterations are caused in the brain by DM such as increased adiposity, inflammation, hormonal dysregulation, uncontrolled hyperphagia, insulin and leptin resistance, and dysregulation of neurotransmitters and declined neurogenesis in the hippocampus and we describe how exercise corrects these alterations in animal models. The results of changes in the brain environment differ according to voluntary, involuntary running exercises and resistance exercise, and gender in the animal studies. These factors have been mentioned in this review, and this review will be a good reference for studying how exercise can be used with therapy for treating DM. PMID:25987956

  6. Modeling the biomechanics of articular eminence function in anthropoid primates

    PubMed Central

    Terhune, Claire E

    2011-01-01

    One of the most prominent features of the cranial component of the temporomandibular joint (TMJ) is the articular eminence (AE). This bar of bone is the primary surface upon which the condyle translates and rotates during movements of the mandible, and is therefore the primary point at which forces are transmitted from the mandible to the cranium during loading of the masticatory apparatus. The shape of the AE is highly variable across primates, and the raised eminence of humans has often been considered a defining feature of the human TMJ, yet few data exist to address whether this variation is functionally significant. This study used a broad interspecific sample of anthropoid primates to elaborate upon and test the predictions of a previously proposed model of AE function. This model suggests that AE inclination acts to resist non-normal forces at the TMJ, thereby maximizing bite forces (BFs). AE inclination was predicted to covary with two specific features of the masticatory apparatus: height of the TMJ above the occlusal plane; and inclination of the masticatory muscles. A correlate of this model is that taxa utilizing more resistant food objects should also exhibit relatively more inclined AEs. Results of the correlation analyses found that AE inclination is strongly correlated with height of the TMJ above the occlusal plane, but less so with inclination of the masticatory muscles. Furthermore, pairwise comparisons of closely related taxa with documented dietary differences found that the AE is consistently more inclined in taxa that utilize more resistant food items. These data preliminarily suggest that variation in AE morphology across anthropoid primates is functionally related to maximizing BFs, and add to the growing dataset of masticatory morphologies linked to feeding behavior. PMID:21923720

  7. Informing soil models using pedotransfer functions: challenges and perspectives

    NASA Astrophysics Data System (ADS)

    Pachepsky, Yakov; Romano, Nunzio

    2015-04-01

    Pedotransfer functions (PTFs) are empirical relationships between parameters of soil models and more easily obtainable data on soil properties. PTFs have become an indispensable tool in modeling soil processes. As alternative methods to direct measurements, they bridge the data we have and data we need by using soil survey and monitoring data to enable modeling for real-world applications. Pedotransfer is extensively used in soil models addressing the most pressing environmental issues. The following is an attempt to provoke a discussion by listing current issues that are faced by PTF development. 1. As more intricate biogeochemical processes are being modeled, development of PTFs for parameters of those processes becomes essential. 2. Since the equations to express PTF relationships are essentially unknown, there has been a trend to employ highly nonlinear equations, e.g. neural networks, which in theory are flexible enough to simulate any dependence. This, however, comes with the penalty of large number of coefficients that are difficult to estimate reliably. A preliminary classification applied to PTF inputs and PTF development for each of the resulting groups may provide simple, transparent, and more reliable pedotransfer equations. 3. The multiplicity of models, i.e. presence of several models producing the same output variables, is commonly found in soil modeling, and is a typical feature in the PTF research field. However, PTF intercomparisons are lagging behind PTF development. This is aggravated by the fact that coefficients of PTF based on machine-learning methods are usually not reported. 4. The existence of PTFs is the result of some soil processes. Using models of those processes to generate PTFs, and more general, developing physics-based PTFs remains to be explored. 5. Estimating the variability of soil model parameters becomes increasingly important, as the newer modeling technologies such as data assimilation, ensemble modeling, and model

  8. Predictions of Geospace Drivers By the Probability Distribution Function Model

    NASA Astrophysics Data System (ADS)

    Bussy-Virat, C.; Ridley, A. J.

    2014-12-01

    Geospace drivers like the solar wind speed, interplanetary magnetic field (IMF), and solar irradiance have a strong influence on the density of the thermosphere and the near-Earth space environment. This has important consequences on the drag on satellites that are in low orbit and therefore on their position. One of the basic problems with space weather prediction is that these drivers can only be measured about one hour before they affect the environment. In order to allow for adequate planning for some members of the commercial, military, or civilian communities, reliable long-term space weather forecasts are needed. The study presents a model for predicting geospace drivers up to five days in advance. This model uses the same general technique to predict the solar wind speed, the three components of the IMF, and the solar irradiance F10.7. For instance, it uses Probability distribution functions (PDFs) to relate the current solar wind speed and slope to the future solar wind speed, as well as the solar wind speed to the solar wind speed one solar rotation in the future. The PDF Model has been compared to other models for predictions of the speed. It has been found that it is better than using the current solar wind speed (i.e., persistence), and better than the Wang-Sheeley-Arge Model for prediction horizons of 24 hours. Once the drivers are predicted, and the uncertainty on the drivers are specified, the density in the thermosphere can be derived using various models of the thermosphere, such as the Global Ionosphere Thermosphere Model. In addition, uncertainties on the densities can be estimated, based on ensembles of simulations. From the density and uncertainty predictions, satellite positions, as well as the uncertainty in those positions can be estimated. These can assist operators in determining the probability of collisions between objects in low Earth orbit.

  9. Exact maps in density functional theory for lattice models

    NASA Astrophysics Data System (ADS)

    Dimitrov, Tanja; Appel, Heiko; Fuks, Johanna I.; Rubio, Angel

    2016-08-01

    In the present work, we employ exact diagonalization for model systems on a real-space lattice to explicitly construct the exact density-to-potential and graphically illustrate the complete exact density-to-wavefunction map that underly the Hohenberg–Kohn theorem in density functional theory. Having the explicit wavefunction-to-density map at hand, we are able to construct arbitrary observables as functionals of the ground-state density. We analyze the density-to-potential map as the distance between the fragments of a system increases and the correlation in the system grows. We observe a feature that gradually develops in the density-to-potential map as well as in the density-to-wavefunction map. This feature is inherited by arbitrary expectation values as functional of the ground-state density. We explicitly show the excited-state energies, the excited-state densities, and the correlation entropy as functionals of the ground-state density. All of them show this exact feature that sharpens as the coupling of the fragments decreases and the correlation grows. We denominate this feature as intra-system steepening and discuss how it relates to the well-known inter-system derivative discontinuity. The inter-system derivative discontinuity is an exact concept for coupled subsystems with degenerate ground state. However, the coupling between subsystems as in charge transfer processes can lift the degeneracy. An important conclusion is that for such systems with a near-degenerate ground state, the corresponding cut along the particle number N of the exact density functionals is differentiable with a well-defined gradient near integer particle number.

  10. New models for analyzing mast cell functions in vivo.

    PubMed

    Reber, Laurent L; Marichal, Thomas; Galli, Stephen J

    2012-12-01

    In addition to their well-accepted role as critical effector cells in anaphylaxis and other acute IgE-mediated allergic reactions, mast cells (MCs) have been implicated in a wide variety of processes that contribute to disease or help to maintain health. Although some of these roles were first suggested by analyses of MC products or functions in vitro, it is critical to determine whether, and under which circumstances, such potential roles actually can be performed by MCs in vivo. This review discusses recent advances in the development and analysis of mouse models to investigate the roles of MCs and MC-associated products during biological responses in vivo, and comments on some of the similarities and differences in the results obtained with these newer versus older models of MC deficiency. PMID:23127755

  11. Spherical collapse and halo mass function in the symmetron model

    NASA Astrophysics Data System (ADS)

    Taddei, Laura; Catena, Riccardo; Pietroni, Massimo

    2014-01-01

    We study the gravitational clustering of spherically symmetric overdensities and the statistics of the resulting dark matter halos in the "symmetron model," in which a new long range force is mediated by a Z2 symmetric scalar field. Depending on the initial radius of the overdensity, we identify two distinct regimes: for small initial radii the symmetron mediated force affects the spherical collapse at all redshifts; for initial radii larger than some critical size this force vanishes before collapse because of the symmetron screening mechanism. As a consequence, halos with initial radii smaller than some critical value collapse earlier than in the ΛCDM and statistically tend to form more massive dark matter halos. Regarding the halo mass function of these objects, we observe departures from standard ΛCDM predictions at the few percent level. The formalism developed here can be easily applied to other models where fifth forces participate to the dynamics of the gravitational collapse.

  12. Verbal Neuropsychological Functions in Aphasia: An Integrative Model.

    PubMed

    Vigliecca, Nora Silvana; Báez, Sandra

    2015-12-01

    A theoretical framework which considers the verbal functions of the brain under a multivariate and comprehensive cognitive model was statistically analyzed. A confirmatory factor analysis was performed to verify whether some recognized aphasia constructs can be hierarchically integrated as latent factors from a homogenously verbal test. The Brief Aphasia Evaluation was used. A sample of 65 patients with left cerebral lesions, and two supplementary samples comprising 35 patients with right cerebral lesions and 30 healthy participants were studied. A model encompassing an all inclusive verbal organizer and two successive organizers was validated. The two last organizers were: three factors of comprehension, expression and a "complementary" verbal factor which included praxia, attention, and memory; followed by the individual (and correlated) factors of auditory comprehension, repetition, naming, speech, reading, writing, and the "complementary" factor. By following this approach all the patients fall inside the classification system; consequently, theoretical improvement is guaranteed. PMID:25168953

  13. Models for predicting objective function weights in prostate cancer IMRT

    SciTech Connect

    Boutilier, Justin J. Lee, Taewoo; Craig, Tim; Sharpe, Michael B.; Chan, Timothy C. Y.

    2015-04-15

    Purpose: To develop and evaluate the clinical applicability of advanced machine learning models that simultaneously predict multiple optimization objective function weights from patient geometry for intensity-modulated radiation therapy of prostate cancer. Methods: A previously developed inverse optimization method was applied retrospectively to determine optimal objective function weights for 315 treated patients. The authors used an overlap volume ratio (OV) of bladder and rectum for different PTV expansions and overlap volume histogram slopes (OVSR and OVSB for the rectum and bladder, respectively) as explanatory variables that quantify patient geometry. Using the optimal weights as ground truth, the authors trained and applied three prediction models: logistic regression (LR), multinomial logistic regression (MLR), and weighted K-nearest neighbor (KNN). The population average of the optimal objective function weights was also calculated. Results: The OV at 0.4 cm and OVSR at 0.1 cm features were found to be the most predictive of the weights. The authors observed comparable performance (i.e., no statistically significant difference) between LR, MLR, and KNN methodologies, with LR appearing to perform the best. All three machine learning models outperformed the population average by a statistically significant amount over a range of clinical metrics including bladder/rectum V53Gy, bladder/rectum V70Gy, and dose to the bladder, rectum, CTV, and PTV. When comparing the weights directly, the LR model predicted bladder and rectum weights that had, on average, a 73% and 74% relative improvement over the population average weights, respectively. The treatment plans resulting from the LR weights had, on average, a rectum V70Gy that was 35% closer to the clinical plan and a bladder V70Gy that was 29% closer, compared to the population average weights. Similar results were observed for all other clinical metrics. Conclusions: The authors demonstrated that the KNN and MLR

  14. Constructing biological pathway models with hybrid functional Petri nets.

    PubMed

    Doi, Atsushi; Fujita, Sachie; Matsuno, Hiroshi; Nagasaki, Masao; Miyano, Satoru

    2004-01-01

    In many research projects on modeling and analyzing biological pathways, the Petri net has been recognized as a promising method for representing biological pathways. From the pioneering works by Reddy et al., 1993, and Hofestädt, 1994, that model metabolic pathways by traditional Petri net, several enhanced Petri nets such as colored Petri net, stochastic Petri net, and hybrid Petri net have been used for modeling biological phenomena. Recently, Matsuno et al., 2003b, introduced the hybrid functional Petri net (HFPN) in order to give a more intuitive and natural modeling method for biological pathways than these existing Petri nets. Although the paper demonstrates the effectiveness of HFPN with two examples of gene regulation mechanism for circadian rhythms and apoptosis signaling pathway, there has been no detailed explanation about the method of HFPN construction for these examples. The purpose of this paper is to describe method to construct biological pathways with the HFPN step-by-step. The method is demonstrated by the well-known glycolytic pathway controlled by the lac operon gene regulatory mechanism. PMID:15724280

  15. Modeling functional piezoelectricity in perovskite superlattices with competing instabilities

    NASA Astrophysics Data System (ADS)

    Swartz, Charles; Wu, Xifan

    2012-02-01

    Multi-component Perovskite Superlattices (SLs) of the form ABO3, provide a very promising avenue for the design of materials with multifunctional properties. Furthermore the interfaces of such multi-component SLs are home to competing anti-ferrodistortive and ferroelectric instabilities which can produce unexpected functionalities. However, at present first principles calculations exceeding more than 10 units cells, are particularly costly as they scale with the valence electrons as N^3. We present a first-principles modeling technique that allows us to accurately model the piezoelectric strains of paraelectric/ferroelectric SLs, BaTiO3/CaTiO3 and PbTiO3/SrTiO3, under a fixed displacement field. The model is based on a maximally localized wannier center layer polarization technique, as well as a truncated cluster expansion, that makes use of the fact that such PE/FE SLs have been shown to have highly localized ionic and electronic interface effects. The prediction of the piezoelectricity for a SL of an arbitrary stacking sequence will be demonstrated. We also use our model to conduct a systemic study of the interface effects on piezoelectric response in the above SLs paying special attention to a strong non-linear effect observed in Bulk SrTiO3.

  16. Engelmann spruce site index models: a comparison of model functions and parameterizations.

    PubMed

    Nigh, Gordon

    2015-01-01

    Engelmann spruce (Picea engelmannii Parry ex Engelm.) is a high-elevation species found in western Canada and western USA. As this species becomes increasingly targeted for harvesting, better height growth information is required for good management of this species. This project was initiated to fill this need. The objective of the project was threefold: develop a site index model for Engelmann spruce; compare the fits and modelling and application issues between three model formulations and four parameterizations; and more closely examine the grounded-Generalized Algebraic Difference Approach (g-GADA) model parameterization. The model fitting data consisted of 84 stem analyzed Engelmann spruce site trees sampled across the Engelmann Spruce - Subalpine Fir biogeoclimatic zone. The fitted models were based on the Chapman-Richards function, a modified Hossfeld IV function, and the Schumacher function. The model parameterizations that were tested are indicator variables, mixed-effects, GADA, and g-GADA. Model evaluation was based on the finite-sample corrected version of Akaike's Information Criteria and the estimated variance. Model parameterization had more of an influence on the fit than did model formulation, with the indicator variable method providing the best fit, followed by the mixed-effects modelling (9% increase in the variance for the Chapman-Richards and Schumacher formulations over the indicator variable parameterization), g-GADA (optimal approach) (335% increase in the variance), and the GADA/g-GADA (with the GADA parameterization) (346% increase in the variance). Factors related to the application of the model must be considered when selecting the model for use as the best fitting methods have the most barriers in their application in terms of data and software requirements. PMID:25853472

  17. Engelmann Spruce Site Index Models: A Comparison of Model Functions and Parameterizations

    PubMed Central

    Nigh, Gordon

    2015-01-01

    Engelmann spruce (Picea engelmannii Parry ex Engelm.) is a high-elevation species found in western Canada and western USA. As this species becomes increasingly targeted for harvesting, better height growth information is required for good management of this species. This project was initiated to fill this need. The objective of the project was threefold: develop a site index model for Engelmann spruce; compare the fits and modelling and application issues between three model formulations and four parameterizations; and more closely examine the grounded-Generalized Algebraic Difference Approach (g-GADA) model parameterization. The model fitting data consisted of 84 stem analyzed Engelmann spruce site trees sampled across the Engelmann Spruce – Subalpine Fir biogeoclimatic zone. The fitted models were based on the Chapman-Richards function, a modified Hossfeld IV function, and the Schumacher function. The model parameterizations that were tested are indicator variables, mixed-effects, GADA, and g-GADA. Model evaluation was based on the finite-sample corrected version of Akaike’s Information Criteria and the estimated variance. Model parameterization had more of an influence on the fit than did model formulation, with the indicator variable method providing the best fit, followed by the mixed-effects modelling (9% increase in the variance for the Chapman-Richards and Schumacher formulations over the indicator variable parameterization), g-GADA (optimal approach) (335% increase in the variance), and the GADA/g-GADA (with the GADA parameterization) (346% increase in the variance). Factors related to the application of the model must be considered when selecting the model for use as the best fitting methods have the most barriers in their application in terms of data and software requirements. PMID:25853472

  18. The integrated Earth System Model Version 1: formulation and functionality

    SciTech Connect

    Collins, William D.; Craig, Anthony P.; Truesdale, John E.; Di Vittorio, Alan; Jones, Andrew D.; Bond-Lamberty, Benjamin; Calvin, Katherine V.; Edmonds, James A.; Kim, Son H.; Thomson, Allison M.; Patel, Pralit L.; Zhou, Yuyu; Mao, Jiafu; Shi, Xiaoying; Thornton, Peter E.; Chini, Louise M.; Hurtt, George C.

    2015-07-23

    The integrated Earth System Model (iESM) has been developed as a new tool for pro- jecting the joint human/climate system. The iESM is based upon coupling an Integrated Assessment Model (IAM) and an Earth System Model (ESM) into a common modeling in- frastructure. IAMs are the primary tool for describing the human–Earth system, including the sources of global greenhouse gases (GHGs) and short-lived species, land use and land cover change, and other resource-related drivers of anthropogenic climate change. ESMs are the primary scientific tools for examining the physical, chemical, and biogeochemical impacts of human-induced changes to the climate system. The iESM project integrates the economic and human dimension modeling of an IAM and a fully coupled ESM within a sin- gle simulation system while maintaining the separability of each model if needed. Both IAM and ESM codes are developed and used by large communities and have been extensively applied in recent national and international climate assessments. By introducing heretofore- omitted feedbacks between natural and societal drivers, we can improve scientific under- standing of the human–Earth system dynamics. Potential applications include studies of the interactions and feedbacks leading to the timing, scale, and geographic distribution of emissions trajectories and other human influences, corresponding climate effects, and the subsequent impacts of a changing climate on human and natural systems. This paper de- scribes the formulation, requirements, implementation, testing, and resulting functionality of the first version of the iESM released to the global climate community.

  19. The integrated Earth system model version 1: formulation and functionality

    DOE PAGESBeta

    Collins, W. D.; Craig, A. P.; Truesdale, J. E.; Di Vittorio, A. V.; Jones, A. D.; Bond-Lamberty, B.; Calvin, K. V.; Edmonds, J. A.; Kim, S. H.; Thomson, A. M.; et al

    2015-07-23

    The integrated Earth system model (iESM) has been developed as a new tool for projecting the joint human/climate system. The iESM is based upon coupling an integrated assessment model (IAM) and an Earth system model (ESM) into a common modeling infrastructure. IAMs are the primary tool for describing the human–Earth system, including the sources of global greenhouse gases (GHGs) and short-lived species (SLS), land use and land cover change (LULCC), and other resource-related drivers of anthropogenic climate change. ESMs are the primary scientific tools for examining the physical, chemical, and biogeochemical impacts of human-induced changes to the climate system. Themore » iESM project integrates the economic and human-dimension modeling of an IAM and a fully coupled ESM within a single simulation system while maintaining the separability of each model if needed. Both IAM and ESM codes are developed and used by large communities and have been extensively applied in recent national and international climate assessments. By introducing heretofore-omitted feedbacks between natural and societal drivers, we can improve scientific understanding of the human–Earth system dynamics. Potential applications include studies of the interactions and feedbacks leading to the timing, scale, and geographic distribution of emissions trajectories and other human influences, corresponding climate effects, and the subsequent impacts of a changing climate on human and natural systems. This paper describes the formulation, requirements, implementation, testing, and resulting functionality of the first version of the iESM released to the global climate community.« less

  20. The integrated Earth system model version 1: formulation and functionality

    NASA Astrophysics Data System (ADS)

    Collins, W. D.; Craig, A. P.; Truesdale, J. E.; Di Vittorio, A. V.; Jones, A. D.; Bond-Lamberty, B.; Calvin, K. V.; Edmonds, J. A.; Kim, S. H.; Thomson, A. M.; Patel, P.; Zhou, Y.; Mao, J.; Shi, X.; Thornton, P. E.; Chini, L. P.; Hurtt, G. C.

    2015-07-01

    The integrated Earth system model (iESM) has been developed as a new tool for projecting the joint human/climate system. The iESM is based upon coupling an integrated assessment model (IAM) and an Earth system model (ESM) into a common modeling infrastructure. IAMs are the primary tool for describing the human-Earth system, including the sources of global greenhouse gases (GHGs) and short-lived species (SLS), land use and land cover change (LULCC), and other resource-related drivers of anthropogenic climate change. ESMs are the primary scientific tools for examining the physical, chemical, and biogeochemical impacts of human-induced changes to the climate system. The iESM project integrates the economic and human-dimension modeling of an IAM and a fully coupled ESM within a single simulation system while maintaining the separability of each model if needed. Both IAM and ESM codes are developed and used by large communities and have been extensively applied in recent national and international climate assessments. By introducing heretofore-omitted feedbacks between natural and societal drivers, we can improve scientific understanding of the human-Earth system dynamics. Potential applications include studies of the interactions and feedbacks leading to the timing, scale, and geographic distribution of emissions trajectories and other human influences, corresponding climate effects, and the subsequent impacts of a changing climate on human and natural systems. This paper describes the formulation, requirements, implementation, testing, and resulting functionality of the first version of the iESM released to the global climate community.

  1. Informing soil models using pedotransfer functions: challenges and perspectives

    NASA Astrophysics Data System (ADS)

    Pachepsky, Yakov; Romano, Nunzio

    2015-04-01

    Pedotransfer functions (PTFs) are empirical relationships between parameters of soil models and more easily obtainable data on soil properties. PTFs have become an indispensable tool in modeling soil processes. As alternative methods to direct measurements, they bridge the data we have and data we need by using soil survey and monitoring data to enable modeling for real-world applications. Pedotransfer is extensively used in soil models addressing the most pressing environmental issues. The following is an attempt to provoke a discussion by listing current issues that are faced by PTF development. 1. As more intricate biogeochemical processes are being modeled, development of PTFs for parameters of those processes becomes essential. 2. Since the equations to express PTF relationships are essentially unknown, there has been a trend to employ highly nonlinear equations, e.g. neural networks, which in theory are flexible enough to simulate any dependence. This, however, comes with the penalty of large number of coefficients that are difficult to estimate reliably. A preliminary classification applied to PTF inputs and PTF development for each of the resulting groups may provide simple, transparent, and more reliable pedotransfer equations. 3. The multiplicity of models, i.e. presence of several models producing the same output variables, is commonly found in soil modeling, and is a typical feature in the PTF research field. However, PTF intercomparisons are lagging behind PTF development. This is aggravated by the fact that coefficients of PTF based on machine-learning methods are usually not reported. 4. The existence of PTFs is the result of some soil processes. Using models of those processes to generate PTFs, and more general, developing physics-based PTFs remains to be explored. 5. Estimating the variability of soil model parameters becomes increasingly important, as the newer modeling technologies such as data assimilation, ensemble modeling, and model

  2. Computer Modeling of the Earliest Cellular Structures and Functions

    NASA Astrophysics Data System (ADS)

    Pohorille, Andrew

    2000-03-01

    In the absence of extinct or extant record of protocells (the earliest ancestors of contemporary cells), the most direct way to test ourunderstanding of the origin of cellular life is to construct laboratory models of protocells. Such efforts are currently underway in the NASA Astrobiology Program. They are accompanied by computational studies aimed at explaining self-organization of simple molecules into ordered structures and developing designs for molecules that perform protocellular functions. Many of these functions, such as import of nutrients, capture and storage of energy, and response to changes in the environment are carried out by proteins bound to membranes. We will discuss a series of large-scale, molecular-level computer simulations which demonstrate (a) how small proteins (peptides)organize themselves into ordered structures at water-membrane interfaces and insert into membranes, (b) how these peptides aggregate to form membrane-spanning structures (e.g. channels), and (c) by what mechanisms such aggregates perform essential protocellular functions, such as proton transport of protons across cell walls, a key step in cellular bioenergetics. The simulations were performed using the molecular dynamics method, in which Newton's equations of motion for each atom in the system are solved iteratively. The problems of interest required simulations on multi-nanosecond time scales, which corresponded to 10^6-10^8 time steps.

  3. Computer Modeling of the Earliest Cellular Structures and Functions

    NASA Technical Reports Server (NTRS)

    Pohorille, Andrew; Chipot, Christophe; Schweighofer, Karl

    2000-01-01

    In the absence of extinct or extant record of protocells (the earliest ancestors of contemporary cells). the most direct way to test our understanding of the origin of cellular life is to construct laboratory models of protocells. Such efforts are currently underway in the NASA Astrobiology Program. They are accompanied by computational studies aimed at explaining self-organization of simple molecules into ordered structures and developing designs for molecules that perform proto-cellular functions. Many of these functions, such as import of nutrients, capture and storage of energy. and response to changes in the environment are carried out by proteins bound to membrane< We will discuss a series of large-scale, molecular-level computer simulations which demonstrate (a) how small proteins (peptides) organize themselves into ordered structures at water-membrane interfaces and insert into membranes, (b) how these peptides aggregate to form membrane-spanning structures (eg. channels), and (c) by what mechanisms such aggregates perform essential proto-cellular functions, such as proton transport of protons across cell walls, a key step in cellular bioenergetics. The simulations were performed using the molecular dynamics method, in which Newton's equations of motion for each item in the system are solved iteratively. The problems of interest required simulations on multi-nanosecond time scales, which corresponded to 10(exp 6)-10(exp 8) time steps.

  4. Modeling the Galaxy Three-Point Correlation Function

    SciTech Connect

    Marin, Felipe; Wechsler, Risa; Frieman, Joshua A.; Nichol, Robert; /Portsmouth U., ICG

    2007-06-05

    We present new theoretical predictions for the galaxy three-point correlation function (3PCF) using high-resolution dissipationless cosmological simulations of a flat Lambda CDM Universe which resolve galaxy-size halos and subhalos. We create realistic mock galaxy catalogs by assigning luminosities and colors to dark matter halos and subhalos, and we measure the reduced 3PCF as a function of luminosity and color in both real and redshift space. As galaxy luminosity and color are varied, we find small differences in the amplitude and shape dependence of the reduced 3PCF, at a level qualitatively consistent with recent measurements from the SDSS and 2dFGRS. We confirm that discrepancies between previous 3PCF measurements can be explained in part by differences in binning choices. We explore the degree to which a simple local bias model can fit the simulated 3PCF. The agreement between the model predictions and galaxy 3PCF measurements lends further credence to the straightforward association of galaxies with CDM halos and subhalos.

  5. Plant functional type mapping for earth system models

    NASA Astrophysics Data System (ADS)

    Poulter, B.; Ciais, P.; Hodson, E.; Lischke, H.; Maignan, F.; Plummer, S.; Zimmermann, N. E.

    2011-08-01

    The sensitivity of global carbon and water cycling to climate variability is coupled directly to land cover and the distribution of vegetation. To investigate biogeochemistry-climate interactions, earth system models require a representation of vegetation distributions that are either prescribed from remote sensing data or simulated via biogeography models. However, the abstraction of earth system state variables in models means that data products derived from remote sensing need to be post-processed for model-data assimilation. Dynamic global vegetation models (DGVM) rely on the concept of plant functional types (PFT) to group shared traits of thousands of plant species into just several classes. Available databases of observed PFT distributions must be relevant to existing satellite sensors and their derived products, and to the present day distribution of managed lands. Here, we develop four PFT datasets based on land-cover information from three satellite sensors (EOS-MODIS 1 km and 0.5 km, SPOT4-VEGETATION 1 km, and ENVISAT-MERIS 0.3 km spatial resolution) that are merged with spatially-consistent Köppen-Geiger climate zones. Using a beta (β) diversity metric to assess reclassification similarity, we find that the greatest uncertainty in PFT classifications occur most frequently between cropland and grassland categories, and in dryland systems between shrubland, grassland and forest categories because of differences in the minimum threshold required for forest cover. The biogeography-biogeochemistry DGVM, LPJmL, is used in diagnostic mode with the four PFT datasets prescribed to quantify the effect of land-cover uncertainty on climatic sensitivity of gross primary productivity (GPP) and transpiration fluxes. Our results show that land-cover uncertainty has large effects in arid regions, contributing up to 30 % (20 %) uncertainty in the sensitivity of GPP (transpiration) to precipitation. The availability of plant functional type datasets that are consistent

  6. Incorporating Functional Gene Quantification into Traditional Decomposition Models

    NASA Astrophysics Data System (ADS)

    Todd-Brown, K. E.; Zhou, J.; Yin, H.; Wu, L.; Tiedje, J. M.; Schuur, E. A. G.; Konstantinidis, K.; Luo, Y.

    2014-12-01

    Incorporating new genetic quantification measurements into traditional substrate pool models represents a substantial challenge. These decomposition models are built around the idea that substrate availablity, with environmental drivers, limit carbon dioxide respiration rates. In this paradigm, microbial communities optimally adapt to a given substrate and environment on much shorter time scales then the carbon flux of interest. By characterizing the relative shift in biomass of these microbial communities, we informed previously poorly constrained parameters in traditional decomposition models. In this study we coupled a 9 month laboratory incubation study with quantitative gene measurements with traditional CO2 flux measurements plus initial soil organic carbon quantification. GeoChip 5.0 was used to quantify the functional genes associated with carbon cycling at 2 weeks, 3 months and 9 months. We then combined the genes which 'collapsed' over the experiment and assumed that this tracked the relative change in the biomass associated with the 'fast' pool. We further assumed that this biomass was proportional to the 'fast' SOC pool and thus were able to constrain the relative change in the fast SOC pool in our 3-pool decomposition model. We found that biomass quantification described above, combined with traditional CO2 flux and SOC measurements, improve the transfer coefficient estimation in traditional decomposition models. Transfer coefficients are very difficult to characterized using traditional CO2 flux measurements, thus DNA quantification provides new and significant information about the system. Over a 100 year simulation, these new biologically informed parameters resulted in an additional 10% of SOC loss over the traditionally informed parameters.

  7. Exact Potts model partition functions on ladder graphs

    NASA Astrophysics Data System (ADS)

    Shrock, Robert

    2000-08-01

    We present exact calculations of the partition function Z of the q-state Potts model and its generalization to real q, for arbitrary temperature on n-vertex ladder graphs, i.e., strips of the square lattice with width Ly=2 and arbitrary length Lx, with free, cyclic, and Möbius longitudinal boundary conditions. These partition functions are equivalent to Tutte/Whitney polynomials for these graphs. The free energy is calculated exactly for the infinite-length limit of these ladder graphs and the thermodynamics is discussed. By comparison with strip graphs of other widths, we analyze how the singularities at the zero-temperature critical point of the ferromagnet on infinite-length, finite-width strips depend on the width. We point out and study the following noncommutativity at certain special values q s: lim n→∞ limq→q s Z 1/n≠ limq→q s limn→∞ Z 1/n. It is shown that the Potts antiferromagnet on both the infinite-length line and ladder graphs with cyclic or Möbius boundary conditions exhibits a phase transition at finite temperature if 0< q<2, but with unphysical properties, including negative specific heat and non-existence, in the low-temperature phase, of an n→∞ limit for thermodynamic functions that is independent of boundary conditions. Considering the full generalization to arbitrary complex q and temperature, we determine the singular locus B in the corresponding C2 space, arising as the accumulation set of partition function zeros as n→∞. In particular, we study the connection with the T=0 limit of the Potts antiferromagnet where B reduces to the accumulation set of chromatic zeros. Certain properties of the complex-temperature phase diagrams are shown to exhibit close connections with those of the model on the square lattice, showing that exact solutions on infinite-length strips provide a way of gaining insight into these complex-temperature phase diagrams.

  8. Modeling root reinforcement using root-failure Weibull survival function

    NASA Astrophysics Data System (ADS)

    Schwarz, M.; Giadrossich, F.; Cohen, D.

    2013-03-01

    Root networks contribute to slope stability through complicated interactions that include mechanical compression and tension. Due to the spatial heterogeneity of root distribution and the dynamic of root turnover, the quantification of root reinforcement on steep slope is challenging and consequently the calculation of slope stability as well. Although the considerable advances in root reinforcement modeling, some important aspect remain neglected. In this study we address in particular to the role of root strength variability on the mechanical behaviors of a root bundle. Many factors may contribute to the variability of root mechanical properties even considering a single class of diameter. This work presents a new approach for quantifying root reinforcement that considers the variability of mechanical properties of each root diameter class. Using the data of laboratory tensile tests and field pullout tests, we calibrate the parameters of the Weibull survival function to implement the variability of root strength in a numerical model for the calculation of root reinforcement (RBMw). The results show that, for both laboratory and field datasets, the parameters of the Weibull distribution may be considered constant with the exponent equal to 2 and the normalized failure displacement equal to 1. Moreover, the results show that the variability of root strength in each root diameter class has a major influence on the behavior of a root bundle with important implications when considering different approaches in slope stability calculation. Sensitivity analysis shows that the calibration of the tensile force and the elasticity of the roots are the most important equations, as well as the root distribution. The new model allows the characterization of root reinforcement in terms of maximum pullout force, stiffness, and energy. Moreover, it simplifies the implementation of root reinforcement in slope stability models. The realistic quantification of root reinforcement for

  9. Dynamic density functional theory of solid tumor growth: Preliminary models.

    PubMed

    Chauviere, Arnaud; Hatzikirou, Haralambos; Kevrekidis, Ioannis G; Lowengrub, John S; Cristini, Vittorio

    2012-03-01

    Cancer is a disease that can be seen as a complex system whose dynamics and growth result from nonlinear processes coupled across wide ranges of spatio-temporal scales. The current mathematical modeling literature addresses issues at various scales but the development of theoretical methodologies capable of bridging gaps across scales needs further study. We present a new theoretical framework based on Dynamic Density Functional Theory (DDFT) extended, for the first time, to the dynamics of living tissues by accounting for cell density correlations, different cell types, phenotypes and cell birth/death processes, in order to provide a biophysically consistent description of processes across the scales. We present an application of this approach to tumor growth. PMID:22489279

  10. From genomes to function: haloarchaea as model organisms.

    PubMed

    Soppa, Jörg

    2006-03-01

    Haloarchaea are adapted to high-salt environments and accumulate equally high salt concentrations in the cytoplasm. The genomes of representatives of six haloarchaeal genera have been fully or partially sequenced, allowing the analysis of haloarchaeal properties in silico. Transcriptome and proteome analyses have been established for Halobacterium salinarum and Haloferax volcanii. Genetic systems are available including methods that allow the fast in-frame deletion or modification of chromosomal genes. The high-efficiency transformation system of Hf. volcanii allows the isolation of genes essential for a biological process by complementation of loss-of-function mutants. For the analysis of haloarchaeal biology many molecular genetic, biochemical, structural and cell biological methods have been adapted to application at high salt concentrations. Recently it has become clear that several different mechanisms allow the adaptation of proteins to the high salt concentration of the cytoplasm. Taken together, the wealth of techniques available make haloarchaea excellent archaeal model species. PMID:16514139

  11. Drosophila Cancer Models Identify Functional Differences between Ret Fusions.

    PubMed

    Levinson, Sarah; Cagan, Ross L

    2016-09-13

    We generated and compared Drosophila models of RET fusions CCDC6-RET and NCOA4-RET. Both RET fusions directed cells to migrate, delaminate, and undergo EMT, and both resulted in lethality when broadly expressed. In all phenotypes examined, NCOA4-RET was more severe than CCDC6-RET, mirroring their effects on patients. A functional screen against the Drosophila kinome and a library of cancer drugs found that CCDC6-RET and NCOA4-RET acted through different signaling networks and displayed distinct drug sensitivities. Combining data from the kinome and drug screens identified the WEE1 inhibitor AZD1775 plus the multi-kinase inhibitor sorafenib as a synergistic drug combination that is specific for NCOA4-RET. Our work emphasizes the importance of identifying and tailoring a patient's treatment to their specific RET fusion isoform and identifies a multi-targeted therapy that may prove effective against tumors containing the NCOA4-RET fusion. PMID:27626672

  12. Correlation functions of the Aharony-Bergman-Jafferis-Maldacena model

    NASA Astrophysics Data System (ADS)

    Lee, Bum-Hoon; Gwak, Bogeun; Park, Chanyong

    2013-04-01

    In the Aharony-Bergman-Jafferis-Maldacena model, we study the three-point function of two heavy operators and an (ir)relevant one. Following the AdS/CFT correspondence, the structure constant in the large ’t Hooft coupling limit can be factorized into two parts. One is the structure constant with a marginal operator, which is fully determined by the physical quantities of heavy operators and gives rise to a result that is consistent with the renormalization-group analysis. The other can be expressed as the universal form depending only on the conformal dimension of an (ir)relevant operator. We also investigate the new size effect of a circular string dual to a certain closed spin chain.

  13. Human haptoglobin structure and function--a molecular modelling study.

    PubMed

    Polticelli, F; Bocedi, A; Minervini, G; Ascenzi, P

    2008-11-01

    Hemoglobin is the most prominent protein in blood, transporting O(2) and facilitating reactive oxygen and nitrogen species detoxification. Hemoglobin metabolism leads to the release of extra-erythrocytic hemoglobin, with potentially severe consequences for health. Extra-erythrocytic hemoglobin is complexed to haptoglobin for clearance by tissue macrophages. The human gene for haptoglobin consists of three structural alleles: Hp1F, Hp1S and Hp2. The products of the Hp1F and Hp1S alleles differ by only one amino acid, whereas the Hp2 allele is the result of a fusion of the Hp1F and Hp1S alleles, is present only in humans and gives rise to a longer alpha-chain. Haptoglobin consists of a dimer of alphabeta-chains covalently linked by a disulphide bond between the Cys15 residue of each alpha-chain. However, the presence of the Hp1 and Hp2 alleles in humans gives rise to HPT1-1 dimers (covalently linked by Cys15 residues), HPT1-2 hetero-oligomers and HPT2-2 oligomers. In fact, the HPT2 variant displays two free Cys residues (Cys15 and Cys74) whose participation in intermolecular disulphide bonds gives rise to higher-order covalent multimers. Here, the complete modelling of both haptoglobin variants, together with their basic quaternary structure arrangements (i.e. HPT1 dimer and HPT2 trimer), is reported. The structural details of the models, which represent the first complete view of the molecular details of human haptoglobin variants, are discussed in relation to the known haptoglobin function(s). PMID:18959750

  14. A continuous function model for path prediction of entities

    NASA Astrophysics Data System (ADS)

    Nanda, S.; Pray, R.

    2007-04-01

    As militaries across the world continue to evolve, the roles of humans in various theatres of operation are being increasingly targeted by military planners for substitution with automation. Forward observation and direction of supporting arms to neutralize threats from dynamic adversaries is one such example. However, contemporary tracking and targeting systems are incapable of serving autonomously for they do not embody the sophisticated algorithms necessary to predict the future positions of adversaries with the accuracy offered by the cognitive and analytical abilities of human operators. The need for these systems to incorporate methods characterizing such intelligence is therefore compelling. In this paper, we present a novel technique to achieve this goal by modeling the path of an entity as a continuous polynomial function of multiple variables expressed as a Taylor series with a finite number of terms. We demonstrate the method for evaluating the coefficient of each term to define this function unambiguously for any given entity, and illustrate its use to determine the entity's position at any point in time in the future.

  15. Bidirectional texture function modeling: a state of the art survey.

    PubMed

    Filip, Jirí; Haindl, Michal

    2009-11-01

    An ever-growing number of real-world computer vision applications require classification, segmentation, retrieval, or realistic rendering of genuine materials. However, the appearance of real materials dramatically changes with illumination and viewing variations. Thus, the only reliable representation of material visual properties requires capturing of its reflectance in as wide range of light and camera position combinations as possible. This is a principle of the recent most advanced texture representation, the Bidirectional Texture Function (BTF). Multispectral BTF is a seven-dimensional function that depends on view and illumination directions as well as on planar texture coordinates. BTF is typically obtained by measurement of thousands of images covering many combinations of illumination and viewing angles. However, the large size of such measurements has prohibited their practical exploitation in any sensible application until recently. During the last few years, the first BTF measurement, compression, modeling, and rendering methods have emerged. In this paper, we categorize, critically survey, and psychophysically compare such approaches, which were published in this newly arising and important computer vision and graphics area. PMID:19762922

  16. A three-stage model of Golgi structure and function.

    PubMed

    Day, Kasey J; Staehelin, L Andrew; Glick, Benjamin S

    2013-09-01

    The Golgi apparatus contains multiple classes of cisternae that differ in structure, composition, and function, but there is no consensus about the number and definition of these classes. A useful way to classify Golgi cisternae is according to the trafficking pathways by which the cisternae import and export components. By this criterion, we propose that Golgi cisternae can be divided into three classes that correspond to functional stages of maturation. First, cisternae at the cisternal assembly stage receive COPII vesicles from the ER and recycle components to the ER in COPI vesicles. At this stage, new cisternae are generated. Second, cisternae at the carbohydrate synthesis stage exchange material with one another via COPI vesicles. At this stage, most of the glycosylation and polysaccharide synthesis reactions occur. Third, cisternae at the carrier formation stage produce clathrin-coated vesicles and exchange material with endosomes. At this stage, biosynthetic cargo proteins are packaged into various transport carriers, and the cisternae ultimately disassemble. Discrete transitions occur as a cisterna matures from one stage to the next. Within each stage, the structure and composition of a cisterna can evolve, but the trafficking pathways remain unchanged. This model offers a unified framework for understanding the properties of the Golgi in diverse organisms. PMID:23881164

  17. Plant functional type mapping for earth system models

    NASA Astrophysics Data System (ADS)

    Poulter, B.; Ciais, P.; Hodson, E.; Lischke, H.; Maignan, F.; Plummer, S.; Zimmermann, N. E.

    2011-11-01

    The sensitivity of global carbon and water cycling to climate variability is coupled directly to land cover and the distribution of vegetation. To investigate biogeochemistry-climate interactions, earth system models require a representation of vegetation distributions that are either prescribed from remote sensing data or simulated via biogeography models. However, the abstraction of earth system state variables in models means that data products derived from remote sensing need to be post-processed for model-data assimilation. Dynamic global vegetation models (DGVM) rely on the concept of plant functional types (PFT) to group shared traits of thousands of plant species into usually only 10-20 classes. Available databases of observed PFT distributions must be relevant to existing satellite sensors and their derived products, and to the present day distribution of managed lands. Here, we develop four PFT datasets based on land-cover information from three satellite sensors (EOS-MODIS 1 km and 0.5 km, SPOT4-VEGETATION 1 km, and ENVISAT-MERIS 0.3 km spatial resolution) that are merged with spatially-consistent Köppen-Geiger climate zones. Using a beta (ß) diversity metric to assess reclassification similarity, we find that the greatest uncertainty in PFT classifications occur most frequently between cropland and grassland categories, and in dryland systems between shrubland, grassland and forest categories because of differences in the minimum threshold required for forest cover. The biogeography-biogeochemistry DGVM, LPJmL, is used in diagnostic mode with the four PFT datasets prescribed to quantify the effect of land-cover uncertainty on climatic sensitivity of gross primary productivity (GPP) and transpiration fluxes. Our results show that land-cover uncertainty has large effects in arid regions, contributing up to 30% (20%) uncertainty in the sensitivity of GPP (transpiration) to precipitation. The availability of PFT datasets that are consistent with current

  18. Assessment of Differential Item Functioning under Cognitive Diagnosis Models: The DINA Model Example

    ERIC Educational Resources Information Center

    Li, Xiaomin; Wang, Wen-Chung

    2015-01-01

    The assessment of differential item functioning (DIF) is routinely conducted to ensure test fairness and validity. Although many DIF assessment methods have been developed in the context of classical test theory and item response theory, they are not applicable for cognitive diagnosis models (CDMs), as the underlying latent attributes of CDMs are…

  19. Investigating Gravity Wave-Ionosphere Interactions Using The Transfer Function Model And An Ionosphere Model

    NASA Astrophysics Data System (ADS)

    Bruntz, R. J.; Paxton, L. J.; Miller, E. S.; Bust, G. S.; Mayr, H. G.

    2015-12-01

    The Transfer Function Model (TFM) has been used in numerous studies to simulate gravity waves. In the TFM, the time dependence is formulated in terms of frequencies, and the horizontal wave pattern on the globe is formulated in terms of vector spherical harmonics. For a wide range of frequencies, the equations of mass, energy and momentum conservation are solved to compile a transfer function. The transfer function can then be easily combined with a time-dependent source whose spatial extent is also expressed in spherical harmonics, to produce a global atmospheric response, including gravity waves. This approach has significant benefits in that the solution is grid-independent (without any inherent limits on resolution), and the solutions do not suffer from singularities at the poles. We will show results from our simulations that couple the output of the TFM to an ionospheric model, to predict traveling ionospheric disturbances (TIDs) driven by the simulated gravity waves.

  20. Finite state model of locomotion for functional electrical stimulation systems.

    PubMed

    Popović, D B

    1993-01-01

    A finite state model of locomotion was developed to simplify a controller design for motor activities of handicapped humans. This paper presents a model developed for real time control of locomotion with functional electrical stimulation (FES) assistive systems. Hierarchical control of locomotion was adopted with three levels: voluntary, coordination and actuator level. This paper deals only with coordination level of control. In our previous studies we demonstrated that a skill-based expert system can be used for coordination level of control in multi-joint FES systems. Basic elements in this skill-based expert system are production rules. Production rules have the form of If-Then conditional expressions. A technique of automatic determination of these conditional expressions is presented in this paper. This technique for automatic synthesis of production rules uses fuzzy logic and artificial neural networks (ANN). The special class of fuzzy logic elements used in this research is called preferential neurons. The preferential neurons were used to estimate the relevance of each of the sensory inputs to the recognition of patterns defined as finite states. The combination of preferential neurons forms a preferential neural network. The preferential neural network belongs to a class of ANNs. The preferential neural network determined the set of finite states convenient for a skill-based expert system for different modalities of locomotion. PMID:8234764

  1. Function of Hexagenia (Mayfly) Burrows: Fluid Model Suggests Bacterial Gardening

    NASA Astrophysics Data System (ADS)

    Traynham, B.; Furbish, D.; Miller, M.; White, D.

    2006-12-01

    Lake and stream bottoms experience an array of physical, chemical, and biological processes that create spatial variations both in the fluid column and in the sediment that provide a physical template for distinct niches. Burrowing insects are major ecological engineers of communities where they structure large areas of the benthic habitat through bioturbation and other activities including respiration, feeding, and defecation. The burrowing mayfly Hexagenia, when present in high densities, has a large impact on food-web dynamics and provides essential ecosystem services within the fluid column and benthic substrate, including sediment mixing, nutrient cycling, and ultimately, energy flow through the freshwater food web. It has long been recognized that particular benthic species are important in linking detrital energy resources to higher trophic levels and for determining how organic matter is processed in freshwater ecosystems; however, the unique contributions made by individual benthic species is largely absent from the literature. Here we present a model that describes the structure and function of a Hexagenia burrow. If testing supports this hypothesis, the model suggests that when high food concentration is available to Hexagenia, there exists a favorable tube length for harvesting bacteria that grow on the burrow walls. The burrow microhabitat created by Hexagenia serves as a case-study in understanding the influence of benthic burrowers on both energy flow through freshwater food webs and nutrient cycling.

  2. Applying the luminosity function statistics in the fireshell model

    NASA Astrophysics Data System (ADS)

    Rangel Lemos, L. J.; Bianco, C. L.; Ruffini, R.

    2015-12-01

    The luminosity function (LF) statistics applied to the data of BATSE, GBM/Fermi and BAT/Swift is the theme approached in this work. The LF is a strong statistical tool to extract useful information from astrophysical samples, and the key point of this statistical analysis is in the detector sensitivity, where we have performed careful analysis. We applied the tool of the LF statistics to three GRB classes predicted by the Fireshell model. We produced, by LF statistics, predicted distributions of: peak ux N(Fph pk), redshift N(z) and peak luminosity N(Lpk) for the three GRB classes predicted by Fireshell model; we also used three GRB rates. We looked for differences among the distributions, and in fact we found. We performed a comparison between the distributions predicted and observed (with and without redshifts), where we had to build a list with 217 GRBs with known redshifts. Our goal is transform the GRBs in a standard candle, where a alternative is find a correlation between the isotropic luminosity and the Band peak spectral energy (Liso - Epk).

  3. Electron Spectral Function for the t-J Model.

    NASA Astrophysics Data System (ADS)

    McMullen, T.; Gibbs, Zane P.; Bishop, Marilyn F.

    1996-03-01

    Computed electron spectral functions for the t-J model(Z. Wang, Y. Bang, and G. Kotliar, Phys. Rev. Lett. 67), 2733, (1991). are presented. Large-\\cal N expansion techniques are used in which all self energies are evaluated to leading order in 1/\\cal N. Slave bosons are employed to enforce the non-double-occupancy constraint. Results are given for several values of the exchange coupling J/t and doping δ, including those appropriate to cuprate superconductors. A sharp dispersive quasiparticle peak is found near the Fermi energy. Additional spectral weight occurs at lower frequencies, which arises from the form of the normal self-energy. This is qualitatively similar to the self-energy obtained by Kampf and Schrieffer(A. Kampf and J. R. Schrieffer, Phys. Rev. B 41), 6399 (1990). from a parameterized model of an electron coupled to antiferromagnetic spin fluctuations, which is characterized by shadow bands. The lower shadow band in their calculation is analogous to the lower band in our results.

  4. Neocaridina denticulata: A Decapod Crustacean Model for Functional Genomics.

    PubMed

    Mykles, Donald L; Hui, Jerome H L

    2015-11-01

    A decapod crustacean model is needed for understanding the molecular mechanisms underlying physiological processes, such as reproduction, sex determination, molting and growth, immunity, regeneration, and response to stress. Criteria for selection are: life-history traits, adult size, availability and ease of culture, and genomics and genetic manipulation. Three freshwater species are considered: cherry shrimp, Neocaridina denticulata; red swamp crayfish, Procambarus clarkii; and redclaw crayfish, Cherax quadricarinatus. All three are readily available, reproduce year round, and grow rapidly. The crayfish species require more space for culture than does N. denticulata. The transparent cuticle of cherry shrimp provides for direct assessment of reproductive status, stage of molt, and tissue-specific expression of reporter genes, and facilitates screening of mutations affecting phenotype. Moreover, a preliminary genome of N. denticulata is available and efforts toward complete genome sequencing and transcriptome sequencing have been initiated. Neocaridina denticulata possesses the best combination of traits that make it most suitable as a model for functional genomics. The next step is to obtain the complete genome sequence and to develop molecular technologies for the screening of mutants and for manipulating tissue-specific gene expression. PMID:26002561

  5. Bidirectional reflectance function in coastal waters: modeling and validation

    NASA Astrophysics Data System (ADS)

    Gilerson, Alex; Hlaing, Soe; Harmel, Tristan; Tonizzo, Alberto; Arnone, Robert; Weidemann, Alan; Ahmed, Samir

    2011-11-01

    The current operational algorithm for the correction of bidirectional effects from the satellite ocean color data is optimized for typical oceanic waters. However, versions of bidirectional reflectance correction algorithms, specifically tuned for typical coastal waters and other case 2 conditions, are particularly needed to improve the overall quality of those data. In order to analyze the bidirectional reflectance distribution function (BRDF) of case 2 waters, a dataset of typical remote sensing reflectances was generated through radiative transfer simulations for a large range of viewing and illumination geometries. Based on this simulated dataset, a case 2 water focused remote sensing reflectance model is proposed to correct above-water and satellite water leaving radiance data for bidirectional effects. The proposed model is first validated with a one year time series of in situ above-water measurements acquired by collocated multi- and hyperspectral radiometers which have different viewing geometries installed at the Long Island Sound Coastal Observatory (LISCO). Match-ups and intercomparisons performed on these concurrent measurements show that the proposed algorithm outperforms the algorithm currently in use at all wavelengths.

  6. Model-based HSF using by target point control function

    NASA Astrophysics Data System (ADS)

    Kim, Seongjin; Do, Munhoe; An, Yongbae; Choi, Jaeseung; Yang, Hyunjo; Yim, Donggyu

    2015-03-01

    As the technology node shrinks, ArF Immersion reaches the limitation of wafer patterning, furthermore weak point during the mask processing is generated easily. In order to make strong patterning result, the design house conducts lithography rule checking (LRC). Despite LRC processing, we found the weak point at the verification stage of optical proximity correction (OPC). It is called the hot spot point (HSP). In order to fix the HSP, many studies have been performed. One of the most general hot spot fixing (HSF) methods is that the modification bias which consists of "Line-Resizing" and "Space-Resizing". In addition to the general rule biasing method, resolution enhancement techniques (RET) which includes the inverse lithography technology (ILT) and model based assist feature (MBAF) have been adapted to remove the hot spot and to maximize the process window. If HSP is found during OPC verification stage, various HSF methods can be applied. However, HSF process added on regular OPC procedure makes OPC turn-around time (TAT) increased. In this paper, we introduce a new HSF method that is able to make OPC TAT shorter than the common HSF method. The new HSF method consists of two concepts. The first one is that OPC target point is controlled to fix HSP. Here, the target point should be moved to optimum position at where the edge placement error (EPE) can be 0 at critical points. Many parameters such as a model accuracy or an OPC recipe become the cause of larger EPE. The second one includes controlling of model offset error through target point adjustment. Figure 1 shows the case EPE is not 0. It means that the simulation contour was not targeted well after OPC process. On the other hand, Figure 2 shows the target point is moved -2.5nm by using target point control function. As a result, simulation contour is matched to the original layout. This function can be powerfully adapted to OPC procedure of memory and logic devices.

  7. The FEATURE framework for protein function annotation: modeling new functions, improving performance, and extending to novel applications

    PubMed Central

    Halperin, Inbal; Glazer, Dariya S; Wu, Shirley; Altman, Russ B

    2008-01-01

    Structural genomics efforts contribute new protein structures that often lack significant sequence and fold similarity to known proteins. Traditional sequence and structure-based methods may not be sufficient to annotate the molecular functions of these structures. Techniques that combine structural and functional modeling can be valuable for functional annotation. FEATURE is a flexible framework for modeling and recognition of functional sites in macromolecular structures. Here, we present an overview of the main components of the FEATURE framework, and describe the recent developments in its use. These include automating training sets selection to increase functional coverage, coupling FEATURE to structural diversity generating methods such as molecular dynamics simulations and loop modeling methods to improve performance, and using FEATURE in large-scale modeling and structure determination efforts. PMID:18831785

  8. Homology Modeling: Generating Structural Models to Understand Protein Function and Mechanism

    NASA Astrophysics Data System (ADS)

    Ramachandran, Srinivas; Dokholyan, Nikolay V.

    Geneticists and molecular and cell biologists routinely uncover new proteins important in specific biological processes/pathways. However, either the molecular functions or the functional mechanisms of many of these proteins are unclear due to a lack of knowledge of their atomic structures. Yet, determining experimental structures of many proteins presents technical challenges. The current methods for obtaining atomic-resolution structures of biomolecules (X-ray crystallography and NMR spectroscopy) require pure preparations of proteins at concentrations much higher than those at which the proteins exist in a physiological environment. Additionally, NMR has size limitations, with current technology limited to the determination of structures of proteins with masses of up to 15 kDa. Due to these reasons, atomic structures of many medically and biologically important proteins do not exist. However, the structures of these proteins are essential for several purposes, including in silico drug design [1], understanding the effects of disease mutations [2], and designing experiments to probe the functional mechanisms of proteins. Comparative modeling has gained importance as a tool for bridging the gap between sequence and structure space, allowing researchers to build structural models of proteins that are difficult to crystallize or for which structure determination by NMR spectroscopy is not tractable. Comparative modeling, or homology modeling, exploits the fact that two proteins whose sequences are evolutionarily connected display similar structural features [3]. Thus, the known structure of a protein (template) can be used to generate a molecular model of the protein (query) whose experimental structure is notknown.

  9. Uterine glands: development, function and experimental model systems.

    PubMed

    Cooke, Paul S; Spencer, Thomas E; Bartol, Frank F; Hayashi, Kanako

    2013-09-01

    Development of uterine glands (adenogenesis) in mammals typically begins during the early post-natal period and involves budding of nascent glands from the luminal epithelium and extensive cell proliferation in these structures as they grow into the surrounding stroma, elongate and mature. Uterine glands are essential for pregnancy, as demonstrated by the infertility that results from inhibiting the development of these glands through gene mutation or epigenetic strategies. Several genes, including forkhead box A2, beta-catenin and members of the Wnt and Hox gene families, are implicated in uterine gland development. Progestins inhibit uterine epithelial proliferation, and this has been employed as a strategy to develop a model in which progestin treatment of ewes for 8 weeks from birth produces infertile adults lacking uterine glands. More recently, mouse models have been developed in which neonatal progestin treatment was used to permanently inhibit adenogenesis and adult fertility. These studies revealed a narrow and well-defined window in which progestin treatments induced permanent infertility by impairing neonatal gland development and establishing endometrial changes that result in implantation defects. These model systems are being utilized to better understand the molecular mechanisms underlying uterine adenogenesis and endometrial function. The ability of neonatal progestin treatment in sheep and mice to produce infertility suggests that an approach of this kind may provide a contraceptive strategy with application in other species. Recent studies have defined the temporal patterns of adenogenesis in uteri of neonatal and juvenile dogs and work is underway to determine whether neonatal progestin or other steroid hormone treatments might be a viable contraceptive approach in this species. PMID:23619340

  10. Uterine glands: development, function and experimental model systems

    PubMed Central

    Cooke, Paul S.; Spencer, Thomas E.; Bartol, Frank F.; Hayashi, Kanako

    2013-01-01

    Development of uterine glands (adenogenesis) in mammals typically begins during the early post-natal period and involves budding of nascent glands from the luminal epithelium and extensive cell proliferation in these structures as they grow into the surrounding stroma, elongate and mature. Uterine glands are essential for pregnancy, as demonstrated by the infertility that results from inhibiting the development of these glands through gene mutation or epigenetic strategies. Several genes, including forkhead box A2, beta-catenin and members of the Wnt and Hox gene families, are implicated in uterine gland development. Progestins inhibit uterine epithelial proliferation, and this has been employed as a strategy to develop a model in which progestin treatment of ewes for 8 weeks from birth produces infertile adults lacking uterine glands. More recently, mouse models have been developed in which neonatal progestin treatment was used to permanently inhibit adenogenesis and adult fertility. These studies revealed a narrow and well-defined window in which progestin treatments induced permanent infertility by impairing neonatal gland development and establishing endometrial changes that result in implantation defects. These model systems are being utilized to better understand the molecular mechanisms underlying uterine adenogenesis and endometrial function. The ability of neonatal progestin treatment in sheep and mice to produce infertility suggests that an approach of this kind may provide a contraceptive strategy with application in other species. Recent studies have defined the temporal patterns of adenogenesis in uteri of neonatal and juvenile dogs and work is underway to determine whether neonatal progestin or other steroid hormone treatments might be a viable contraceptive approach in this species. PMID:23619340

  11. Annotation and retrieval system of CAD models based on functional semantics

    NASA Astrophysics Data System (ADS)

    Wang, Zhansong; Tian, Ling; Duan, Wenrui

    2014-11-01

    CAD model retrieval based on functional semantics is more significant than content-based 3D model retrieval during the mechanical conceptual design phase. However, relevant research is still not fully discussed. Therefore, a functional semantic-based CAD model annotation and retrieval method is proposed to support mechanical conceptual design and design reuse, inspire designer creativity through existing CAD models, shorten design cycle, and reduce costs. Firstly, the CAD model functional semantic ontology is constructed to formally represent the functional semantics of CAD models and describe the mechanical conceptual design space comprehensively and consistently. Secondly, an approach to represent CAD models as attributed adjacency graphs(AAG) is proposed. In this method, the geometry and topology data are extracted from STEP models. On the basis of AAG, the functional semantics of CAD models are annotated semi-automatically by matching CAD models that contain the partial features of which functional semantics have been annotated manually, thereby constructing CAD Model Repository that supports model retrieval based on functional semantics. Thirdly, a CAD model retrieval algorithm that supports multi-function extended retrieval is proposed to explore more potential creative design knowledge in the semantic level. Finally, a prototype system, called Functional Semantic-based CAD Model Annotation and Retrieval System(FSMARS), is implemented. A case demonstrates that FSMARS can successfully botain multiple potential CAD models that conform to the desired function. The proposed research addresses actual needs and presents a new way to acquire CAD models in the mechanical conceptual design phase.

  12. The Functional Transitions Model: Maximizing Ability in the Context of Progressive Disability Associated with Alzheimer's Disease

    ERIC Educational Resources Information Center

    Slaughter, Susan; Bankes, Jane

    2007-01-01

    The Functional Transitions Model (FTM) integrates the theoretical notions of progressive functional decline associated with Alzheimer's disease (AD), excess disability, and transitions occurring intermittently along the trajectory of functional decline. Application of the Functional Transitions Model to clinical practice encompasses the paradox of…

  13. Wightman function and vacuum fluctuations in higher dimensional brane models

    SciTech Connect

    Saharian, Aram A.

    2006-02-15

    The Wightman function and the vacuum expectation value of the field square are evaluated for a massive scalar field with a general curvature coupling parameter subject to Robin boundary conditions on two codimension-one parallel branes located on a (D+1)-dimensional background spacetime AdS{sub D{sub 1}}{sub +1}x{sigma} with a warped internal space {sigma}. The general case of different Robin coefficients on separate branes is considered. The application of the generalized Abel-Plana formula for the series over zeros of combinations of cylinder functions allows us to manifestly extract the part due to the bulk without boundaries. Unlike the purely anti-de Sitter (AdS) bulk, the vacuum expectation value of the field square induced by a single brane, in addition to the distance from the brane, depends also on the position of the brane in the bulk. The brane induced part in this expectation value vanishes when the brane position tends to the AdS horizon or the AdS boundary. The asymptotic behavior of the vacuum densities near the branes and at large distances is investigated. The contribution of Kaluza-Klein modes along {sigma} is discussed in various limiting cases. In the limit when the curvature radius for the AdS spacetime tends to infinity, we derive the results for two parallel Robin plates on the background spacetime R{sup (D{sub 1},1)}x{sigma}. For strong gravitational fields corresponding to large values of the AdS energy scale, both the single brane and interference parts of the expectation values integrated over the internal space are exponentially suppressed. As an example the case {sigma}=S{sup 1} is considered, corresponding to the AdS{sub D+1} bulk with one compactified dimension. An application to the higher dimensional generalization of the Randall-Sundrum brane model with arbitrary mass terms on the branes is discussed.

  14. Application of Gaussian Process Modeling to Analysis of Functional Unreliability

    SciTech Connect

    R. Youngblood

    2014-06-01

    This paper applies Gaussian Process (GP) modeling to analysis of the functional unreliability of a “passive system.” GPs have been used widely in many ways [1]. The present application uses a GP for emulation of a system simulation code. Such an emulator can be applied in several distinct ways, discussed below. All applications illustrated in this paper have precedents in the literature; the present paper is an application of GP technology to a problem that was originally analyzed [2] using neural networks (NN), and later [3, 4] by a method called “Alternating Conditional Expectations” (ACE). This exercise enables a multifaceted comparison of both the processes and the results. Given knowledge of the range of possible values of key system variables, one could, in principle, quantify functional unreliability by sampling from their joint probability distribution, and performing a system simulation for each sample to determine whether the function succeeded for that particular setting of the variables. Using previously available system simulation codes, such an approach is generally impractical for a plant-scale problem. It has long been recognized, however, that a well-trained code emulator or surrogate could be used in a sampling process to quantify certain performance metrics, even for plant-scale problems. “Response surfaces” were used for this many years ago. But response surfaces are at their best for smoothly varying functions; in regions of parameter space where key system performance metrics may behave in complex ways, or even exhibit discontinuities, response surfaces are not the best available tool. This consideration was one of several that drove the work in [2]. In the present paper, (1) the original quantification of functional unreliability using NN [2], and later ACE [3], is reprised using GP; (2) additional information provided by the GP about uncertainty in the limit surface, generally unavailable in other representations, is discussed

  15. Density functional theory modeling of multilayer "epitaxial" graphene oxide.

    PubMed

    Zhou, Si; Bongiorno, Angelo

    2014-11-18

    CONSPECTUS: Graphene oxide (GO) is a complex material of both fundamental and applied interest. Elucidating the structure of GO is crucial to achieve control over its properties and technological applications. GO is a nonstoichiometric and hygroscopic material with a lamellar structure, and its physical chemical properties depend critically on synthesis procedures and postsynthesis treatments. Numerous efforts are in place to both understand and exploit this versatile layered carbon material. This Account reports on recent density functional theory (DFT) studies of "epitaxial" graphene oxide (hereafter EGO), a type of GO obtained by oxidation of graphene films grown epitaxially on silicon carbide. Here, we rely on selected X-ray photoelectron spectroscopy (XPS), infrared spectroscopy (IR), and X-ray diffraction (XRD) measurements of EGO, and we discuss in great detail how we utilized DFT-based techniques to project out from the experimental data basic atomistic information about the chemistry and structure of these films. This Account provides an example as to how DFT modeling can be used to elucidate complex materials such as GO from a limited set of experimental information. EGO exhibits a uniform layered structure, consisting of a stack of graphene planes hosting predominantly epoxide and hydroxyl groups, and water molecules intercalated between the oxidized carbon layers. Here, we first focus on XPS measurements of EGO, and we use DFT to generate realistic model structures, calculate core-level chemical shifts, and through the comparison with experiment, gain insight on the chemical composition and metastability characteristics of EGO. DFT calculations are then used to devise a simplistic but accurate simulation scheme to study thermodynamic and kinetic stability and to predict the intralayer structure of EGO films aged at room temperature. Our simulations show that aged EGO encompasses layers with nanosized oxidized domains presenting a high concentration of

  16. Dicentric chromosomes: unique models to study centromere function and inactivation

    PubMed Central

    Stimpson, Kaitlin M.; Matheny, Justyne E.

    2013-01-01

    Dicentric chromosomes are products of genome rearrangement that place two centromeres on the same chromosome. Depending on the organism, dicentric stability varies after formation. In humans, dicentrics occur naturally in a substantial portion of the population and usually segregate successfully in mitosis and meiosis. Their stability has been attributed to inactivation of one of the two centromeres, creating a functionally monocentric chromosome that can segregate normally during cell division. The molecular basis for centromere inactivation is not well under-stood, although studies in model organisms and in humans suggest that genomic and epigenetic mechanisms can be involved. Furthermore, constitutional dicentric chromosomes ascertained in patients presumably represent the most stable chromosomes, so the spectrum of dicentric fates, if it exists, is not entirely clear. Studies of engineered or induced dicentrics in budding yeast and plants have provided significant insight into the fate of dicentric chromosomes. And, more recently, studies have shown that dicentrics in humans can also undergo multiple fates after formation. Here, we discuss current experimental evidence from various organisms that has deepened our understanding of dicentric behavior and the intriguingly complex process of centromere inactivation. PMID:22801777

  17. PTEN recruitment controls synaptic and cognitive function in Alzheimer's models.

    PubMed

    Knafo, Shira; Sánchez-Puelles, Cristina; Palomer, Ernest; Delgado, Igotz; Draffin, Jonathan E; Mingo, Janire; Wahle, Tina; Kaleka, Kanwardeep; Mou, Liping; Pereda-Perez, Inmaculada; Klosi, Edvin; Faber, Erik B; Chapman, Heidi M; Lozano-Montes, Laura; Ortega-Molina, Ana; Ordóñez-Gutiérrez, Lara; Wandosell, Francisco; Viña, Jose; Dotti, Carlos G; Hall, Randy A; Pulido, Rafael; Gerges, Nashaat Z; Chan, Andrew M; Spaller, Mark R; Serrano, Manuel; Venero, César; Esteban, José A

    2016-03-01

    Dyshomeostasis of amyloid-β peptide (Aβ) is responsible for synaptic malfunctions leading to cognitive deficits ranging from mild impairment to full-blown dementia in Alzheimer's disease. Aβ appears to skew synaptic plasticity events toward depression. We found that inhibition of PTEN, a lipid phosphatase that is essential to long-term depression, rescued normal synaptic function and cognition in cellular and animal models of Alzheimer's disease. Conversely, transgenic mice that overexpressed PTEN displayed synaptic depression that mimicked and occluded Aβ-induced depression. Mechanistically, Aβ triggers a PDZ-dependent recruitment of PTEN into the postsynaptic compartment. Using a PTEN knock-in mouse lacking the PDZ motif, and a cell-permeable interfering peptide, we found that this mechanism is crucial for Aβ-induced synaptic toxicity and cognitive dysfunction. Our results provide fundamental information on the molecular mechanisms of Aβ-induced synaptic malfunction and may offer new mechanism-based therapeutic targets to counteract downstream Aβ signaling. PMID:26780512

  18. Modeling of Red Blood Cells and Related Spleen Function

    NASA Astrophysics Data System (ADS)

    Peng, Zhangli; Pivkin, Igor; Dao, Ming

    2011-11-01

    A key function of the spleen is to clear red blood cells (RBCs) with abnormal mechanical properties from the circulation. These abnormal mechanical properties may be due to RBC aging or RBC diseases, e.g., malaria and sickle cell anemia. Specifically, 10% of RBCs passing through the spleen are forced to squeeze into the narrow slits between the endothelial cells, and stiffer cells which get stuck are killed and digested by macrophages. To investigate this important physiological process, we employ three different approaches to study RBCs passage through these small slits, including analytical theory, Dissipative Particle Dynamics (DPD) simulation and Multiscale Finite Element Method (MS-FEM). By applying the analytical theory, we estimate the critical limiting geometries RBCs can pass. By using the DPD method, we study the full fluid-structure interaction problem, and compute RBC deformation under different pressure gradients. By employing the MS-FEM approach, we model the lipid bilayer and the cytoskeleton as two distinct layers, and focus on the cytoskeleton deformation and the bilayer-skeleton interaction force at the molecular level. Finally the results of these three approaches are compared to each other and correlated to the experimental observations.

  19. Vesicle formation and endocytosis: function, machinery, mechanisms, and modeling.

    PubMed

    Parkar, Nihal S; Akpa, Belinda S; Nitsche, Ludwig C; Wedgewood, Lewis E; Place, Aaron T; Sverdlov, Maria S; Chaga, Oleg; Minshall, Richard D

    2009-06-01

    Vesicle formation provides a means of cellular entry for extracellular substances and for recycling of membrane constituents. Mechanisms governing the two primary endocytic pathways (i.e., caveolae- and clathrin-mediated endocytosis, as well as newly emerging vesicular pathways) have become the focus of intense investigation to improve our understanding of nutrient, hormone, and drug delivery, as well as opportunistic invasion of pathogens. In this review of endocytosis, we broadly discuss the structural and signaling proteins that compose the molecular machinery governing endocytic vesicle formation (budding, invagination, and fission from the membrane), with some regard for the specificity observed in certain cell types and species. Important biochemical functions of endocytosis and diseases caused by their disruption also are discussed, along with the structures of key components of endocytic pathways and their known mechanistic contributions. The mechanisms by which principal components of the endocytic machinery are recruited to the plasma membrane, where they interact to induce vesicle formation, are discussed, together with computational approaches used to simulate simplified versions of endocytosis with the hope of clarifying aspects of vesicle formation that may be difficult to determine experimentally. Finally, we pose several unanswered questions intended to stimulate further research interest in the cell biology and modeling of endocytosis. PMID:19113823

  20. Vesicle Formation and Endocytosis: Function, Machinery, Mechanisms, and Modeling

    PubMed Central

    Parkar, Nihal S.; Akpa, Belinda S.; Nitsche, Ludwig C.; Wedgewood, Lewis E.; Place, Aaron T.; Sverdlov, Maria S.; Chaga, Oleg

    2009-01-01

    Abstract Vesicle formation provides a means of cellular entry for extracellular substances and for recycling of membrane constituents. Mechanisms governing the two primary endocytic pathways (i.e., caveolae- and clathrin-mediated endocytosis, as well as newly emerging vesicular pathways) have become the focus of intense investigation to improve our understanding of nutrient, hormone, and drug delivery, as well as opportunistic invasion of pathogens. In this review of endocytosis, we broadly discuss the structural and signaling proteins that compose the molecular machinery governing endocytic vesicle formation (budding, invagination, and fission from the membrane), with some regard for the specificity observed in certain cell types and species. Important biochemical functions of endocytosis and diseases caused by their disruption also are discussed, along with the structures of key components of endocytic pathways and their known mechanistic contributions. The mechanisms by which principal components of the endocytic machinery are recruited to the plasma membrane, where they interact to induce vesicle formation, are discussed, together with computational approaches used to simulate simplified versions of endocytosis with the hope of clarifying aspects of vesicle formation that may be difficult to determine experimentally. Finally, we pose several unanswered questions intended to stimulate further research interest in the cell biology and modeling of endocytosis. Antioxid. Redox Signal. 11, 1301–1312. PMID:19113823

  1. Applying Quality Function Deployment Model in Burn Unit Service Improvement.

    PubMed

    Keshtkaran, Ali; Hashemi, Neda; Kharazmi, Erfan; Abbasi, Mehdi

    2014-10-13

    Quality function deployment (QFD) is one of the most effective quality design tools. This study applies QFD technique to improve the quality of the burn unit services in Ghotbedin Hospital in Shiraz, Iran. First, the patients' expectations of burn unit services and their priorities were determined through Delphi method. Thereafter, burn unit service specifications were determined through Delphi method. Further, the relationships between the patients' expectations and service specifications and also the relationships between service specifications were determined through an expert group's opinion. Last, the final importance scores of service specifications were calculated through simple additive weighting method. The findings show that burn unit patients have 40 expectations in six different areas. These expectations are in 16 priority levels. Burn units also have 45 service specifications in six different areas. There are four-level relationships between the patients' expectations and service specifications and four-level relationships between service specifications. The most important burn unit service specifications have been identified in this study. The QFD model developed in the study can be a general guideline for QFD planners and executives. PMID:23884047

  2. A quantitative confidence signal detection model: 1. Fitting psychometric functions.

    PubMed

    Yi, Yongwoo; Merfeld, Daniel M

    2016-04-01

    Perceptual thresholds are commonly assayed in the laboratory and clinic. When precision and accuracy are required, thresholds are quantified by fitting a psychometric function to forced-choice data. The primary shortcoming of this approach is that it typically requires 100 trials or more to yield accurate (i.e., small bias) and precise (i.e., small variance) psychometric parameter estimates. We show that confidence probability judgments combined with a model of confidence can yield psychometric parameter estimates that are markedly more precise and/or markedly more efficient than conventional methods. Specifically, both human data and simulations show that including confidence probability judgments for just 20 trials can yield psychometric parameter estimates that match the precision of those obtained from 100 trials using conventional analyses. Such an efficiency advantage would be especially beneficial for tasks (e.g., taste, smell, and vestibular assays) that require more than a few seconds for each trial, but this potential benefit could accrue for many other tasks. PMID:26763777

  3. Stepwise building of plankton functional type (PFT) models: A feasible route to complex models?

    NASA Astrophysics Data System (ADS)

    Frede Thingstad, T.; Strand, Espen; Larsen, Aud

    2010-01-01

    We discuss the strategy of building models of the lower part of the planktonic food web in a stepwise manner: starting with few plankton functional types (PFTs) and adding resolution and complexity while carrying along the insight and results gained from simpler models. A central requirement for PFT models is that they allow sustained coexistence of the PFTs. Here we discuss how this identifies a need to consider predation, parasitism and defence mechanisms together with nutrient acquisition and competition. Although the stepwise addition of complexity is assumed to be useful and feasible, a rapid increase in complexity strongly calls for alternative approaches able to model emergent system-level features without a need for detailed representation of all the underlying biological detail.

  4. Functional Competency Development Model for Academic Personnel Based on International Professional Qualification Standards in Computing Field

    ERIC Educational Resources Information Center

    Tumthong, Suwut; Piriyasurawong, Pullop; Jeerangsuwan, Namon

    2016-01-01

    This research proposes a functional competency development model for academic personnel based on international professional qualification standards in computing field and examines the appropriateness of the model. Specifically, the model consists of three key components which are: 1) functional competency development model, 2) blended training…

  5. Functional Linear Models for Zero-Inflated Count Data with Application to Modeling Hospitalizations in Patients on Dialysis

    PubMed Central

    Şentürk, Damla; Dalrymple, Lorien S.; Nguyen, Danh V.

    2014-01-01

    Summary We propose functional linear models for zero-inflated count data with a focus on the functional hurdle and functional zero-inflated Poisson (ZIP) models. While the hurdle model assumes the counts come from a mixture of a degenerate distribution at zero and a zero-truncated Poisson distribution, the ZIP model considers a mixture of a degenerate distribution at zero and a standard Poisson distribution. We extend the generalized functional linear model framework with a functional predictor and multiple cross-sectional predictors to model counts generated by a mixture distribution. We propose an estimation procedure for functional hurdle and ZIP models, called penalized reconstruction (PR), geared towards error-prone and sparsely observed longitudinal functional predictors. The approach relies on dimension reduction and pooling of information across subjects involving basis expansions and penalized maximum likelihood techniques. The developed functional hurdle model is applied to modeling hospitalizations within the first two years from initiation of dialysis, with a high percentage of zeros, in the Comprehensive Dialysis Study participants. Hospitalization counts are modeled as a function of sparse longitudinal measurements of serum albumin concentrations, patient demographics and comorbidities. Simulation studies are used to study finite sample properties of the proposed method and include comparisons with an adaptation of standard principal components regression (PCR). PMID:24942314

  6. Mouse alpha-macroglobulin. Structure, function and a molecular model.

    PubMed Central

    Hudson, N W; Kehoe, J M; Koo, P H

    1987-01-01

    Mouse alpha-macroglobulin (M-AMG) is believed to be a functional homologue of human alpha 2-macroglobulin (h-alpha 2M). The subunit composition, the tryptic cleavage pattern before and after methylamine incorporation and the two-dimensional tryptic-peptide mapping, however, indicate that these two proteins are structurally distinct. M-AMG is composed of two major types of polypeptides (Mr 163,000 and 35,000) together with a minor polypeptide (Mr 185,000), whereas h-alpha 2M has only one type of polypeptide (Mr 185,000). After incorporation of methylamine, there is no change in the normal tryptic-cleavage pattern of M-AMG; however, tryptic cleavage of h-alpha 2M is severely retarded [Hudson & Koo (1982) Biochim. Biophys. Acta 704, 290-303]. The N-terminal sequence of the 163,000-Mr polypeptide of M-AMG shows sequence homology with the N-terminal sequence of h-alpha 2M. The amino acid compositions of M-AMG and its two major polypeptide chains are compared. Thermal fragmentation studies show that the 163,000-Mr polypeptide is broken down into 125,000-Mr and 29,000-Mr fragments. Trypsin-binding studies show that M-AMG can bind two molecules of trypsin/molecule. Inactivations of the trypsin-binding property of M-AMG and h-alpha 2M with methylamine show similar kinetics of inhibition at 4 degrees C. A structural model of M-AMG is proposed, based on accumulated data. Images Fig. 3. PMID:2449173

  7. Crustal structure beneath northeast India inferred from receiver function modeling

    NASA Astrophysics Data System (ADS)

    Borah, Kajaljyoti; Bora, Dipok K.; Goyal, Ayush; Kumar, Raju

    2016-09-01

    We estimated crustal shear velocity structure beneath ten broadband seismic stations of northeast India, by using H-Vp/Vs stacking method and a non-linear direct search approach, Neighbourhood Algorithm (NA) technique followed by joint inversion of Rayleigh wave group velocity and receiver function, calculated from teleseismic earthquakes data. Results show significant variations of thickness, shear velocities (Vs) and Vp/Vs ratio in the crust of the study region. The inverted shear wave velocity models show crustal thickness variations of 32-36 km in Shillong Plateau (North), 36-40 in Assam Valley and ∼44 km in Lesser Himalaya (South). Average Vp/Vs ratio in Shillong Plateau is less (1.73-1.77) compared to Assam Valley and Lesser Himalaya (∼1.80). Average crustal shear velocity beneath the study region varies from 3.4 to 3.5 km/s. Sediment structure beneath Shillong Plateau and Assam Valley shows 1-2 km thick sediment layer with low Vs (2.5-2.9 km/s) and high Vp/Vs ratio (1.8-2.1), while it is observed to be of greater thickness (4 km) with similar Vs and high Vp/Vs (∼2.5) in RUP (Lesser Himalaya). Both Shillong Plateau and Assam Valley show thick upper and middle crust (10-20 km), and thin (4-9 km) lower crust. Average Vp/Vs ratio in Assam Valley and Shillong Plateau suggest that the crust is felsic-to-intermediate and intermediate-to-mafic beneath Shillong Plateau and Assam Valley, respectively. Results show that lower crust rocks beneath the Shillong Plateau and Assam Valley lies between mafic granulite and mafic garnet granulite.

  8. Operator function modeling: Cognitive task analysis, modeling and intelligent aiding in supervisory control systems

    NASA Technical Reports Server (NTRS)

    Mitchell, Christine M.

    1990-01-01

    The design, implementation, and empirical evaluation of task-analytic models and intelligent aids for operators in the control of complex dynamic systems, specifically aerospace systems, are studied. Three related activities are included: (1) the models of operator decision making in complex and predominantly automated space systems were used and developed; (2) the Operator Function Model (OFM) was used to represent operator activities; and (3) Operator Function Model Expert System (OFMspert), a stand-alone knowledge-based system was developed, that interacts with a human operator in a manner similar to a human assistant in the control of aerospace systems. OFMspert is an architecture for an operator's assistant that uses the OFM as its system and operator knowledge base and a blackboard paradigm of problem solving to dynamically generate expectations about upcoming operator activities and interpreting actual operator actions. An experiment validated the OFMspert's intent inferencing capability and showed that it inferred the intentions of operators in ways comparable to both a human expert and operators themselves. OFMspert was also augmented with control capabilities. An interface allowed the operator to interact with OFMspert, delegating as much or as little control responsibility as the operator chose. With its design based on the OFM, OFMspert's control capabilities were available at multiple levels of abstraction and allowed the operator a great deal of discretion over the amount and level of delegated control. An experiment showed that overall system performance was comparable for teams consisting of two human operators versus a human operator and OFMspert team.

  9. Relation between transverse momentum dependent distribution functions and parton distribution functions in the covariant parton model approach

    SciTech Connect

    Efremov, A. V.; Teryaev, O. V.; Schweitzer, P.; Zavada, P.

    2011-03-01

    We derive relations between transverse momentum dependent distribution functions and the usual parton distribution functions in the 3D covariant parton model, which follow from Lorentz invariance and the assumption of a rotationally symmetric distribution of parton momenta in the nucleon rest frame. Using the known parton distribution functions f{sub 1}{sup a}(x) and g{sub 1}{sup a}(x) as input we predict the x- and p{sub T}-dependence of all twist-2 T-even transverse momentum dependent distribution functions.

  10. Fabrication, Characterization and Modeling of Functionally Graded Materials

    NASA Astrophysics Data System (ADS)

    Lee, Po-Hua

    In the past few decades, a number of theoretical and experimental studies for design, fabrication and performance analysis of solar panel systems (photovoltaic/thermal systems) have been documented. The existing literature shows that the use of solar energy provides a promising solution to alleviate the shortage of natural resources and the environmental pollution associated with electricity generation. A hybrid solar panel has been invented to integrate photovoltaic (PV) cells onto a substrate through a functionally graded material (FGM) with water tubes cast inside, through which water flow serves as both a heat sink and a solar heat collector. Due to the unique and graded material properties of FGMs, this novel design not only supplies efficient thermal harvest and electrical production, but also provides benefits such as structural integrity and material efficiency. In this work, a sedimentation method has been used to fabricate aluminum (Al) and high-density polyethylene (HDPE) FGMs. The size effect of aluminum powder on the material gradation along the depth direction is investigated. Aluminum powder or the mixture of Al and HDPE powder is thoroughly mixed and uniformly dispersed in ethanol and then subjected to sedimentation. During the sedimentation process, the concentration of Al and HDPE particles temporally and spatially changes in the depth direction due to the non-uniform motion of particles; this change further affects the effective viscosity of the suspension and thus changes the drag force of particles. A Stokes' law based model is developed to simulate the sedimentation process, demonstrate the effect of manufacturing parameters on sedimentation, and predict the graded microstructure of deposition in the depth direction. In order to improve the modeling for sedimentation behavior of particles, the Eshelby's equivalent inclusion method (EIM) is presented to determine the interaction between particles, which is not considered in a Stokes' law based

  11. Lawrence Livermore National Security Cost Model Functional Management Assessment

    SciTech Connect

    Tevis, J; Hirahara, J; Thomas, B; Mendez, M

    2008-06-12

    The scope of the Functional Management Assessment of the cost model included a review of the plan and progress of the Cost Model Review Team. The review focused on processes in place to ensure simplicity, compliance with cost accounting standards and indirect cost allocation methodology, and the change management plan. This was intended to be a high-level initial review in order to provide recommendations for a subsequent more comprehensive review. The single document reviewed by the team during the assessment was the Indirect Cost Recovery Model Review, which describes how the indirect rate restructure and new organizational structure have resulted in streamlined charging practices to better understand and strategically manage costs. ISSUE 1: The cost model focuses heavily on rate structure but not on cost management. Significant progress has been made to simplify the rate structure. The number of indirect rates has been reduced from 67 different indirect rates used under the prior contract to 32 rates in the first year of the LLNS contract, with a goal of further reduction to 16 for FY09. The reductions are being recommended by a broad-based Working Group driven by Lab leadership desiring a simplified rate structure that would make it easier to analyze the true cost of overhead, be viewed as equitable, and ensure appropriate use of Service, i.e., operations, Centers. This has been a real challenge due to the significant change in approach from one that previously involved a very complex rate structure. Under this prior approach, the goal was to manage the rates, and rates were established at very detailed levels that would 'shine the light' on pools of overhead costs. As long as rates stayed constant or declined, not as much attention tended to be given to them, particularly with so many pools to review (184 indirect rate pools in FY05). However, as difficult and important as simplifying the rate structure has been, the fundamental reason for the simplification

  12. Partition function of the elliptic solid-on-solid model as a single determinant

    NASA Astrophysics Data System (ADS)

    Galleas, W.

    2016-07-01

    In this Rapid Communication we express the partition function of the integrable elliptic solid-on-solid model with domain-wall boundary conditions as a single determinant. This representation appears naturally as the solution of a system of functional equations governing the model's partition function.

  13. A Theoretical Framework for Research in Algebra: Modification of Janvier's "Star" Model of Function Understanding.

    ERIC Educational Resources Information Center

    Bowman, Anita H.

    A pentagonal model, based on the star model of function understanding of C. Janvier (1987), is presented as a framework for the design and interpretation of research in the area of learning the concept of mathematical function. The five vertices of the pentagon correspond to five common representations of mathematical function: (1) graph; (2)…

  14. Dreaming: The functional state-shift hypothesis. A neuropsychophysiological model.

    PubMed

    Koukkou, M; Lehmann, D

    1983-03-01

    The different brain functional states during sleep and wakefulness are associated with differences in processing strategies, memory stores, and EEG patterns. Shifts of functional state occur spontaneously or as orienting reactions to processed information, and cause the formal characteristics of dreams. Forgetting of dreams is a function of the magnitude of the difference between states during storage and recall. Based on EEG similarities between sleep stages and developmental stages, brain states during sleep in adults are proposed to correspond functionally with waking states during childhood. Repeated functional regressions occur during sleep, with access to earlier memory material and cognitive strategies unavailable during waking life, so that earlier experiences can be used for current problems. This dream work constitutes the biological significance of sleep. PMID:6860875

  15. Modeling mixtures of thyroid gland function disruptors in a vertebrate alternative model, the zebrafish eleutheroembryo

    SciTech Connect

    Thienpont, Benedicte; Barata, Carlos; Raldúa, Demetrio

    2013-06-01

    Maternal thyroxine (T4) plays an essential role in fetal brain development, and even mild and transitory deficits in free-T4 in pregnant women can produce irreversible neurological effects in their offspring. Women of childbearing age are daily exposed to mixtures of chemicals disrupting the thyroid gland function (TGFDs) through the diet, drinking water, air and pharmaceuticals, which has raised the highest concern for the potential additive or synergic effects on the development of mild hypothyroxinemia during early pregnancy. Recently we demonstrated that zebrafish eleutheroembryos provide a suitable alternative model for screening chemicals impairing the thyroid hormone synthesis. The present study used the intrafollicular T4-content (IT4C) of zebrafish eleutheroembryos as integrative endpoint for testing the hypotheses that the effect of mixtures of TGFDs with a similar mode of action [inhibition of thyroid peroxidase (TPO)] was well predicted by a concentration addition concept (CA) model, whereas the response addition concept (RA) model predicted better the effect of dissimilarly acting binary mixtures of TGFDs [TPO-inhibitors and sodium-iodide symporter (NIS)-inhibitors]. However, CA model provided better prediction of joint effects than RA in five out of the six tested mixtures. The exception being the mixture MMI (TPO-inhibitor)-KClO{sub 4} (NIS-inhibitor) dosed at a fixed ratio of EC{sub 10} that provided similar CA and RA predictions and hence it was difficult to get any conclusive result. There results support the phenomenological similarity criterion stating that the concept of concentration addition could be extended to mixture constituents having common apical endpoints or common adverse outcomes. - Highlights: • Potential synergic or additive effect of mixtures of chemicals on thyroid function. • Zebrafish as alternative model for testing the effect of mixtures of goitrogens. • Concentration addition seems to predict better the effect of

  16. MODELS-3/CMAQ APPLICATIONS WHICH ILLUSTRATE CAPABILITY AND FUNCTIONALITY

    EPA Science Inventory

    The Models-3/CMAQ developed by the U.S. Environmental Protections Agency (USEPA) is a third generation multiscale, multi-pollutant air quality modeling system within a high-level, object-oriented computer framework (Models-3). It has been available to the scientific community ...

  17. Modeling the fundamental characteristics and processes of the spacecraft functioning

    NASA Technical Reports Server (NTRS)

    Bazhenov, V. I.; Osin, M. I.; Zakharov, Y. V.

    1986-01-01

    The fundamental aspects of modeling of spacecraft characteristics by using computing means are considered. Particular attention is devoted to the design studies, the description of physical appearance of the spacecraft, and simulated modeling of spacecraft systems. The fundamental questions of organizing the on-the-ground spacecraft testing and the methods of mathematical modeling were presented.

  18. Models of the Protocellular Structures, Functions and Evolution

    NASA Technical Reports Server (NTRS)

    Pohorille, Andrew; New, Michael; Keefe, Anthony; Szostak, Jack W.; Lanyi, Janos F.; DeVincenzi, Donald L. (Technical Monitor)

    2000-01-01

    In the absence of extinct or extant record of protocells, the most direct way to test our understanding of the origin of cellular life is to construct laboratory models that capture important features of protocellular systems. Such efforts are currently underway in a collaborative project between NASA-Ames, Harvard medical School and University of California. They are accompanied by computational studies aimed at explaining self-organization of simple molecules into ordered structures. The centerpiece of this project is a method for the in vitro evolution of protein enzymes toward arbitrary catalytic targets. A similar approach has already been developed for nucleic acids: First, a very large population of candidate molecules is generated using a random synthetic approach. Next, the small numbers of molecules that can accomplish the desired task are selected. These molecules are next vastly multiplied using the polymerase chain reaction. A mutagenic approach, in which the sequences of selected molecules are randomly altered, can yield further improvements in performance or alterations of specificities. Unfortunately, the catalytic potential of nucleic acids is rather limited. Proteins are more catalytically capable but cannot be directly amplified. In the new technique, this problem is circumvented by covalently linking each protein of the initial, diverse, pool to the RNA sequence that codes for it. Then, selection is performed on the proteins, but the nucleic acids are replicated. To date, we have obtained "a proof of concept" by evolving simple, novel proteins capable of selectively binding adenosine tri-phosphate (ATP). Our next goal is to create an enzyme that can phosphorylate amino acids and another to catalyze the formation of peptide bonds in the absence of nucleic acid templates. This latter reaction does not take place in contemporary cells. once developed, these enzymes will be encapsulated in liposomes so that they will function in a simulated cellular

  19. Simple model potential and model wave functions for (H-alkali)+ and (alkali-alkali)+ ions

    NASA Astrophysics Data System (ADS)

    Patil, S. H.; Tang, K. T.

    2000-07-01

    A simple model potential is proposed to describe the interaction of a valence electron with the alkali core, which incorporates the correct asymptotic behavior in terms of dipolar polarizabilities, and the short-range exchange effects in terms of a hard core adjusted to give the correct energy for the valence electron. Based on this potential, simple wave functions are developed to describe the (H-alkali)+ and (alkali-alkali)+ ions. These wave functions exhibit some important structures of the ions, and provide a universal description of the properties of all (H-alkali)+ and (alkali-alkali)+ ions, in particular, the equilibrium separations of the nuclei and the corresponding dissociation energies. They also allow us to calculate the dipolar polarizabilities of Li2+, Na2+, K2+, Rb2+, and Cs2+.

  20. Web services and model-data comparison for the Functional Test Platform

    NASA Astrophysics Data System (ADS)

    Krassovski, Misha; Wang, Dali

    2015-04-01

    Web services and model-data comparison for the Functional Test Platform. The realistic representation of key biogeophysical and biogeochemical function is the fundamental on process based ecosystem models. A Functional Test Platform is designed to create direct linkages between site measurements and process-based ecosystem model within the Community Earth System Models (CESM). The platform consists of three major parts: 1) interactive user interfaces, 2) functional test models and 3) observational datasets. The purpose of the observational datasets is to provide an interactive search and visualization capability for direct model-data comparison. The proposed presentation is going to show how web services can be used to feed model-data comparison using AmeriFlux data collection provided by Carbon Dioxide Information Analysis Center (CDIAC) and the way it is coupled with Functional Test Platform for the Community Land Model.

  1. Fatigue Crack Growth Analysis Models for Functionally Graded Materials

    SciTech Connect

    Dag, Serkan; Yildirim, Bora; Sabuncuoglu, Baris

    2008-02-15

    The objective of this study is to develop crack growth analysis methods for functionally graded materials (FGMs) subjected to mode I cyclic loading. The study presents finite elements based computational procedures for both two and three dimensional problems to examine fatigue crack growth in functionally graded materials. Developed methods allow the computation of crack length and generation of crack front profile for a graded medium subjected to fluctuating stresses. The results presented for an elliptical crack embedded in a functionally graded medium, illustrate the competing effects of ellipse aspect ratio and material property gradation on the fatigue crack growth behavior.

  2. MODELING FUNCTIONALLY GRADED INTERPHASE REGIONS IN CARBON NANOTUBE REINFORCED COMPOSITES

    NASA Technical Reports Server (NTRS)

    Seidel, G. D.; Lagoudas, D. C.; Frankland, S. J. V.; Gates, T. S.

    2006-01-01

    A combination of micromechanics methods and molecular dynamics simulations are used to obtain the effective properties of the carbon nanotube reinforced composites with functionally graded interphase regions. The multilayer composite cylinders method accounts for the effects of non-perfect load transfer in carbon nanotube reinforced polymer matrix composites using a piecewise functionally graded interphase. The functional form of the properties in the interphase region, as well as the interphase thickness, is derived from molecular dynamics simulations of carbon nanotubes in a polymer matrix. Results indicate that the functional form of the interphase can have a significant effect on all the effective elastic constants except for the effective axial modulus for which no noticeable effects are evident.

  3. Polarized and Unpolarized Structure Functions in the Valon Model

    NASA Astrophysics Data System (ADS)

    Arash, Firooz

    2006-02-01

    Hadrons are considered as the bound states of their structureful constituents, the Valons. The valon structure is calculated perturbatively in QCD; which is universal and independent of the hosting hadron. This structure is used to calculate Proton and pion structure functions. For the case of polarized structure function, the valon representation, not only gives all the available data on gp,n,d1, but also requires a sizable orbital angular momentum associated with the partonic structure of the valon.

  4. A bimodal model for the galaxy luminosity function

    NASA Technical Reports Server (NTRS)

    Schaeffer, R.; Silk, J.

    1988-01-01

    The galaxy luminosity function in the Virgo cluster has been recently found to show a clear separation between bright galaxies and dwarf galaxies. Here, consideration is given to the effect on the luminosity function of galaxy binding energy which allows gas to be retained and star formation to proceed over about 1 Gyr in massive galaxies, but implies wind-driven mass loss and inefficient star formation in dwarf galaxies.

  5. Building a predictive model of galaxy formation - I. Phenomenological model constrained to the z = 0 stellar mass function

    NASA Astrophysics Data System (ADS)

    Benson, Andrew J.

    2014-11-01

    We constrain a highly simplified semi-analytic model of galaxy formation using the z ≈ 0 stellar mass function of galaxies. Particular attention is paid to assessing the role of random and systematic errors in the determination of stellar masses, to systematic uncertainties in the model, and to correlations between bins in the measured and modelled stellar mass functions, in order to construct a realistic likelihood function. We derive constraints on model parameters and explore which aspects of the observational data constrain particular parameter combinations. We find that our model, once constrained, provides a remarkable match to the measured evolution of the stellar mass function to z = 1, although fails dramatically to match the local galaxy H I mass function. Several `nuisance parameters' contribute significantly to uncertainties in model predictions. In particular, systematic errors in stellar mass estimate are the dominant source of uncertainty in model predictions at z ≈ 1, with additional, non-negligble contributions arising from systematic uncertainties in halo mass functions and the residual uncertainties in cosmological parameters. Ignoring any of these sources of uncertainties could lead to viable models being erroneously ruled out. Additionally, we demonstrate that ignoring the significant covariance between bins the observed stellar mass function leads to significant biases in the constraints derived on model parameters. Careful treatment of systematic and random errors in the constraining data, and in the model being constrained, is crucial if this methodology is to be used to test hypotheses relating to the physics of galaxy formation.

  6. Microroughness, statistical surface models, and bidirectional reflection distribution function (BRDF): functions of smooth surfaces

    NASA Astrophysics Data System (ADS)

    Harnisch, Bernd; Weigel, Thomas

    1994-09-01

    The calculation of the BRDF (Bi-Directional-Reflection-Distribution-Function) from profile measurements was performed theoretically and verified by measurements on a BK7 sample. The assumptions on the surface topography and approximations done are highlighted.

  7. Probability Weighting Functions Derived from Hyperbolic Time Discounting: Psychophysical Models and Their Individual Level Testing

    PubMed Central

    Takemura, Kazuhisa; Murakami, Hajime

    2016-01-01

    A probability weighting function (w(p)) is considered to be a nonlinear function of probability (p) in behavioral decision theory. This study proposes a psychophysical model of probability weighting functions derived from a hyperbolic time discounting model and a geometric distribution. The aim of the study is to show probability weighting functions from the point of view of waiting time for a decision maker. Since the expected value of a geometrically distributed random variable X is 1/p, we formulized the probability weighting function of the expected value model for hyperbolic time discounting as w(p) = (1 − k log p)−1. Moreover, the probability weighting function is derived from Loewenstein and Prelec's (1992) generalized hyperbolic time discounting model. The latter model is proved to be equivalent to the hyperbolic-logarithmic weighting function considered by Prelec (1998) and Luce (2001). In this study, we derive a model from the generalized hyperbolic time discounting model assuming Fechner's (1860) psychophysical law of time and a geometric distribution of trials. In addition, we develop median models of hyperbolic time discounting and generalized hyperbolic time discounting. To illustrate the fitness of each model, a psychological experiment was conducted to assess the probability weighting and value functions at the level of the individual participant. The participants were 50 university students. The results of individual analysis indicated that the expected value model of generalized hyperbolic discounting fitted better than previous probability weighting decision-making models. The theoretical implications of this finding are discussed. PMID:27303338

  8. Probability Weighting Functions Derived from Hyperbolic Time Discounting: Psychophysical Models and Their Individual Level Testing.

    PubMed

    Takemura, Kazuhisa; Murakami, Hajime

    2016-01-01

    A probability weighting function (w(p)) is considered to be a nonlinear function of probability (p) in behavioral decision theory. This study proposes a psychophysical model of probability weighting functions derived from a hyperbolic time discounting model and a geometric distribution. The aim of the study is to show probability weighting functions from the point of view of waiting time for a decision maker. Since the expected value of a geometrically distributed random variable X is 1/p, we formulized the probability weighting function of the expected value model for hyperbolic time discounting as w(p) = (1 - k log p)(-1). Moreover, the probability weighting function is derived from Loewenstein and Prelec's (1992) generalized hyperbolic time discounting model. The latter model is proved to be equivalent to the hyperbolic-logarithmic weighting function considered by Prelec (1998) and Luce (2001). In this study, we derive a model from the generalized hyperbolic time discounting model assuming Fechner's (1860) psychophysical law of time and a geometric distribution of trials. In addition, we develop median models of hyperbolic time discounting and generalized hyperbolic time discounting. To illustrate the fitness of each model, a psychological experiment was conducted to assess the probability weighting and value functions at the level of the individual participant. The participants were 50 university students. The results of individual analysis indicated that the expected value model of generalized hyperbolic discounting fitted better than previous probability weighting decision-making models. The theoretical implications of this finding are discussed. PMID:27303338

  9. Relation between transverse momentum dependent distribution functions and parton distribution functions in the covariant parton model approach

    SciTech Connect

    A.V. Efremov, P. Schweitzer, O.V. Teryaev, P. Zavada

    2011-03-01

    We derive relations between transverse momentum dependent distribution functions (TMDs) and the usual parton distribution functions (PDFs) in the 3D covariant parton model, which follow from Lorentz invariance and the assumption of a rotationally symmetric distribution of parton momenta in the nucleon rest frame. Using the known PDFs f_1(x) and g_1(x) as input we predict the x- and pT-dependence of all twist-2 T-even TMDs.

  10. A Comparison of Land Surface Model Soil Hydraulic Properties Estimated by Inverse Modeling and Pedotransfer Functions

    NASA Technical Reports Server (NTRS)

    Gutmann, Ethan D.; Small, Eric E.

    2007-01-01

    Soil hydraulic properties (SHPs) regulate the movement of water in the soil. This in turn plays an important role in the water and energy cycles at the land surface. At present, SHPS are commonly defined by a simple pedotransfer function from soil texture class, but SHPs vary more within a texture class than between classes. To examine the impact of using soil texture class to predict SHPS, we run the Noah land surface model for a wide variety of measured SHPs. We find that across a range of vegetation cover (5 - 80% cover) and climates (250 - 900 mm mean annual precipitation), soil texture class only explains 5% of the variance expected from the real distribution of SHPs. We then show that modifying SHPs can drastically improve model performance. We compare two methods of estimating SHPs: (1) inverse method, and (2) soil texture class. Compared to texture class, inverse modeling reduces errors between measured and modeled latent heat flux from 88 to 28 w/m(exp 2). Additionally we find that with increasing vegetation cover the importance of SHPs decreases and that the van Genuchten m parameter becomes less important, while the saturated conductivity becomes more important.

  11. Basic Life Functions Instructional Program Model. Field Copy.

    ERIC Educational Resources Information Center

    Wisconsin State Dept. of Public Instruction, Madison. Div. for Handicapped Children.

    Presented is a model, designed by the Wisconsin Department of Public Instruction, for development of an instructional program in basic living skills for trainable mentally retarded children (2- to 20-years-old). The model identifies the following instructional goals: to communicate ideas, to understand one's self and interact with others, to…

  12. A Functional Model for the Treatment of Primary Enuresis.

    ERIC Educational Resources Information Center

    Goldstein, Sam; Book, Robert

    1983-01-01

    The present model, based upon Alexander and Barton's two-phase model for family therapy, was developed to provide the practicing school psychologist with an efficient, manageable program maximizing successful outcome. The program enables psychologists to adapt primary enuresis intervention strategies to suit their styles and the individual needs…

  13. Modelling Transformations of Quadratic Functions: A Proposal of Inductive Inquiry

    ERIC Educational Resources Information Center

    Sokolowski, Andrzej

    2013-01-01

    This paper presents a study about using scientific simulations to enhance the process of mathematical modelling. The main component of the study is a lesson whose major objective is to have students mathematise a trajectory of a projected object and then apply the model to formulate other trajectories by using the properties of function…

  14. Putting the brakes on inhibitory models of frontal lobe function

    PubMed Central

    Hampshire, Adam

    2015-01-01

    There has been much recent debate regarding the neural basis of motor response inhibition. An influential hypothesis from the last decade proposes that a module within the right inferior frontal cortex (RIFC) of the human brain is dedicated to supporting response inhibition. However, there is growing evidence to support the alternative view that response inhibition is just one prominent example of the many cognitive control processes that are supported by the same set of ‘domain general’ functional networks. Here, I test directly between the modular and network accounts of motor response inhibition by applying a combination of data-driven, event-related and functional connectivity analyses to fMRI data from a variety of attention and inhibition tasks. The results demonstrate that there is no inhibitory module within the RIFC. Instead, response inhibition recruits a functionally heterogeneous ensemble of RIFC networks, which can be dissociated from each other in the context of other task demands. PMID:25818684

  15. Modeling Functional Motions of Biological Systems by Customized Natural Moves.

    PubMed

    Demharter, Samuel; Knapp, Bernhard; Deane, Charlotte M; Minary, Peter

    2016-08-23

    Simulating the functional motions of biomolecular systems requires large computational resources. We introduce a computationally inexpensive protocol for the systematic testing of hypotheses regarding the dynamic behavior of proteins and nucleic acids. The protocol is based on natural move Monte Carlo, a highly efficient conformational sampling method with built-in customization capabilities that allows researchers to design and perform a large number of simulations to investigate functional motions in biological systems. We demonstrate the use of this protocol on both a protein and a DNA case study. Firstly, we investigate the plasticity of a class II major histocompatibility complex in the absence of a bound peptide. Secondly, we study the effects of the epigenetic mark 5-hydroxymethyl on cytosine on the structure of the Dickerson-Drew dodecamer. We show how our customized natural moves protocol can be used to investigate causal relationships of functional motions in biological systems. PMID:27558715

  16. Discrete two-sex models of population dynamics: On modelling the mating function

    NASA Astrophysics Data System (ADS)

    Bessa-Gomes, Carmen; Legendre, Stéphane; Clobert, Jean

    2010-09-01

    Although sexual reproduction has long been a central subject of theoretical ecology, until recently its consequences for population dynamics were largely overlooked. This is now changing, and many studies have addressed this issue, showing that when the mating system is taken into account, the population dynamics depends on the relative abundance of males and females, and is non-linear. Moreover, sexual reproduction increases the extinction risk, namely due to the Allee effect. Nevertheless, different studies have identified diverse potential consequences, depending on the choice of mating function. In this study, we investigate the consequences of three alternative mating functions that are frequently used in discrete population models: the minimum; the harmonic mean; and the modified harmonic mean. We consider their consequences at three levels: on the probability that females will breed; on the presence and intensity of the Allee effect; and on the extinction risk. When we consider the harmonic mean, the number of times the individuals of the least abundant sex mate exceeds their mating potential, which implies that with variable sex-ratios the potential reproductive rate is no longer under the modeller's control. Consequently, the female breeding probability exceeds 1 whenever the sex-ratio is male-biased, which constitutes an obvious problem. The use of the harmonic mean is thus only justified if we think that this parameter should be re-defined in order to represent the females' breeding rate and the fact that females may reproduce more than once per breeding season. This phenomenon buffers the Allee effect, and reduces the extinction risk. However, when we consider birth-pulse populations, such a phenomenon is implausible because the number of times females can reproduce per birth season is limited. In general, the minimum or modified harmonic mean mating functions seem to be more suitable for assessing the impact of mating systems on population dynamics.

  17. Integrating the switching, inhibition, and updating model of executive function with the Cattell-Horn-Carroll model.

    PubMed

    Jewsbury, Paul A; Bowden, Stephen C; Strauss, Milton E

    2016-02-01

    Executive function is an important concept in neuropsychological and cognitive research, and is often viewed as central to effective clinical assessment of cognition. However, the construct validity of executive function tests is controversial. The switching, inhibition, and updating model is the most empirically supported and replicated factor model of executive function (Miyake et al., 2000). To evaluate the relation between executive function constructs and nonexplicitly executive cognitive constructs, we used confirmatory factor reanalysis guided by the comprehensive Cattell-Horn-Carroll (CHC) model of cognitive abilities. Data from 7 of the best studies supporting the executive function model were reanalyzed, contrasting executive function models and CHC models. Where possible, we examined the effect of specifying executive function factors in addition to the CHC factors. The results suggested that little evidence is available to support updating as a separate factor from general memory factors; that inhibition does not separate from general speed; and that switching is supported as a narrow factor under general speed, but with a more restricted definition than some clinicians and researchers have conceptualized. The replicated executive function factor structure was integrated with the larger body of research on individual difference in cognition, as represented by the CHC model. PMID:26569128

  18. Pump function curve shape for a model lymphatic vessel.

    PubMed

    Bertram, C D; Macaskill, C; Moore, J E

    2016-07-01

    The transport capacity of a contractile segment of lymphatic vessel is defined by its pump function curve relating mean flow-rate and adverse pressure difference. Numerous system characteristics affect curve shape and the magnitude of the generated flow-rates and pressures. Some cannot be varied experimentally, but their separate and interacting effects can be systematically revealed numerically. This paper explores variations in the rate of change of active tension and the form of the relation between active tension and muscle length, factors not known from experiment to functional precision. Whether the pump function curve bends toward or away from the origin depends partly on the curvature of the passive pressure-diameter relation near zero transmural pressure, but rather more on the form of the relation between active tension and muscle length. A pump function curve bending away from the origin defines a well-performing pump by maximum steady output power. This behaviour is favoured by a length/active-tension relationship which sustains tension at smaller lengths. Such a relationship also favours high peak mechanical efficiency, defined as output power divided by the input power obtained from the lymphangion diameter changes and active-tension time-course. The results highlight the need to pin down experimentally the form of the length/active-tension relationship. PMID:27185045

  19. Peak functions for modeling high resolution soil profile data

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Parametric and non-parametric depth functions have been used to estimate continuous soil profile properties. However, some soil properties, such as those seen in weathered loess, have complex peaked and anisotropic depth distributions. These distributions are poorly handled by common parametric func...

  20. Intracerebral hemorrhage in mouse models: therapeutic interventions and functional recovery

    PubMed Central

    Carmichael, S. Thomas

    2014-01-01

    There has been strong pre-clinical research on mechanisms of initial cell death and tissue injury in intracerebral hemorrhage (ICH). This data has led to the evaluation of several therapeutics for neuroprotection or the mitigation of early tissue damage. Most of these studies have been done in the rat. Also, there has been little study of the mechanisms of tissue repair and recovery. This review examines the testing of candidate therapeutics in mouse models of ICH for their effect on tissue protection and repair. This review will help the readers compare it to the extensively researched rat model of ICH and thus enhance work that are pending in mouse model. PMID:24810632

  1. Introducing a domain flexing function in the Jiles-Atherton hysteresis model

    NASA Astrophysics Data System (ADS)

    Miljavec, Damijan; Zidarič, Bogomir

    The Jiles-Atherton hysteresis model (J-A model) exhibits a certain unphysical behavior when magnetic excitation reaches or reverses from the extremity of the hysteresis loop. Introducing a domain flexing function, coherent with the magnetic excitation level, improves accuracy of the J-A hysteresis model and at the same time prevents its unphysical behavior. Moreover, applying this function also improves representation of inner (lower excitation level) hysteresis loops. Implementation of magnetic excitation dependence in the domain flexing function adds a valuable parameter to the J-A original model on the way towards its further optimization. In the proposed hysteresis model, genetic algorithms are used in parameters optimization.

  2. Relationships between Perceptions of Personal and Family Functioning, Defensive Functioning, and Working Models of Caregiving.

    ERIC Educational Resources Information Center

    Meyers, Steven A.; And Others

    Current psychological literature suggests that positive representations of self and others are associated with sensitivity of caregiving. This study was designed to examine the relationship among self-perceptions, perceptions of family functioning, and caregiving schemata in 618 undergraduates (437 females, 181 males) enrolled in Introductory…

  3. Correspondence between Traditional Models of Functional Analysis and a Functional Analysis of Manding Behavior

    ERIC Educational Resources Information Center

    LaRue, Robert H.; Sloman, Kimberly N.; Weiss, Mary Jane; Delmolino, Lara; Hansford, Amy; Szalony, Jill; Madigan, Ryan; Lambright, Nathan M.

    2011-01-01

    Functional analysis procedures have been effectively used to determine the maintaining variables for challenging behavior and subsequently develop effective interventions. However, fear of evoking dangerous topographies of maladaptive behavior and concerns for reinforcing infrequent maladaptive behavior present challenges for people working in…

  4. Rational polynomial functions for modeling E. coli and bromide breakthrough

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Fecal bacteria peak concentrations and breakthrough times through preferential flow to tile drainage systems following irrigation or rainfall events are important when assessing the risk of contamination. Process-based, convective-dispersive modeling of microbial organism transport through preferent...

  5. Functional Testing Protocols for Commercial Building Efficiency Baseline Modeling Software

    SciTech Connect

    Jump, David; Price, Phillip N.; Granderson, Jessica; Sohn, Michael

    2013-09-06

    This document describes procedures for testing and validating proprietary baseline energy modeling software accuracy in predicting energy use over the period of interest, such as a month or a year. The procedures are designed according to the methodology used for public domain baselining software in another LBNL report that was (like the present report) prepared for Pacific Gas and Electric Company: ?Commercial Building Energy Baseline Modeling Software: Performance Metrics and Method Testing with Open Source Models and Implications for Proprietary Software Testing Protocols? (referred to here as the ?Model Analysis Report?). The test procedure focuses on the quality of the software?s predictions rather than on the specific algorithms used to predict energy use. In this way the software vendor is not required to divulge or share proprietary information about how their software works, while enabling stakeholders to assess its performance.

  6. Improving plant functional groups for dynamic models of biodiversity: at the crossroads between functional and community ecology.

    PubMed

    Isabelle, Boulangeat; Pauline, Philippe; Sylvain, Abdulhak; Roland, Douzet; Luc, Garraud; Sébastien, Lavergne; Sandra, Lavorel; Jérémie, Van Es; Pascal, Vittoz; Wilfried, Thuiller

    2012-11-01

    The pace of on-going climate change calls for reliable plant biodiversity scenarios. Traditional dynamic vegetation models use plant functional types that are summarized to such an extent that they become meaningless for biodiversity scenarios. Hybrid dynamic vegetation models of intermediate complexity (hybrid-DVMs) have recently been developed to address this issue. These models, at the crossroads between phenomenological and process-based models, are able to involve an intermediate number of well-chosen plant functional groups (PFGs). The challenge is to build meaningful PFGs that are representative of plant biodiversity, and consistent with the parameters and processes of hybrid-DVMs. Here, we propose and test a framework based on few selected traits to define a limited number of PFGs, which are both representative of the diversity (functional and taxonomic) of the flora in the Ecrins National Park, and adapted to hybrid-DVMs. This new classification scheme, together with recent advances in vegetation modeling, constitutes a step forward for mechanistic biodiversity modeling. PMID:24403847

  7. Coarse-Grained Models Reveal Functional Dynamics - I. Elastic Network Models – Theories, Comparisons and Perspectives

    PubMed Central

    Yang, Lee-Wei; Chng, Choon-Peng

    2008-01-01

    In this review, we summarize the progress on coarse-grained elastic network models (CG-ENMs) in the past decade. Theories were formulated to allow study of conformational dynamics in time/space frames of biological interest. Several highlighted models and their underlined hypotheses are introduced in physical depth. Important ENM offshoots, motivated to reproduce experimental data as well as to address the slow-mode-encoded configurational transitions, are also introduced. With the theoretical developments, computational cost is significantly reduced due to simplified potentials and coarse-grained schemes. Accumulating wealth of data suggest that ENMs agree equally well with experiment in describing equilibrium dynamics despite their distinct potentials and levels of coarse-graining. They however do differ in the slowest motional components that are essential to address large conformational changes of functional significance. The difference stems from the dissimilar curvatures of the harmonic energy wells described for each model. We also provide our views on the predictability of ‘open to close’ (open→close) transitions of biomolecules on the basis of conformational selection theory. Lastly, we address the limitations of the ENM formalism which are partially alleviated by the complementary CG-MD approach, to be introduced in the second paper of this two-part series. PMID:19812764

  8. Global land model development: time to shift from a plant functional type to a plant functional trait approach

    NASA Astrophysics Data System (ADS)

    Reich, P. B.; Butler, E. E.

    2015-12-01

    This project will advance global land models by shifting from the current plant functional type approach to one that better utilizes what is known about the importance and variability of plant traits, within a framework of simultaneously improving fundamental physiological relations that are at the core of model carbon cycling algorithms. Existing models represent the global distribution of vegetation types using the Plant Functional Typeconcept. Plant Functional Types are classes of plant species with similar evolutionary and life history withpresumably similar responses to environmental conditions like CO2, water and nutrient availability. Fixedproperties for each Plant Functional Type are specified through a collection of physiological parameters, or traits.These traits, mostly physiological in nature (e.g., leaf nitrogen and longevity) are used in model algorithms to estimate ecosystem properties and/or drive calculated process rates. In most models, 5 to 15 functional types represent terrestrial vegetation; in essence, they assume there are a total of only 5 to 15 different kinds of plants on the entire globe. This assumption of constant plant traits captured within the functional type concept has serious limitations, as a single set of traits does not reflect trait variation observed within and between species and communities. While this simplification was necessary decades past, substantial improvement is now possible. Rather than assigning a small number of constant parameter values to all grid cells in a model, procedures will be developed that predict a frequency distribution of values for any given grid cell. Thus, the mean and variance, and how these change with time, will inform and improve model performance. The trait-based approach will improve land modeling by (1) incorporating patterns and heterogeneity of traits into model parameterization, thus evolving away from a framework that considers large areas of vegetation to have near identical trait

  9. Pion structure function F2π in the valon model

    NASA Astrophysics Data System (ADS)

    Arash, Firooz

    2003-03-01

    Partonic structure of constituent quark (or valon) in the next-to-leading order is used to calculate pion structure function. This is a further demonstration of the finding that the constituent quark structure is universal, and once it is calculated, the structure of any hadron can be predicted thereafter, using a convolution method, without introducing any new free parameter. The results are compared with the pion structure function from ZEUS Collaboration leading neutron production in e+p collisions at HERA. We found good agreement with the experiment. A resolution for the issue of normalization of the experimental data is suggested. In addition, the proportionality of F2π and F2p, which have caused confusion in the normalization of ZEUS data is discussed and resolved.

  10. A Model-Based Approach to Constructing Music Similarity Functions

    NASA Astrophysics Data System (ADS)

    West, Kris; Lamere, Paul

    2006-12-01

    Several authors have presented systems that estimate the audio similarity of two pieces of music through the calculation of a distance metric, such as the Euclidean distance, between spectral features calculated from the audio, related to the timbre or pitch of the signal. These features can be augmented with other, temporally or rhythmically based features such as zero-crossing rates, beat histograms, or fluctuation patterns to form a more well-rounded music similarity function. It is our contention that perceptual or cultural labels, such as the genre, style, or emotion of the music, are also very important features in the perception of music. These labels help to define complex regions of similarity within the available feature spaces. We demonstrate a machine-learning-based approach to the construction of a similarity metric, which uses this contextual information to project the calculated features into an intermediate space where a music similarity function that incorporates some of the cultural information may be calculated.

  11. Density functional theory an effective method to model polythiophenes

    NASA Astrophysics Data System (ADS)

    Venkateswaran, S.

    The luminescent polymer, poly[2-(3-thienyl)ethanol butoxycarbonyl-methyl urethane, called popularly as PURET, has rekindled research interests due to the recent discovery of its ability for detection of explosives at trace levels of molecules in their vapor phase. In this computational study, Hartree-Fock and/or Density Functional Theory (DFT) methods are applied, using Gaussian09 W software, for calculating the HOMO-LUMO energy levels, the Dipole Moment, and the UV-Vis and IR spectra for the Oligomers of PURET monomer, dimer, and trimer. Similar calculations for a few other Thiophene derivatives, such as TAA. TMA, 3HT, and TTZ, are also shown. DFT-based calculations, employing especially the B3LYP functional, are shown to systematically converge to experimental levels of accuracy for PURET Oligomers.

  12. Critical Function Models for Operation of the International Space Station

    SciTech Connect

    Nelson, William Roy; Bagian, T. M.

    2000-11-01

    Long duration and exploration class space missions will place new requirements on human performance when compared to current space shuttle missions. Specifically, assembly and operation of the International Space Station (ISS) will place significant new demands on the crew. For example, maintenance of systems that provide habitability will become an ongoing activity for the international flight crews. Tasks for maintaining space station habitability will need to be integrated with tasks associated with scientific research. In addition, tasks and resources will need to be prioritized and allocated dynamically in response to changing operational conditions and unplanned system breakdowns. This paper describes an ongoing program to develop a habitability index (HI) for space operations based on the critical function approach. This pilot project focuses on adaptation of the critical function approach to develop a habitability index specifically tailored for space operations. Further work will then be needed to expand and validate the habitability index for application in the ISS operational environment.

  13. Evaluation of Analytical Modeling Functions for the Phonation Onset Process.

    PubMed

    Petermann, Simon; Kniesburges, Stefan; Ziethe, Anke; Schützenberger, Anne; Döllinger, Michael

    2016-01-01

    The human voice originates from oscillations of the vocal folds in the larynx. The duration of the voice onset (VO), called the voice onset time (VOT), is currently under investigation as a clinical indicator for correct laryngeal functionality. Different analytical approaches for computing the VOT based on endoscopic imaging were compared to determine the most reliable method to quantify automatically the transient vocal fold oscillations during VO. Transnasal endoscopic imaging in combination with a high-speed camera (8000 fps) was applied to visualize the phonation onset process. Two different definitions of VO interval were investigated. Six analytical functions were tested that approximate the envelope of the filtered or unfiltered glottal area waveform (GAW) during phonation onset. A total of 126 recordings from nine healthy males and 210 recordings from 15 healthy females were evaluated. Three criteria were analyzed to determine the most appropriate computation approach: (1) reliability of the fit function for a correct approximation of VO; (2) consistency represented by the standard deviation of VOT; and (3) accuracy of the approximation of VO. The results suggest the computation of VOT by a fourth-order polynomial approximation in the interval between 32.2 and 67.8% of the saturation amplitude of the filtered GAW. PMID:27066108

  14. Evaluation of Analytical Modeling Functions for the Phonation Onset Process

    PubMed Central

    Petermann, Simon; Kniesburges, Stefan; Ziethe, Anke; Schützenberger, Anne; Döllinger, Michael

    2016-01-01

    The human voice originates from oscillations of the vocal folds in the larynx. The duration of the voice onset (VO), called the voice onset time (VOT), is currently under investigation as a clinical indicator for correct laryngeal functionality. Different analytical approaches for computing the VOT based on endoscopic imaging were compared to determine the most reliable method to quantify automatically the transient vocal fold oscillations during VO. Transnasal endoscopic imaging in combination with a high-speed camera (8000 fps) was applied to visualize the phonation onset process. Two different definitions of VO interval were investigated. Six analytical functions were tested that approximate the envelope of the filtered or unfiltered glottal area waveform (GAW) during phonation onset. A total of 126 recordings from nine healthy males and 210 recordings from 15 healthy females were evaluated. Three criteria were analyzed to determine the most appropriate computation approach: (1) reliability of the fit function for a correct approximation of VO; (2) consistency represented by the standard deviation of VOT; and (3) accuracy of the approximation of VO. The results suggest the computation of VOT by a fourth-order polynomial approximation in the interval between 32.2 and 67.8% of the saturation amplitude of the filtered GAW. PMID:27066108

  15. Computer Modeling of Protocellular Functions: Peptide Insertion in Membranes

    NASA Technical Reports Server (NTRS)

    Rodriquez-Gomez, D.; Darve, E.; Pohorille, A.

    2006-01-01

    Lipid vesicles became the precursors to protocells by acquiring the capabilities needed to survive and reproduce. These include transport of ions, nutrients and waste products across cell walls and capture of energy and its conversion into a chemically usable form. In modem organisms these functions are carried out by membrane-bound proteins (about 30% of the genome codes for this kind of proteins). A number of properties of alpha-helical peptides suggest that their associations are excellent candidates for protobiological precursors of proteins. In particular, some simple a-helical peptides can aggregate spontaneously and form functional channels. This process can be described conceptually by a three-step thermodynamic cycle: 1 - folding of helices at the water-membrane interface, 2 - helix insertion into the lipid bilayer and 3 - specific interactions of these helices that result in functional tertiary structures. Although a crucial step, helix insertion has not been adequately studied because of the insolubility and aggregation of hydrophobic peptides. In this work, we use computer simulation methods (Molecular Dynamics) to characterize the energetics of helix insertion and we discuss its importance in an evolutionary context. Specifically, helices could self-assemble only if their interactions were sufficiently strong to compensate the unfavorable Free Energy of insertion of individual helices into membranes, providing a selection mechanism for protobiological evolution.

  16. Theta function solutions of the quantum Knizhnik-Zamolodchikov-Bernard equation for a face model

    NASA Astrophysics Data System (ADS)

    Finch, Peter E.; Weston, Robert; Zinn-Justin, Paul

    2016-02-01

    We consider the quantum Knizhnik-Zamolodchikov-Bernard equation for a face model with elliptic weights, the SOS model. We provide explicit solutions as theta functions. On the so-called combinatorial line, in which the model is equivalent to the three-colour model, these solutions are shown to be eigenvectors of the transfer matrix with periodic boundary conditions.

  17. Modeling the Transfer Function for the Dark Energy Survey

    DOE PAGESBeta

    Chang, C.

    2015-03-04

    We present a forward-modeling simulation framework designed to model the data products from the Dark Energy Survey (DES). This forward-model process can be thought of as a transfer function—a mapping from cosmological/astronomical signals to the final data products used by the scientists. Using output from the cosmological simulations (the Blind Cosmology Challenge), we generate simulated images (the Ultra Fast Image Simulator) and catalogs representative of the DES data. In this work we demonstrate the framework by simulating the 244 deg2 coadd images and catalogs in five bands for the DES Science Verification data. The simulation output is compared with themore » corresponding data to show that major characteristics of the images and catalogs can be captured. We also point out several directions of future improvements. Two practical examples—star-galaxy classification and proximity effects on object detection—are then used to illustrate how one can use the simulations to address systematics issues in data analysis. With clear understanding of the simplifications in our model, we show that one can use the simulations side-by-side with data products to interpret the measurements. This forward modeling approach is generally applicable for other upcoming and future surveys. It provides a powerful tool for systematics studies that is sufficiently realistic and highly controllable.« less

  18. Predicting and correcting ataxia using a model of cerebellar function

    PubMed Central

    Bhanpuri, Nasir H.; Okamura, Allison M.

    2014-01-01

    Cerebellar damage results in uncoordinated, variable and dysmetric movements known as ataxia. Here we show that we can reliably model single-joint reaching trajectories of patients (n = 10), reproduce patient-like deficits in the behaviour of controls (n = 11), and apply patient-specific compensations that improve reaching accuracy (P < 0.02). Our approach was motivated by the theory that the cerebellum is essential for updating and/or storing an internal dynamic model that relates motor commands to changes in body state (e.g. arm position and velocity). We hypothesized that cerebellar damage causes a mismatch between the brain’s modelled dynamics and the actual body dynamics, resulting in ataxia. We used both behavioural and computational approaches to demonstrate that specific cerebellar patient deficits result from biased internal models. Our results strongly support the idea that an intact cerebellum is critical for maintaining accurate internal models of dynamics. Importantly, we demonstrate how subject-specific compensation can improve movement in cerebellar patients, who are notoriously unresponsive to treatment. PMID:24812203

  19. Modeling the Transfer Function for the Dark Energy Survey

    NASA Astrophysics Data System (ADS)

    Chang, C.; Busha, M. T.; Wechsler, R. H.; Refregier, A.; Amara, A.; Rykoff, E.; Becker, M. R.; Bruderer, C.; Gamper, L.; Leistedt, B.; Peiris, H.; Abbott, T.; Abdalla, F. B.; Balbinot, E.; Banerji, M.; Bernstein, R. A.; Bertin, E.; Brooks, D.; Carnero, A.; Desai, S.; da Costa, L. N.; Cunha, C. E.; Eifler, T.; Evrard, A. E.; Fausti Neto, A.; Gerdes, D.; Gruen, D.; James, D.; Kuehn, K.; Maia, M. A. G.; Makler, M.; Ogando, R.; Plazas, A.; Sanchez, E.; Santiago, B.; Schubnell, M.; Sevilla-Noarbe, I.; Smith, C.; Soares-Santos, M.; Suchyta, E.; Swanson, M. E. C.; Tarle, G.; Zuntz, J.

    2015-03-01

    We present a forward-modeling simulation framework designed to model the data products from the Dark Energy Survey (DES). This forward-model process can be thought of as a transfer function—a mapping from cosmological/astronomical signals to the final data products used by the scientists. Using output from the cosmological simulations (the Blind Cosmology Challenge), we generate simulated images (the Ultra Fast Image Simulator) and catalogs representative of the DES data. In this work we demonstrate the framework by simulating the 244 deg2 coadd images and catalogs in five bands for the DES Science Verification data. The simulation output is compared with the corresponding data to show that major characteristics of the images and catalogs can be captured. We also point out several directions of future improvements. Two practical examples—star-galaxy classification and proximity effects on object detection—are then used to illustrate how one can use the simulations to address systematics issues in data analysis. With clear understanding of the simplifications in our model, we show that one can use the simulations side-by-side with data products to interpret the measurements. This forward modeling approach is generally applicable for other upcoming and future surveys. It provides a powerful tool for systematics studies that is sufficiently realistic and highly controllable.

  20. An anatomical and functional model of the human tracheobronchial tree.

    PubMed

    Florens, M; Sapoval, B; Filoche, M

    2011-03-01

    The human tracheobronchial tree is a complex branched distribution system in charge of renewing the air inside the acini, which are the gas exchange units. We present here a systematic geometrical model of this system described as a self-similar assembly of rigid pipes. It includes the specific geometry of the upper bronchial tree and a self-similar intermediary tree with a systematic branching asymmetry. It ends by the terminal bronchioles whose generations range from 8 to 22. Unlike classical models, it does not rely on a simple scaling law. With a limited number of parameters, this model reproduces the morphometric data from various sources (Horsfield K, Dart G, Olson DE, Filley GF, Cumming G. J Appl Physiol 31: 207-217, 1971; Weibel ER. Morphometry of the Human Lung. New York: Academic Press, 1963) and the main characteristics of the ventilation. Studying various types of random variations of the airway sizes, we show that strong correlations are needed to reproduce the measured distributions. Moreover, the ventilation performances are observed to be robust against anatomical variability. The same methodology applied to the rat also permits building a geometrical model that reproduces the anatomical and ventilation characteristics of this animal. This simple model can be directly used as a common description of the entire tree in analytical or numerical studies such as the computation of air flow distribution or aerosol transport. PMID:21183626

  1. A functional circuit model of interaural time difference processing.

    PubMed

    McColgan, Thomas; Shah, Sahil; Köppl, Christine; Carr, Catherine; Wagner, Hermann

    2014-12-01

    Inputs from the two sides of the brain interact to create maps of interaural time difference (ITD) in the nucleus laminaris of birds. How inputs from each side are matched with high temporal precision in ITD-sensitive circuits is unknown, given the differences in input path lengths from each side. To understand this problem in birds, we modeled the geometry of the input axons and their corresponding conduction velocities and latencies. Consistent with existing physiological data, we assumed a common latency up to the border of nucleus laminaris. We analyzed two biological implementations of the model, the single ITD map in chickens and the multiple maps of ITD in barn owls. For binaural inputs, since ipsi- and contralateral initial common latencies were very similar, we could restrict adaptive regulation of conduction velocity to within the nucleus. Other model applications include the simultaneous derivation of multiple conduction velocities from one set of measurements and the demonstration that contours with the same ITD cannot be parallel to the border of nucleus laminaris in the owl. Physiological tests of the predictions of the model demonstrate its validity and robustness. This model may have relevance not only for auditory processing but also for other computational tasks that require adaptive regulation of conduction velocity. PMID:25185809

  2. A functional circuit model of interaural time difference processing

    PubMed Central

    McColgan, Thomas; Shah, Sahil; Köppl, Christine; Carr, Catherine

    2014-01-01

    Inputs from the two sides of the brain interact to create maps of interaural time difference (ITD) in the nucleus laminaris of birds. How inputs from each side are matched with high temporal precision in ITD-sensitive circuits is unknown, given the differences in input path lengths from each side. To understand this problem in birds, we modeled the geometry of the input axons and their corresponding conduction velocities and latencies. Consistent with existing physiological data, we assumed a common latency up to the border of nucleus laminaris. We analyzed two biological implementations of the model, the single ITD map in chickens and the multiple maps of ITD in barn owls. For binaural inputs, since ipsi- and contralateral initial common latencies were very similar, we could restrict adaptive regulation of conduction velocity to within the nucleus. Other model applications include the simultaneous derivation of multiple conduction velocities from one set of measurements and the demonstration that contours with the same ITD cannot be parallel to the border of nucleus laminaris in the owl. Physiological tests of the predictions of the model demonstrate its validity and robustness. This model may have relevance not only for auditory processing but also for other computational tasks that require adaptive regulation of conduction velocity. PMID:25185809

  3. Modeling intracellular signaling underlying striatal function in health and disease

    PubMed Central

    Nair, Anu G; Gutierrez-Arenas, Omar; Eriksson, Olivia; Jauhiainen, Alexandra; Blackwell, Kim T; Kotaleski, Jeanette Hellgren

    2014-01-01

    Striatum, which is the input nucleus of the basal ganglia, integrates cortical and thalamic glutamatergic inputs with dopaminergic afferents from the substantia nigra pars compacta. The combination of dopamine and glutamate strongly modulates molecular and cellular properties of striatal neurons and the strength of corticostriatal synapses. These actions are performed via intracellular signaling networks, containing several intertwined feedback loops. Understanding the role of dopamine and other neuromodulators requires the development of quantitative dynamical models for describing the intracellular signaling, in order to provide precise unambiguous descriptions and quantitative predictions. Building such models requires integration of data from multiple data sources containing information regarding the molecular interactions, the strength of these interactions, and the subcellular localization of the molecules. Due to the uncertainty, variability, and sparseness of these data, parameter estimation techniques are critical for inferring or constraining the unknown parameters, and sensitivity analysis evaluates which parameters are most critical for a given observed macroscopic behavior. Here, we briefly review the modeling approaches and tools that have been used to investigate biochemical signaling in the striatum, along with some of the models built around striatum. We also suggest a future direction for the development of such models from the, now becoming abundant, high-throughput data. PMID:24560149

  4. Modeling the Transfer Function for the Dark Energy Survey

    SciTech Connect

    Chang, C.

    2015-03-04

    We present a forward-modeling simulation framework designed to model the data products from the Dark Energy Survey (DES). This forward-model process can be thought of as a transfer function—a mapping from cosmological/astronomical signals to the final data products used by the scientists. Using output from the cosmological simulations (the Blind Cosmology Challenge), we generate simulated images (the Ultra Fast Image Simulator) and catalogs representative of the DES data. In this work we demonstrate the framework by simulating the 244 deg2 coadd images and catalogs in five bands for the DES Science Verification data. The simulation output is compared with the corresponding data to show that major characteristics of the images and catalogs can be captured. We also point out several directions of future improvements. Two practical examples—star-galaxy classification and proximity effects on object detection—are then used to illustrate how one can use the simulations to address systematics issues in data analysis. With clear understanding of the simplifications in our model, we show that one can use the simulations side-by-side with data products to interpret the measurements. This forward modeling approach is generally applicable for other upcoming and future surveys. It provides a powerful tool for systematics studies that is sufficiently realistic and highly controllable.

  5. Modeling intracellular signaling underlying striatal function in health and disease.

    PubMed

    Nair, Anu G; Gutierrez-Arenas, Omar; Eriksson, Olivia; Jauhiainen, Alexandra; Blackwell, Kim T; Kotaleski, Jeanette H

    2014-01-01

    Striatum, which is the input nucleus of the basal ganglia, integrates cortical and thalamic glutamatergic inputs with dopaminergic afferents from the substantia nigra pars compacta. The combination of dopamine and glutamate strongly modulates molecular and cellular properties of striatal neurons and the strength of corticostriatal synapses. These actions are performed via intracellular signaling networks, containing several intertwined feedback loops. Understanding the role of dopamine and other neuromodulators requires the development of quantitative dynamical models for describing the intracellular signaling, in order to provide precise unambiguous descriptions and quantitative predictions. Building such models requires integration of data from multiple data sources containing information regarding the molecular interactions, the strength of these interactions, and the subcellular localization of the molecules. Due to the uncertainty, variability, and sparseness of these data, parameter estimation techniques are critical for inferring or constraining the unknown parameters, and sensitivity analysis evaluates which parameters are most critical for a given observed macroscopic behavior. Here, we briefly review the modeling approaches and tools that have been used to investigate biochemical signaling in the striatum, along with some of the models built around striatum. We also suggest a future direction for the development of such models from the, now becoming abundant, high-throughput data. PMID:24560149

  6. A Caenorhabditis elegans model for ether lipid biosynthesis and function[S

    PubMed Central

    Shi, Xun; Tarazona, Pablo; Brock, Trisha J.; Browse, John; Feussner, Ivo; Watts, Jennifer L.

    2016-01-01

    Ether lipids are widespread in nature, and they are structurally and functionally important components of membranes. The roundworm, Caenorhabditis elegans, synthesizes numerous lipid species containing alkyl and alkenyl ether bonds. We isolated C. elegans strains carrying loss-of-function mutations in three genes encoding the proteins required for the initial three steps in the ether lipid biosynthetic pathway, FARD-1/FAR1, ACL-7/GNPAT, and ADS-1/AGPS. Analysis of the mutant strains show that they lack ether lipids, but possess the ability to alter their lipid composition in response to lack of ether lipids. We found that increases in de novo fatty acid synthesis and reduction of stearoyl- and palmitoyl-CoA desaturase activity, processes that are at least partially regulated transcriptionally, mediate the altered lipid composition in ether lipid-deficient mutants. Phenotypic analysis demonstrated the importance of ether lipids for optimal fertility, lifespan, survival at cold temperatures, and resistance to oxidative stress.Caenorhabditis PMID:26685325

  7. Modeling mixtures of thyroid gland function disruptors in a vertebrate alternative model, the zebrafish eleutheroembryo.

    PubMed

    Thienpont, Benedicte; Barata, Carlos; Raldúa, Demetrio

    2013-06-01

    Maternal thyroxine (T4) plays an essential role in fetal brain development, and even mild and transitory deficits in free-T4 in pregnant women can produce irreversible neurological effects in their offspring. Women of childbearing age are daily exposed to mixtures of chemicals disrupting the thyroid gland function (TGFDs) through the diet, drinking water, air and pharmaceuticals, which has raised the highest concern for the potential additive or synergic effects on the development of mild hypothyroxinemia during early pregnancy. Recently we demonstrated that zebrafish eleutheroembryos provide a suitable alternative model for screening chemicals impairing the thyroid hormone synthesis. The present study used the intrafollicular T4-content (IT4C) of zebrafish eleutheroembryos as integrative endpoint for testing the hypotheses that the effect of mixtures of TGFDs with a similar mode of action [inhibition of thyroid peroxidase (TPO)] was well predicted by a concentration addition concept (CA) model, whereas the response addition concept (RA) model predicted better the effect of dissimilarly acting binary mixtures of TGFDs [TPO-inhibitors and sodium-iodide symporter (NIS)-inhibitors]. However, CA model provided better prediction of joint effects than RA in five out of the six tested mixtures. The exception being the mixture MMI (TPO-inhibitor)-KClO4 (NIS-inhibitor) dosed at a fixed ratio of EC10 that provided similar CA and RA predictions and hence it was difficult to get any conclusive result. There results support the phenomenological similarity criterion stating that the concept of concentration addition could be extended to mixture constituents having common apical endpoints or common adverse outcomes. PMID:23562343

  8. Modeling of pharmaceuticals mixtures toxicity with deviation ratio and best-fit functions models.

    PubMed

    Wieczerzak, Monika; Kudłak, Błażej; Yotova, Galina; Nedyalkova, Miroslava; Tsakovski, Stefan; Simeonov, Vasil; Namieśnik, Jacek

    2016-11-15

    The present study deals with assessment of ecotoxicological parameters of 9 drugs (diclofenac (sodium salt), oxytetracycline hydrochloride, fluoxetine hydrochloride, chloramphenicol, ketoprofen, progesterone, estrone, androstenedione and gemfibrozil), present in the environmental compartments at specific concentration levels, and their mutual combinations by couples against Microtox® and XenoScreen YES/YAS® bioassays. As the quantitative assessment of ecotoxicity of drug mixtures is an complex and sophisticated topic in the present study we have used two major approaches to gain specific information on the mutual impact of two separate drugs present in a mixture. The first approach is well documented in many toxicological studies and follows the procedure for assessing three types of models, namely concentration addition (CA), independent action (IA) and simple interaction (SI) by calculation of a model deviation ratio (MDR) for each one of the experiments carried out. The second approach used was based on the assumption that the mutual impact in each mixture of two drugs could be described by a best-fit model function with calculation of weight (regression coefficient or other model parameter) for each of the participants in the mixture or by correlation analysis. It was shown that the sign and the absolute value of the weight or the correlation coefficient could be a reliable measure for the impact of either drug A on drug B or, vice versa, of B on A. Results of studies justify the statement, that both of the approaches show similar assessment of the mode of mutual interaction of the drugs studied. It was found that most of the drug mixtures exhibit independent action and quite few of the mixtures show synergic or dependent action. PMID:27479466

  9. Psychometric Properties on Lecturers' Beliefs on Teaching Function: Rasch Model Analysis

    ERIC Educational Resources Information Center

    Mofreh, Samah Ali Mohsen; Ghafar, Mohammed Najib Abdul; Omar, Abdul Hafiz Hj; Mosaku, Monsurat; Ma'ruf, Amar

    2014-01-01

    This paper focuses on the psychometric analysis of lecturers' beliefs on teaching function (LBTF) survey using Rasch Model analysis. The sample comprised 34 Community Colleges' lecturers. The Rasch Model is applied to produce specific measurements on the lecturers' beliefs on teaching function in order to generalize results and inferential…

  10. Defining a Model for Mitochondrial Function in mESC Differentiation

    EPA Science Inventory

    Defining a Model for Mitochondrial Function in mESC DifferentiationDefining a Model for Mitochondrial Function in mESC Differentiation Differentiating embryonic stem cells (ESCs) undergo mitochondrial maturation leading to a switch from a system dependent upon glycolysis to a re...

  11. A Classroom Note on: Modeling Functions with the TI-83/84 Calculator

    ERIC Educational Resources Information Center

    Lubowsky, Jack

    2011-01-01

    In Pre-Calculus courses, students are taught the composition and combination of functions to model physical applications. However, when combining two or more functions into a single more complicated one, students may lose sight of the physical picture which they are attempting to model. A block diagram, or flow chart, in which each block…

  12. A Note on the Equivalence between Observed and Expected Information Functions with Polytomous IRT Models

    ERIC Educational Resources Information Center

    Magis, David

    2015-01-01

    The purpose of this note is to study the equivalence of observed and expected (Fisher) information functions with polytomous item response theory (IRT) models. It is established that observed and expected information functions are equivalent for the class of divide-by-total models (including partial credit, generalized partial credit, rating…

  13. An exactly solvable model of an oscillator with nonlinear coupling and zeros of Bessel functions

    NASA Technical Reports Server (NTRS)

    Dodonov, V. V.; Klimov, A. B.

    1993-01-01

    We consider an oscillator model with nonpolynomial interaction. The model admits exact solutions for two situations: for energy eigenvalues in terms of zeros of Bessel functions, that were considered as functions of the continuous index; and for the corresponding eigenstates in terms of Lommel polynomials.

  14. Functional scale-free networks in the two-dimensional Abelian sandpile model

    NASA Astrophysics Data System (ADS)

    Zarepour, M.; Niry, M. D.; Valizadeh, A.

    2015-07-01

    Recently, the similarity of the functional network of the brain and the Ising model was investigated by Chialvo [Nat. Phys. 6, 744 (2010), 10.1038/nphys1803]. This similarity supports the idea that the brain is a self-organized critical system. In this study we derive a functional network of the two-dimensional Bak-Tang-Wiesenfeld sandpile model as a self-organized critical model, and compare its characteristics with those of the functional network of the brain, obtained from functional magnetic resonance imaging.

  15. Neutron strength functions: the link between resolved resonances and the optical model

    SciTech Connect

    Moldauer, P.A.

    1980-01-01

    Neutron strength functions and scattering radii are useful as energy and channel radius independent parameters that characterize neutron scattering resonances and provide a connection between R-matrix resonance analysis and the optical model. The choice of R-matrix channel radii is discussed, as are limitations on the accuracies of strength functions. New definitions of the p-wave strength function and scattering radius are proposed. For light nuclei, where strength functions display optical model energy variations over the resolved resonances, a doubly reduced partial neutron width is introduced for more meaningful statistical analyses of widths. The systematic behavior of strength functions and scattering radii is discussed.

  16. Voluntary Delay of Reinforcement as a Function of Model Status

    ERIC Educational Resources Information Center

    Walls, Richard T.; Smith, Tennie S.

    1970-01-01

    Adult vocational rehabilitation clients in a resident training program were engaged in a task involving the assemble of bolts, washers, and nuts, and were given their choice of a smaller reward immediately or a delayed larger reward. Subjects tended to imitate the decision of the video-tape model (both high and medium status). (Author)

  17. A Functional Model of Sensemaking in a Neurocognitive Architecture

    PubMed Central

    Lebiere, Christian; Paik, Jaehyon; Rutledge-Taylor, Matthew; Staszewski, James; Anderson, John R.

    2013-01-01

    Sensemaking is the active process of constructing a meaningful representation (i.e., making sense) of some complex aspect of the world. In relation to intelligence analysis, sensemaking is the act of finding and interpreting relevant facts amongst the sea of incoming reports, images, and intelligence. We present a cognitive model of core information-foraging and hypothesis-updating sensemaking processes applied to complex spatial probability estimation and decision-making tasks. While the model was developed in a hybrid symbolic-statistical cognitive architecture, its correspondence to neural frameworks in terms of both structure and mechanisms provided a direct bridge between rational and neural levels of description. Compared against data from two participant groups, the model correctly predicted both the presence and degree of four biases: confirmation, anchoring and adjustment, representativeness, and probability matching. It also favorably predicted human performance in generating probability distributions across categories, assigning resources based on these distributions, and selecting relevant features given a prior probability distribution. This model provides a constrained theoretical framework describing cognitive biases as arising from three interacting factors: the structure of the task environment, the mechanisms and limitations of the cognitive architecture, and the use of strategies to adapt to the dual constraints of cognition and the environment. PMID:24302930

  18. A Simple Model System to Demonstrate Antibody Structure and Functions.

    ERIC Educational Resources Information Center

    O'Kennedy, Richard

    1991-01-01

    A model that can be used to show the arrangement of light and heavy chains, disulfide linkages, domains, and subclass variations in antibodies is given. It can be constructed and modified to illustrate Fab, F(ab')2, and Fc fragments, single domain and bifunctional antibodies, and labeling of antibodies. (Author)

  19. SIR model with general distribution function in the infectious period

    NASA Astrophysics Data System (ADS)

    Gomes, Marcelo F. C.; Gonçalves, Sebastián

    2009-08-01

    The Susceptible-Infected-Removed or SIR model, as it was formulated by Kermack and McKendrick, is the key model for epidemic dynamics. Most applications of such a basic scheme use a constant rate for the removal term. However, that assumption corresponds to the rather unrealistic exponential distribution of infectious times. On the other hand, recent approaches, like numerical simulations, frequently assume a fixed and uniform duration for the infectious state-which is unrealistic too. The extreme assumptions in those different schemes are a hurdle that can frustrate any intention of drawing comparison between results from them. In the present contribution we study the delay equations for the SIR model, comparing the solutions for many typical cases with the simulation counterpart and with the standard SIR model. Using delay equations, where each infected individual is removed at a specific time after being infected, the dynamics for the infected and susceptible agree almost exactly with the numerical implementation. Even in the general case of distributed infective periods, the agreement is excellent.

  20. Modelling the Constraints of Spatial Environment in Fauna Movement Simulations: Comparison of a Boundaries Accurate Function and a Cost Function

    NASA Astrophysics Data System (ADS)

    Jolivet, L.; Cohen, M.; Ruas, A.

    2015-08-01

    Landscape influences fauna movement at different levels, from habitat selection to choices of movements' direction. Our goal is to provide a development frame in order to test simulation functions for animal's movement. We describe our approach for such simulations and we compare two types of functions to calculate trajectories. To do so, we first modelled the role of landscape elements to differentiate between elements that facilitate movements and the ones being hindrances. Different influences are identified depending on landscape elements and on animal species. Knowledge were gathered from ecologists, literature and observation datasets. Second, we analysed the description of animal movement recorded with GPS at fine scale, corresponding to high temporal frequency and good location accuracy. Analysing this type of data provides information on the relation between landscape features and movements. We implemented an agent-based simulation approach to calculate potential trajectories constrained by the spatial environment and individual's behaviour. We tested two functions that consider space differently: one function takes into account the geometry and the types of landscape elements and one cost function sums up the spatial surroundings of an individual. Results highlight the fact that the cost function exaggerates the distances travelled by an individual and simplifies movement patterns. The geometry accurate function represents a good bottom-up approach for discovering interesting areas or obstacles for movements.

  1. Examination of Ventricular Contraction Function Using Electrical Lumped Circuit Model of Circulation System

    NASA Astrophysics Data System (ADS)

    Ito, Mitsuyo; Koya, Yoshiharu; Mizoshiri, Isao

    Presently, many of the already proposed blood circulation models are mainly partial models although they are precise models. A complete model that is a combination of these partial models are difficult to analyze because it is complicated to consider both the viscosity of blood and circulatory details at the same time. So, it is difficult to control the model parameters in order to adapt to various cases of circulatory diseases. This paper proposes a complete circulation model as a lumped electrical circuit, which is comparatively simple. In the circuit model, total blood is modeled as seven lumped capacitors, representing the functions of atriums, ventricles, arteries, veins and lungs. We regard the variation of the ventricle capacitance as the driving force of the complete circulation model. In our model, we considered only the variation of pressure between each part and the blood capacity of each part. In particular, the contraction function of the left ventricle is examined under the consideration of whole blood circulation.

  2. Implementation and identification of Preisach type hysteresis models with Everett Function in closed form

    NASA Astrophysics Data System (ADS)

    Szabó, Zsolt; Füzi, János

    2016-05-01

    The Preisach function is considered as a product of two special one dimensional functions, which allows the closed form evaluation of the Everett integral. The deduced closed form expressions are included in Preisach models, in particular in the static model, moving model and a rate dependent hysteresis model, which can simulate the frequency dependence of the magnetization process. The details of the freely available implementations, which are available online are presented. The identification of the model parameters and the accuracy to describe the magnetization process are discussed and demonstrated by fitting measured data. Transient electric circuit simulation with hysteresis demonstrates the applicability of the developed models.

  3. Why are you telling me that? A conceptual model of the social function of autobiographical memory.

    PubMed

    Alea, Nicole; Bluck, Susan

    2003-03-01

    In an effort to stimulate and guide empirical work within a functional framework, this paper provides a conceptual model of the social functions of autobiographical memory (AM) across the lifespan. The model delineates the processes and variables involved when AMs are shared to serve social functions. Components of the model include: lifespan contextual influences, the qualitative characteristics of memory (emotionality and level of detail recalled), the speaker's characteristics (age, gender, and personality), the familiarity and similarity of the listener to the speaker, the level of responsiveness during the memory-sharing process, and the nature of the social relationship in which the memory sharing occurs (valence and length of the relationship). These components are shown to influence the type of social function served and/or, the extent to which social functions are served. Directions for future empirical work to substantiate the model and hypotheses derived from the model are provided. PMID:12820829

  4. Modelling human musculoskeletal functional movements using ultrasound imaging

    PubMed Central

    2010-01-01

    Background A widespread and fundamental assumption in the health sciences is that muscle functions are related to a wide variety of conditions, for example pain, ischemic and neurological disorder, exercise and injury. It is therefore highly desirable to study musculoskeletal contributions in clinical applications such as the treatment of muscle injuries, post-surgery evaluations, monitoring of progressive degeneration in neuromuscular disorders, and so on. The spatial image resolution in ultrasound systems has improved tremendously in the last few years and nowadays provides detailed information about tissue characteristics. It is now possible to study skeletal muscles in real-time during activity. Methods The ultrasound images are transformed to be congruent and are effectively compressed and stacked in order to be analysed with multivariate techniques. The method is applied to a relevant clinical orthopaedic research field, namely to describe the dynamics in the Achilles tendon and the calf during real-time movements. Results This study introduces a novel method to medical applications that can be used to examine ultrasound image sequences and to detect, visualise and quantify skeletal muscle dynamics and functions. Conclusions This new objective method is a powerful tool to use when visualising tissue activity and dynamics of musculoskeletal ultrasound registrations. PMID:20492648

  5. Knock-out models reveal new aquaporin functions.

    PubMed

    Verkman, Alan S

    2009-01-01

    Knockout mice have been informative in the discovery of unexpected biological functions of aquaporins. Knockout mice have confirmed the predicted roles of aquaporins in transepithelial fluid transport, as in the urinary concentrating mechanism and glandular fluid secretion. A less obvious, though predictable role of aquaporins is in tissue swelling under stress, as in the brain in stroke, tumor and infection. Phenotype analysis of aquaporin knockout mice has revealed several unexpected cellular roles of aquaporins whose mechanisms are being elucidated. Aquaporins facilitate cell migration, as seen in aquaporin-dependent tumor angiogenesis and tumor metastasis, by a mechanism that may involve facilitated water transport in lamellipodia of migrating cells. The ' aquaglyceroporins', aquaporins that transport both glycerol and water, regulate glycerol content in epidermis, fat and other tissues, and lead to a multiplicity of interesting consequences of gene disruption including dry skin, resistance to skin carcinogenesis, impaired cell proliferation and altered fat metabolism. An even more surprising role of a mammalian aquaporin is in neural signal transduction in the central nervous system. The many roles of aquaporins might be exploited for clinical benefit by modulation of aquaporin expression/function - as diuretics, and in the treatment of brain swelling, glaucoma, epilepsy, obesity and cancer. PMID:19096787

  6. Insights from mathematical modeling of renal tubular function.

    PubMed

    Weinstein, A M

    1998-01-01

    Mathematical models of proximal tubule have been developed which represent the important solute species within the constraints of known cytosolic concentrations, transport fluxes, and overall epithelial permeabilities. In general, model simulations have been used to assess the quantitative feasibility of what appear to be qualitatively plausible mechanisms, or alternatively, to identify incomplete rationalization of experimental observations. The examples considered include: (1) proximal water reabsorption, for which the lateral interspace is a locus for solute-solvent coupling; (2) ammonia secretion, for which the issue is prioritizing driving forces - transport on the Na+/H+ exchanger, on the Na,K-ATPase, or ammoniagenesis; (3) formate-stimulated NaCl reabsorption, for which simple addition of a luminal membrane chloride/formate exchanger fails to represent experimental observation, and (4) balancing luminal entry and peritubular exit, in which ATP-dependent peritubular K+ channels have been implicated, but appear unable to account for the bulk of proximal tubule cell volume homeostasis. PMID:9730663

  7. Modelling the structure and function of enzymes by machine learning.

    PubMed

    Sternberg, M J; Lewis, R A; King, R D; Muggleton, S

    1992-01-01

    A machine learning program, GOLEM, has been applied to two problems: (1) the prediction of protein secondary structure from sequence and (2) modelling a quantitative structure-activity relationship in drug design. GOLEM takes as input observations and combines them with background knowledge of chemistry to yield rules expressed as stereochemical principles for prediction. The secondary structure prediction was explored on the alpha/alpha class of proteins; on an unrelated test set it yielded 81% accuracy. The rules from GOLEM defined patterns of residues forming alpha-helices. The system studied for drug design was the activities of trimethoprim analogues binding to E. coli dihydrofolate reductase. The GOLEM rules were a better model than standard regression approaches. More importantly, these rules described the chemical properties of the enzyme-binding site that were in broad agreement with the crystallographic structure. PMID:1290938

  8. Approaches to Modelling the Dynamical Activity of Brain Function Based on the Electroencephalogram

    NASA Astrophysics Data System (ADS)

    Liley, David T. J.; Frascoli, Federico

    The brain is arguably the quintessential complex system as indicated by the patterns of behaviour it produces. Despite many decades of concentrated research efforts, we remain largely ignorant regarding the essential processes that regulate and define its function. While advances in functional neuroimaging have provided welcome windows into the coarse organisation of the neuronal networks that underlie a range of cognitive functions, they have largely ignored the fact that behaviour, and by inference brain function, unfolds dynamically. Modelling the brain's dynamics is therefore a critical step towards understanding the underlying mechanisms of its functioning. To date, models have concentrated on describing the sequential organisation of either abstract mental states (functionalism, hard AI) or the objectively measurable manifestations of the brain's ongoing activity (rCBF, EEG, MEG). While the former types of modelling approach may seem to better characterise brain function, they do so at the expense of not making a definite connection with the actual physical brain. Of the latter, only models of the EEG (or MEG) offer a temporal resolution well matched to the anticipated temporal scales of brain (mental processes) function. This chapter will outline the most pertinent of these modelling approaches, and illustrate, using the electrocortical model of Liley et al, how the detailed application of the methods of nonlinear dynamics and bifurcation theory is central to exploring and characterising their various dynamical features. The rich repertoire of dynamics revealed by such dynamical systems approaches arguably represents a critical step towards an understanding of the complexity of brain function.

  9. Modeling the two-point correlation of the vector stream function

    NASA Technical Reports Server (NTRS)

    Oberlack, M.; Rogers, M. M.; Reynolds, W. C.

    1994-01-01

    A new model for the two-point vector stream function correlation has been developed using tensor invariant arguments and evaluated by the comparison of model predictions with DNS data for incompressible homogeneous turbulent shear flow. This two-point vector stream function model correlation can then be used to calculate the two-point velocity correlation function and other quantities useful in turbulence modeling. The model assumes that the two-point vector stream function correlation can be written in terms of the separation vector and a new tensor function that depends only on the magnitude of the separation vector. The model has a single free model coefficient, which has been chosen by comparison with the DNS data. The relative error of the model predictions of the two-point vector stream function correlation is only a few percent for a broad range of the model coefficient. Predictions of the derivatives of this correlation, which are of interest in turbulence modeling, may not be this accurate.

  10. Moving Kriging shape function modeling of vector TARMA models for modal identification of linear time-varying structural systems

    NASA Astrophysics Data System (ADS)

    Yang, Wu; Liu, Li; Zhou, Si-Da; Ma, Zhi-Sai

    2015-10-01

    This work proposes a Moving Kriging (MK) shape function modeling method for modal identification of linear time-varying (LTV) structural systems based on vector time-dependent autoregressive moving average (VTARMA) models. It aims to avoid the functional subspaces selection of the conventional functional series VTARMA (FS-VTARMA) models. Instead of the common basis functions, it constructs the time-varying coefficients on the time nodes with the MK shape functions in a compact support domain. The merit of the MK shape function is to determine its shape parameters upon vector random vibration signals adaptively. Model identification is effectively dealt with through an optimization scheme that decomposes the identification problem into two subproblems: estimating model parameters via two-stage least squares (2SLS) method and estimating shape function parameters via a discrete-continuous-variable hybrid optimization. In addition, the model order selection is achieved by the optimization scheme. This method has been validated by a Monte Carlo study of simulation case and further by an experimental test case, and the performance and potential advantages are illustrated.

  11. Introducing free-function camera calibration model for central-projection and omni-directional lenses

    NASA Astrophysics Data System (ADS)

    Nekouei Shahraki, M.; Haala, N.

    2015-09-01

    To ensure making valid decisions with high accuracy in machine vision systems such as driver-assistant systems, a primary key factor is to have accurate measurements, which means that we need accurate camera calibration for various optical designs and a very fast approach to analyse the calibration data in real-time. Conventional methods have specific limitations such as limited accuracy, instability by using complex models, difficulties to model the local lens distortions and limitation in real-time calculations that altogether show the necessity to introduce new solutions. We introduce a new model for lens distortion modelling with high accuracies beyond conventional models while yet allowing real-time calculation. The concept is based on Free-Function modelling in a posterior calibration step using the initial distortion estimation and the corresponding residuals on the observations as input information. Free-Function model is the technique of numerically and locally modelling the lens distortion field by assuming unknown functions in our calibration model. This increases the model's flexibility to fit to different optical designs and be able to model the very local lens distortions. Using the Free-Function model one can observe great enhancements in accuracy (in comparison with classical models). Furthermore, by increasing the number of control points and improving their distribution the quality of lens modelling would be improved; a characteristic which is not present in the classical methods.

  12. Assessment of models for pedestrian dynamics with functional principal component analysis

    NASA Astrophysics Data System (ADS)

    Chraibi, Mohcine; Ensslen, Tim; Gottschalk, Hanno; Saadi, Mohamed; Seyfried, Armin

    2016-06-01

    Many agent based simulation approaches have been proposed for pedestrian flow. As such models are applied e.g. in evacuation studies, the quality and reliability of such models is of vital interest. Pedestrian trajectories are functional data and thus functional principal component analysis is a natural tool to assess the quality of pedestrian flow models beyond average properties. In this article we conduct functional Principal Component Analysis (PCA) for the trajectories of pedestrians passing through a bottleneck. In this way it is possible to assess the quality of the models not only on basis of average values but also by considering its fluctuations. We benchmark two agent based models of pedestrian flow against the experimental data using PCA average and stochastic features. Functional PCA proves to be an efficient tool to detect deviation between simulation and experiment and to assess quality of pedestrian models.

  13. Functional imaging of tumor vascular network in small animal models

    NASA Astrophysics Data System (ADS)

    Kalchenko, Vyacheslav; Madar-Balakirski, Noa; Kuznetsov, Yuri; Meglinski, Igor; Harmelin, Alon

    2011-07-01

    In current report we present synchronized in vivo imaging of tumor vascular network and tumor microenvironment obtained by combined use of Dynamic Light Scattering Imaging, Spectrally Enhanced Microscopy, and Fluorescence Intravital Microscopy. Dynamic Light Scattering Imaging is used for functional imaging of the vascular network and blood microcirculation. Spectrally Enhanced Microscopy provides information regarding blood vessel topography. Fluorescence Intravital Microscopy is used for imaging of tumor microvasculature and tumor microenvironment. These well known modalities have been comprehensively validated in the past and are widely used in various bio-medical applications. As shown here, their combined application has great potential for studies of vascular biology. This multi-modal non-invasive diagnostic technique expands our current capacity to investigate blood microcirculation and tumor angiogenesis in vivo, thereby contributing to the development of cancer research and treatment.

  14. Coupled cluster Green function: Model involving single and double excitations

    NASA Astrophysics Data System (ADS)

    Bhaskaran-Nair, Kiran; Kowalski, Karol; Shelton, William A.

    2016-04-01

    In this paper, we report on the development of a parallel implementation of the coupled-cluster (CC) Green function formulation (GFCC) employing single and double excitations in the cluster operator (GFCCSD). A key aspect of this work is the determination of the frequency dependent self-energy, Σ(ω). The detailed description of the underlying algorithm is provided, including approximations used that preserve the pole structure of the full GFCCSD method, thereby reducing the computational costs while maintaining an accurate character of methodology. Furthermore, for systems with strong local correlation, our formulation reveals a diagonally dominate block structure where as the non-local correlation increases, the block size increases proportionally. To demonstrate the accuracy of our approach, several examples including calculations of ionization potentials for benchmark systems are presented and compared against experiment.

  15. Coupled cluster Green function: Model involving single and double excitations.

    PubMed

    Bhaskaran-Nair, Kiran; Kowalski, Karol; Shelton, William A

    2016-04-14

    In this paper, we report on the development of a parallel implementation of the coupled-cluster (CC) Green function formulation (GFCC) employing single and double excitations in the cluster operator (GFCCSD). A key aspect of this work is the determination of the frequency dependent self-energy, Σ(ω). The detailed description of the underlying algorithm is provided, including approximations used that preserve the pole structure of the full GFCCSD method, thereby reducing the computational costs while maintaining an accurate character of methodology. Furthermore, for systems with strong local correlation, our formulation reveals a diagonally dominate block structure where as the non-local correlation increases, the block size increases proportionally. To demonstrate the accuracy of our approach, several examples including calculations of ionization potentials for benchmark systems are presented and compared against experiment. PMID:27083702

  16. Scattering phase function for particulates-in-water: modeling and validation

    NASA Astrophysics Data System (ADS)

    Sahu, Sanjay Kumar; Shanmugam, Palanisamy

    2016-05-01

    Scattering phase function plays a crucial role in studies and calculations based on radiative transfer theory in water as well as atmosphere. A model based on Mie theory is developed for estimating the particulates-in-water scattering phase function for forward angles (0.1° - 90°). Particle size distribution (PSD) slope (ξ) and bulk refractive index (n) are chosen as key inputs for this proposed model. The PSD slope can be estimated from the attenuation spectrum measured directly in-situ and the bulk refractive index can be calculated by an inversion model using measured backscattering ratio (BP) and PSD slope. The attenuation spectrum and backscattering ratio can be easily measured in-situ using commercially available instruments in real time. The entire range of forward angles is divided into two ranges and phase function is modeled separately in the ranges 0.1° - 5° and 5° - 90°, from numerically calculated Volume Scattering Function (VSF) using Mie theory. The division boundary is decided owing to the fact that the scattering phase functions, for different oceanic conditions, exhibit a change in slope at approximately 5°. Performance of the present model is evaluated by comparing with existing empirical and analytical models as well as measured phase functions. The proposed phase function model shows a considerable improvement upon existing models, and will have important applications in remote sensing applications and underwater studies.

  17. The Sandia MEMS Passive Shock Sensor : FY08 testing for functionality, model validation, and technology readiness.

    SciTech Connect

    Walraven, Jeremy Allen; Blecke, Jill; Baker, Michael Sean; Clemens, Rebecca C.; Mitchell, John Anthony; Brake, Matthew Robert; Epp, David S.; Wittwer, Jonathan W.

    2008-10-01

    This report summarizes the functional, model validation, and technology readiness testing of the Sandia MEMS Passive Shock Sensor in FY08. Functional testing of a large number of revision 4 parts showed robust and consistent performance. Model validation testing helped tune the models to match data well and identified several areas for future investigation related to high frequency sensitivity and thermal effects. Finally, technology readiness testing demonstrated the integrated elements of the sensor under realistic environments.

  18. Integrated Medical Model (IMM) 4.0 Enhanced Functionalities

    NASA Technical Reports Server (NTRS)

    Young, M.; Keenan, A. B.; Saile, L.; Boley, L. A.; Walton, M. E.; Shah, R. V.; Kerstman, E. L.; Myers, J. G.

    2015-01-01

    The Integrated Medical Model is a probabilistic simulation model that uses input data on 100 medical conditions to simulate expected medical events, the resources required to treat, and the resulting impact to the mission for specific crew and mission characteristics. The newest development version of IMM, IMM v4.0, adds capabilities that remove some of the conservative assumptions that underlie the current operational version, IMM v3. While IMM v3 provides the framework to simulate whether a medical event occurred, IMMv4 also simulates when the event occurred during a mission timeline. This allows for more accurate estimation of mission time lost and resource utilization. In addition to the mission timeline, IMMv4.0 features two enhancements that address IMM v3 assumptions regarding medical event treatment. Medical events in IMMv3 are assigned the untreated outcome if any resource required to treat the event was unavailable. IMMv4 allows for partially treated outcomes that are proportional to the amount of required resources available, thus removing the dichotomous treatment assumption. An additional capability IMMv4 is to use an alternative medical resource when the primary resource assigned to the condition is depleted, more accurately reflecting the real-world system. The additional capabilities defining IMM v4.0the mission timeline, partial treatment, and alternate drug result in more realistic predicted mission outcomes. The primary model outcomes of IMM v4.0 for the ISS6 mission, including mission time lost, probability of evacuation, and probability of loss of crew life, are be compared to those produced by the current operational version of IMM to showcase enhanced prediction capabilities.

  19. Nano-Transistor Modeling: Two Dimensional Green's Function Method

    NASA Technical Reports Server (NTRS)

    Svizhenko, Alexei; Anantram, M. P.; Govindan, T. R.; Biegel, Bryan

    2001-01-01

    Two quantum mechanical effects that impact the operation of nanoscale transistors are inversion layer energy quantization and ballistic transport. While the qualitative effects of these features are reasonably understood, a comprehensive study of device physics in two dimensions is lacking. Our work addresses this shortcoming and provides: (a) a framework to quantitatively explore device physics issues such as the source-drain and gate leakage currents, DIBL (Drain Induced Barrier Lowering), and threshold voltage shift due to quantization, and b) a means of benchmarking quantum corrections to semiclassical models (such as density-gradient and quantum-corrected MEDICI).

  20. Calculating kaon fragmentation functions from the Nambu-Jona-Lasinio jet model

    SciTech Connect

    Matevosyan, Hrayr H.; Thomas, Anthony W.; Bentz, Wolfgang

    2011-04-01

    The Nambu-Jona-Lasinio (NJL)-jet model provides a sound framework for calculating the fragmentation functions in an effective chiral quark theory, where the momentum and isospin sum rules are satisfied without the introduction of ad hoc parameters. Earlier studies of the pion fragmentation functions using the NJL model within this framework showed qualitative agreement with the empirical parametrizations. Here we extend the NJL-jet model by including the strange quark. The corrections to the pion fragmentation functions and corresponding kaon fragmentation functions are calculated using the elementary quark to quark-meson fragmentation functions from NJL. The results for the kaon fragmentation functions exhibit a qualitative agreement with the empirical parametrizations, while the unfavored strange quark fragmentation to pions is shown to be of the same order of magnitude as the unfavored light quark. The results of these studies are expected to provide important guidance for the analysis of a large variety of semi-inclusive data.

  1. Proton electroreduction catalyzed by cobaloximes: functional models for hydrogenases.

    PubMed

    Razavet, Mathieu; Artero, Vincent; Fontecave, Marc

    2005-06-27

    Cobaloximes have been examined as electrocatalysts for proton reduction in nonaqueous solvent in the presence of triethylammonium chloride. [Co(III)(dmgH)2pyCl], working at moderate potentials (-0.90 V/(Ag/AgCl/3 mol x L(-1) NaCl) and in neutral conditions, is a promising catalyst as compared to other first-row transition metal complexes which generally function at more negative potentials and/or at lower pH. More than 100 turnovers can be achieved during controlled-potential electrolysis without detectable degradation of the catalyst. Cyclic voltammograms simulation is consistent with a heterolytic catalytic mechanism and allowed us to extract related kinetic parameters. Introduction of an electron-donating (electron-withdrawing) substituent in the axial pyridine ligand significantly increases (decreases) the rate constant of the catalytic cycle determining step. This effect linearly correlates with the Hammet coefficients of the introduced substituents. The influence of the equatorial glyoxime ligand was also investigated and the capability of the stabilized BF2-bridged species [Co(dmgBF2)2(OH2)2] for electrocatalyzed hydrogen evolution confirmed. PMID:15962987

  2. Assembly and mechanosensory function of focal adhesions: experiments and models.

    PubMed

    Bershadsky, Alexander D; Ballestrem, Christoph; Carramusa, Letizia; Zilberman, Yuliya; Gilquin, Benoit; Khochbin, Saadi; Alexandrova, Antonina Y; Verkhovsky, Alexander B; Shemesh, Tom; Kozlov, Michael M

    2006-04-01

    Initial integrin-mediated cell-matrix adhesions (focal complexes) appear underneath the lamellipodia, in the regions of the "fast" centripetal flow driven by actin polymerization. Once formed, these adhesions convert the flow behind them into a "slow", myosin II-driven mode. Some focal complexes then turn into elongated focal adhesions (FAs) associated with contractile actomyosin bundles (stress fibers). Myosin II inhibition does not suppress formation of focal complexes but blocks their conversion into mature FAs and further FA growth. Application of external pulling force promotes FA growth even under conditions when myosin II activity is blocked. Thus, individual FAs behave as mechanosensors responding to the application of force by directional assembly. We proposed a thermodynamic model for the mechanosensitivity of FAs, taking into account that an elastic molecular aggregate subject to pulling forces tends to grow in the direction of force application by incorporating additional subunits. This simple model can explain a variety of processes typical of FA behavior. Assembly of FAs is triggered by the small G-protein Rho via activation of two major targets, Rho-associated kinase (ROCK) and the formin homology protein, Dia1. ROCK controls creation of myosin II-driven forces, while Dia1 is involved in the response of FAs to these forces. Expression of the active form of Dia1, allows the external force-induced assembly of mature FAs, even in conditions when Rho is inhibited. Conversely, downregulation of Dia1 by siRNA prevents FA maturation even if Rho is activated. Dia1 and other formins cap barbed (fast growing) ends of actin filaments, allowing insertion of the new actin monomers. We suggested a novel mechanism of such "leaky" capping based on an assumption of elasticity of the formin/barbed end complex. Our model predicts that formin-mediated actin polymerization should be greatly enhanced by application of external pulling force. Thus, the formin-actin complex

  3. Aircraft/Air Traffic Management Functional Analysis Model. Version 2.0; User's Guide

    NASA Technical Reports Server (NTRS)

    Etheridge, Melvin; Plugge, Joana; Retina, Nusrat

    1998-01-01

    The Aircraft/Air Traffic Management Functional Analysis Model, Version 2.0 (FAM 2.0), is a discrete event simulation model designed to support analysis of alternative concepts in air traffic management and control. FAM 2.0 was developed by the Logistics Management Institute (LMI) a National Aeronautics and Space Administration (NASA) contract. This document provides a guide for using the model in analysis. Those interested in making enhancements or modification to the model should consult the companion document, Aircraft/Air Traffic Management Functional Analysis Model, Version 2.0 Technical Description.

  4. Molecular modelling of miraculin: Structural analyses and functional hypotheses.

    PubMed

    Paladino, Antonella; Costantini, Susan; Colonna, Giovanni; Facchiano, Angelo M

    2008-02-29

    Miraculin is a plant protein that displays the peculiar property of modifying taste by swiching sour into a sweet taste. Its monomer is flavourless at all pH as well as at high concentration; the dimer form elicits its taste-modifying activity at acidic pH; a tetrameric form is also reported as active. Two histidine residues, located in exposed regions, are the main responsible of miraculin activity, as demonstrated by mutagenesis studies. Since structural data of miraculin are not available, we have predicted its three-dimensional structure and simulated both its dimer and tetramer forms by comparative modelling and molecular docking techniques. Finally, molecular dynamics simulations at different pH conditions have indicated that at acidic pH the dimer assumes a widely open conformation, in agreement with the hypotheses coming from other studies. PMID:18158914

  5. A Functional Murine Model of Hind Limb Demand Ischemia

    PubMed Central

    Peck, Michael A.; Crawford, Robert S.; Abularrage, Christopher J.; Patel, Virendra I.; Conrad, Mark F.; Yoo, Jin Hyung; Watkins, Michael T.; Albadawi, Hassan

    2010-01-01

    Introduction To date murine models of treadmill exercise have been used to study general exercise physiology and angiogenesis in ischemic hind limbs. The purpose of these experiments was to develop a murine model of demand ischemia in an ischemic limb to mimic claudication in humans. The primary goal was to determine whether treadmill exercise reflected a hemodynamic picture which might be consistent with the hyperemic response observed in humans. Methods Aged hypercholesterolemic ApoE null mice ( ApoE−/−, n=13) were subjected to Femoral Artery Ligation (FAL), and allowed to recover from the acute ischemic response. Peripheral perfusion of the hind limbs at rest was determined by serial evaluation using laser Doppler imaging (LDI) on days 0, 7, and 14 following FAL. During the duration of the experiments, the mice were also assessed on an established 5 point clinical ischemic score which assessed the degree of digital amputation, necrosis, and cyanosis as compared to the non ischemic contralateral limb. After stabilization of the LDI ratio (ischemic limb flux/contralateral non ischemic limb flux) and clinical ischemic score, mice underwent two days of treadmill training (10 min @ 10 m/min, incline of 10°) followed by 60 minutes daily treadmill exercise (13 m/min, incline of 10°) through day 25. An evaluation of pre-exercise and post exercise perfusion using LDI was performed on two separate occasions following the onset of daily exercise. During the immediate 15 minute post exercise evaluation, LDI scanning was obtained in quadruplicate, to allow identification of peak flux ratios. Statistical analysis included unpaired t-tests and ANOVA. Results After FAL, the LDI Flux ratio reached a nadir between days one and two, then stabilized by day 14 and remained stable through day 25. The clinical ischemic score stabilized at day 7, and remained stable throughout the rest of the experiment. Based on stabilization of both the clinical ischemic score and LDI ratio

  6. Modeling the auditory functions in the primary cortex

    NASA Astrophysics Data System (ADS)

    Wang, Kuansan; Shamma, Shihab A.

    1994-03-01

    Neurons in the primary auditory cortex exhibit distinctive selectivities in responses to various acoustic features. Recent physiological studies suggest three spatial dimensions along which the neural response patterns can be systematically organized: the tuning frequencies of the neurons are logarithmically mapped on the tonotopic axis, and the shapes of the tuning curves, in terms of symmetry and bandwidth, vary gradually along two other spatial dimensions. In this report, it is shown that these variations can be effectively modeled by a complex wavelet transform. With such a tie, one can employ well- established wavelet theories into analyzing and understanding how acoustic signals are processed in the auditory system, and thereby design novel engineering applications that are perceptually oriented.

  7. Modeling the auditory functions in the primary cortex

    NASA Astrophysics Data System (ADS)

    Wang, Kuansan; Shamma, Shihab A.

    1994-07-01

    Neurons in the primary auditory cortex exhibit distinctive selectivities in responses to various acoustic features. Recent physiological studies suggest that there are three spatial dimensions along which the neural response patterns can be systematically organized: the tuning frequencies of the neurons are logarithmically mapped on the tonotopic axis, and the shapes of the tuning curves, in terms of symmetry and bandwidth, vary gradually along two other spatial dimensions. It is shown that these variations can be effectively modeled by a complex wavelet transform. With such a tie, one can employ well-established wavelet theories to analyzing and understanding how acoustic signals are processed in the auditory system, and thereby design novel engineering applications that are perceptually oriented.

  8. Insight into the functional versatility of RNA through model-making with applications to data fitting.

    PubMed

    Bevilacqua, Philip C; Cerrone-Szakal, Andrea L; Siegfried, Nathan A

    2007-02-01

    The RNA World hypothesis posits that life emerged from self-replicating RNA molecules. For any single biopolymer to be the basis for life, it must both store information and perform diverse functions. It is well known that RNA can store information. Advances in recent years have revealed that RNA can exhibit remarkable functional versatility as well. In an effort to judge the functional versatility of RNA and thereby the plausibility that RNA was at one point the basis for life, a statistical chemical approach is adopted. Essential biological functions are reduced to simple molecular models in a minimalist, biopolymer-independent fashion. The models dictate requisite states, populations of states, and physical and chemical changes occurring between the states. Next, equations are derived from the models, which lead to complex phenomenological constants such as observed and functional constants that are defined in terms of familiar elementary chemical descriptors: intrinsic rate constants, microscopic ligand equilibrium constants, secondary structure stability, and ligand concentration. Using these equations, simulations of functional behavior are performed. These functional models provide practical frameworks for fitting and organizing real data on functional RNAs such as ribozymes and riboswitches. At the same time, the models allow the suitability of RNA as a basis for life to be judged. We conclude that RNA, while inferior to extant proteins in most, but not all, functional respects, may be more versatile than proteins, performing a wider range of elementary biological functions at a tolerable level. Inspection of the functional models and various RNA structures uncovers several surprising ways in which the nucleobases can conspire to afford chemical catalysis and evolvability. These models support the plausibility that RNA, or a closely related informational biopolymer, could serve as the basis for a fairly simple form of life. PMID:17391549

  9. The Lung Physiome: merging imaging-based measures with predictive computational models of structure and function

    PubMed Central

    Tawhai, Merryn H; Hoffman, Eric A; Lin, Ching-Long

    2009-01-01

    Global measurements of the lung provided by standard pulmonary function tests do not give insight into the regional basis of lung function and lung disease. Advances in imaging methodologies, computer technologies, and subject-specific simulations are creating new opportunities for studying structure-function relationships in the lung through multi-disciplinary research. The digital Human Lung Atlas is an imaging-based resource compiled from male and female subjects spanning several decades of age. The Atlas comprises both structural and functional measures, and includes computational models derived to match individual subjects for personalized prediction of function. The computational models in the Atlas form part of the Lung Physiome project, which is an international effort to develop integrative models of lung function at all levels of biological organization. The computational models provide mechanistic interpretation of imaging measures; the Atlas provides structural data upon which to base model geometry, and functional data against which to test hypotheses. The example of simulating air flow on a subject-specific basis is considered. Methods for deriving multi-scale models of the airway geometry for individual subjects in the Atlas are outlined, and methods for modeling turbulent flows in the airway are reviewed. PMID:20835982

  10. FOAM (Functional Ontology Assignments for Metagenomes): a Hidden Markov Model (HMM) database with environmental focus.

    PubMed

    Prestat, Emmanuel; David, Maude M; Hultman, Jenni; Taş, Neslihan; Lamendella, Regina; Dvornik, Jill; Mackelprang, Rachel; Myrold, David D; Jumpponen, Ari; Tringe, Susannah G; Holman, Elizabeth; Mavromatis, Konstantinos; Jansson, Janet K

    2014-10-29

    A new functional gene database, FOAM (Functional Ontology Assignments for Metagenomes), was developed to screen environmental metagenomic sequence datasets. FOAM provides a new functional ontology dedicated to classify gene functions relevant to environmental microorganisms based on Hidden Markov Models (HMMs). Sets of aligned protein sequences (i.e. 'profiles') were tailored to a large group of target KEGG Orthologs (KOs) from which HMMs were trained. The alignments were checked and curated to make them specific to the targeted KO. Within this process, sequence profiles were enriched with the most abundant sequences available to maximize the yield of accurate classifier models. An associated functional ontology was built to describe the functional groups and hierarchy. FOAM allows the user to select the target search space before HMM-based comparison steps and to easily organize the results into different functional categories and subcategories. FOAM is publicly available at http://portal.nersc.gov/project/m1317/FOAM/. PMID:25260589

  11. FOAM (Functional Ontology Assignments for Metagenomes): A Hidden Markov Model (HMM) database with environmental focus

    SciTech Connect

    Prestat, Emmanuel; David, Maude M.; Hultman, Jenni; Ta , Neslihan; Lamendella, Regina; Dvornik, Jill; Mackelprang, Rachel; Myrold, David D.; Jumpponen, Ari; Tringe, Susannah G.; Holman, Elizabeth; Mavromatis, Konstantinos; Jansson, Janet K.

    2014-09-26

    A new functional gene database, FOAM (Functional Ontology Assignments for Metagenomes), was developed to screen environmental metagenomic sequence datasets. FOAM provides a new functional ontology dedicated to classify gene functions relevant to environmental microorganisms based on Hidden Markov Models (HMMs). Sets of aligned protein sequences (i.e. ‘profiles’) were tailored to a large group of target KEGG Orthologs (KOs) from which HMMs were trained. The alignments were checked and curated to make them specific to the targeted KO. Within this process, sequence profiles were enriched with the most abundant sequences available to maximize the yield of accurate classifier models. An associated functional ontology was built to describe the functional groups and hierarchy. FOAM allows the user to select the target search space before HMM-based comparison steps and to easily organize the results into different functional categories and subcategories. FOAM is publicly available at http://portal.nersc.gov/project/m1317/FOAM/.

  12. Muscle function may depend on model selection in forward simulation of normal walking.

    PubMed

    Xiao, Ming; Higginson, Jill S

    2008-11-14

    The purpose of this study was to quantify how the predicted muscle function would change in a muscle-driven forward simulation of normal walking when changing the number of degrees of freedom in the model. Muscle function was described by individual muscle contributions to the vertical acceleration of the center of mass (COM). We built a two-dimensional (2D) sagittal plane model and a three-dimensional (3D) model in OpenSim and used both models to reproduce the same normal walking data. Perturbation analysis was applied to deduce muscle function in each model. Muscle excitations and contributions to COM support were compared between the 2D and 3D models. We found that the 2D model was able to reproduce similar joint kinematics and kinetics patterns as the 3D model. Individual muscle excitations were different for most of the hip muscles but ankle and knee muscles were able to attain similar excitations. Total induced vertical COM acceleration by muscles and gravity was the same for both models. However, individual muscle contributions to COM support varied, especially for hip muscles. Although there is currently no standard way to validate muscle function predictions, a 3D model seems to be more appropriate for estimating individual hip muscle function. PMID:18804767

  13. Two Models for Exploring the Anti-predator Function of Eyespots.

    ERIC Educational Resources Information Center

    Cundy, J. M.; Allen, J. A.

    1988-01-01

    Describes two working models of moths that can be used to test the eyespot function as an aversive property. Uses simple mechanical and electrical models as the "moths" and wild birds as the predators. Includes diagrams, methods, models, validation statements, and a discussion. (RT)

  14. RIM: A Random Item Mixture Model to Detect Differential Item Functioning

    ERIC Educational Resources Information Center

    Frederickx, Sofie; Tuerlinckx, Francis; De Boeck, Paul; Magis, David

    2010-01-01

    In this paper we present a new methodology for detecting differential item functioning (DIF). We introduce a DIF model, called the random item mixture (RIM), that is based on a Rasch model with random item difficulties (besides the common random person abilities). In addition, a mixture model is assumed for the item difficulties such that the…

  15. A General Model for Preferential and Triadic Choice in Terms of Central F Distribution Functions.

    ERIC Educational Resources Information Center

    Ennis, Daniel M; Johnson, Norman L.

    1994-01-01

    A model for preferential and triadic choice is derived in terms of weighted sums of central F distribution functions. It is a probabilistic generalization of Coombs' (1964) unfolding model from which special cases can be derived easily. This model for binary choice can be easily related to preference ratio judgments. (SLD)

  16. Evaluation of Model Selection Strategies for Cross-Level Two-Way Differential Item Functioning Analysis

    ERIC Educational Resources Information Center

    Patarapichayatham, Chalie; Kamata, Akihito; Kanjanawasee, Sirichai

    2012-01-01

    Model specification issues on the cross-level two-way differential item functioning model were previously investigated by Patarapichayatham et al. (2009). Their study clarified that an incorrect model specification can easily lead to biased estimates of key parameters. The objective of this article is to provide further insights on the issue by…

  17. A Note on the Item Information Function of the Four-Parameter Logistic Model

    ERIC Educational Resources Information Center

    Magis, David

    2013-01-01

    This article focuses on four-parameter logistic (4PL) model as an extension of the usual three-parameter logistic (3PL) model with an upper asymptote possibly different from 1. For a given item with fixed item parameters, Lord derived the value of the latent ability level that maximizes the item information function under the 3PL model. The…

  18. A Bayesian approach to functional-based multilevel modeling of longitudinal data: applications to environmental epidemiology

    PubMed Central

    Berhane, Kiros; Molitor, Nuoo-Ting

    2008-01-01

    Flexible multilevel models are proposed to allow for cluster-specific smooth estimation of growth curves in a mixed-effects modeling format that includes subject-specific random effects on the growth parameters. Attention is then focused on models that examine between-cluster comparisons of the effects of an ecologic covariate of interest (e.g. air pollution) on nonlinear functionals of growth curves (e.g. maximum rate of growth). A Gibbs sampling approach is used to get posterior mean estimates of nonlinear functionals along with their uncertainty estimates. A second-stage ecologic random-effects model is used to examine the association between a covariate of interest (e.g. air pollution) and the nonlinear functionals. A unified estimation procedure is presented along with its computational and theoretical details. The models are motivated by, and illustrated with, lung function and air pollution data from the Southern California Children's Health Study. PMID:18349036

  19. Model Etch Profiles for Ion Energy Distribution Functions in an Inductively Coupled Plasma Reactor

    SciTech Connect

    Abraham-Shrauner, B.; Chen, W.; Woodworth, J.R.

    1998-12-14

    Rectangular trench profiles are modeled with analytic etch rates determined from measured ion distribution functions. The pattern transfer step for this plasma etch is for trilayer lithography. Argon and chlorine angular ion energy distribution functions measured by a spherical collector ring analyzer are fit to a sum of drifting Maxwellian velocity distribution functions with anisotropic temperatures. The fit of the model ion distribution functions by a simulated annealing optimization procedure converges adequately for only two drifting Maxwellians. The etch rates are proportional to analytic expressions for the ion energy flux. Numerical computation of the etch profiles by integration of the characteristic equations for profile points and connection of the profiles points is efficient.

  20. The polarized structure function of the nucleons with a non-extensive statistical quark model

    NASA Astrophysics Data System (ADS)

    Trevisan, Luis A.; Mirez, Carlos

    2013-05-01

    We studied an application of nonextensive thermodynamics to describe the polarized structure function of nucleon, in a model where the usual Fermi-Dirac and Bose-Einstein energy distribution, often used in the statistical models, were replaced by the equivalent functions of the q-statistical. The parameters of the model are given by an effective temperature T, the q parameter (from Tsallis statistics), and the chemical potentials given by the corresponding up (u) and down (d) quark normalization in the nucleon and by Δu and Δd of the polarized functions.

  1. Jump of the minimal site and a new correlation function in the Bak-Sneppen model

    NASA Astrophysics Data System (ADS)

    Yang, C. B.; Cai, X.

    2001-08-01

    A new type of spatio-temporal correlation function for the process approaching the self-organized criticality is investigated within the Bak-Sneppen model for biological evolution. In terms of the ``directional shorter distance'' between the two sites with minimum fitness at two successive updates, the correlation function is defined and studied numerically for the nearest- and random-neighbor versions of the model. Qualitatively different behaviors of the jump of the minimal site in the two models are presented, and the behaviors of the correlation functions are shown also different.

  2. The polarized structure function of the nucleons with a non-extensive statistical quark model

    SciTech Connect

    Trevisan, Luis A.; Mirez, Carlos

    2013-05-06

    We studied an application of nonextensive thermodynamics to describe the polarized structure function of nucleon, in a model where the usual Fermi-Dirac and Bose-Einstein energy distribution, often used in the statistical models, were replaced by the equivalent functions of the q-statistical. The parameters of the model are given by an effective temperature T, the q parameter (from Tsallis statistics), and the chemical potentials given by the corresponding up (u) and down (d) quark normalization in the nucleon and by {Delta}u and {Delta}d of the polarized functions.

  3. New data model with better functionality for VLab

    NASA Astrophysics Data System (ADS)

    da Silveira, P. R.; Wentzcovitch, R. M.; Karki, B. B.

    2009-12-01

    The VLab infrastructure and architecture was further developed to allow for several new features. First, workflows for first principles calculations of thermodynamics properties and static elasticity programmed in Java as Web Services can now be executed by multiple users. Second, jobs generated by these workflows can now be executed in batch in multiple servers. A simple internal schedule was implemented to handle hundreds of execution packages generated by multiple users and avoid the overload on servers. Third, a new data model was implemented to guarantee integrity of a project (workflow execution) in case of failure. The latter can happen in an execution package or in a workflow phase. By recording all executed steps of a project, its execution can be resumed after dynamic alteration of parameters through the VLab Portal. Fourth, batch jobs can also be monitored through the portal. Now, better and faster interaction with servers is achieved using Ajax technology. Finally, plots are now created on the Vlab server using Gnuplot 4.2.2. Research supported by NSF grants ATM 0428774 (VLab). Vlab is hosted by the Minnesota Supercomputing Institute.

  4. Spectral function of the ionic Hubbard model (IHM)

    NASA Astrophysics Data System (ADS)

    Bulut, Sinan; Atkinson, Bill

    2010-03-01

    Using two-pole approximations, which are based on the equation of motion method, we calculate the excitation spectrum of the one dimensional IHM. To be specific, we use the composite operator method and the Roth-approximation. Though very simple in nature, these approximations capture the physics of the IHM qualitatively at least. As is predicted by several other numerical and/or theoretical studies, a bond-order (BO) phase is given by these approximate methods. In the BO phase, atoms in the system are dimerized leading to a gap in the excitation spectrum. We find that the BO phase flattens both low and high-energy bands. When the BO phase is suppressed, however, the system can be driven from the band-insulating phase to the metal one by electron-electron repulsions, which is somewhat counter-intuitive. Additionally, two-pole approximations generate a reasonably good DOS spectrum of this model when compared with exact numerical results for small systems.

  5. Zebrafish as a model to study chemokine function.

    PubMed

    Kochhan, Eva; Siekmann, Arndt F

    2013-01-01

    Zebrafish have emerged as a powerful model organism to study embryo morphogenesis. Due to their optical clarity, they are uniquely suited for time-lapse imaging studies, providing insights into the dynamic processes underlying tissue formation and cell migration. These studies have been tremendously facilitated by the availability of transgenic zebrafish lines, labelling distinct embryonic structures, individual cells, or even subcellular structures, such as the nucleus. Zebrafish studies have revealed that the migration of several different cell types in the embryo is controlled by chemokines, small vertebrate-specific proteins. Here, we report methods to analyze the expression pattern of a given chemokine and its receptor in transgenic zebrafish using fluorescent in situ hybridization in combination with an anti-green fluorescent protein (GFP) antibody staining. We furthermore illustrate how to image migrating cell populations using time-lapse microscopy in double-transgenic embryos. We show how to investigate cell number and direction of migration by using a nuclear-localized GFP. The combination of this transgene with a membrane-targeted red fluorescent protein allows for the simultaneous determination of changes in cell shape, such as the formation of filopodial extensions. We exemplify this by describing how a mutation in the chemokine receptor cxcr4a affects endothelial cell migration and blood vessel formation. Finally, we provide a method to perform fluorescent angiography to monitor blood vessel perfusion in chemokine receptor mutants. PMID:23625497

  6. Evidence supporting the importance of microbial functional groups in decomposition models

    NASA Astrophysics Data System (ADS)

    Todd-Brown, K. E.; Lu, L.; Allison, S. D.

    2010-12-01

    Microbial communities mediate organic carbon decomposition in both soil and marine environments. Decomposition depends on microbes that produce extracellular enzymes to degrade complex organic matter, as well as microbes that mineralize simple organic matter to CO2. Therefore microbes could be represented in Earth system models as functional groups based on the extracellular enzymes they produce. However, the importance of including the functional diversity of microbes in decomposition models has been unclear. In this study we simulated microbial functional diversity with two strains of Pseudomonas fluorescens bacteria, one of which secretes extracellular protease and one that does not. These two strains were competed on several carbon resources including casein-glucose, casamino acids-glucose and glucose over several days. We then fit a series of models to the resulting data: 1) an explicit model representing both biomass and substrate pools, 2) a simplified substrate pool model with two biomass pools and one substrate pool, 3) a simplified biomass pool model with one biomass and two substrate pools, 4) a simplified biomass/substrate pool model with one biomass and one substrate pool, and 5) a single carbon pool model. We found that the explicit model (#1) fit the laboratory data significantly better than the other models, suggesting that functional groups and substrate pools should be represented in global decomposition models with time steps on the order of hours.

  7. Re-Annotation Is an Essential Step in Systems Biology Modeling of Functional Genomics Data

    PubMed Central

    van den Berg, Bart H. J.; McCarthy, Fiona M.; Lamont, Susan J.; Burgess, Shane C.

    2010-01-01

    One motivation of systems biology research is to understand gene functions and interactions from functional genomics data such as that derived from microarrays. Up-to-date structural and functional annotations of genes are an essential foundation of systems biology modeling. We propose that the first essential step in any systems biology modeling of functional genomics data, especially for species with recently sequenced genomes, is gene structural and functional re-annotation. To demonstrate the impact of such re-annotation, we structurally and functionally re-annotated a microarray developed, and previously used, as a tool for disease research. We quantified the impact of this re-annotation on the array based on the total numbers of structural- and functional-annotations, the Gene Annotation Quality (GAQ) score, and canonical pathway coverage. We next quantified the impact of re-annotation on systems biology modeling using a previously published experiment that used this microarray. We show that re-annotation improves the quantity and quality of structural- and functional-annotations, allows a more comprehensive Gene Ontology based modeling, and improves pathway coverage for both the whole array and a differentially expressed mRNA subset. Our results also demonstrate that re-annotation can result in a different knowledge outcome derived from previous published research findings. We propose that, because of this, re-annotation should be considered to be an essential first step for deriving value from functional genomics data. PMID:20498845

  8. Methodology to develop crash modification functions for road safety treatments with fully specified and hierarchical models.

    PubMed

    Chen, Yongsheng; Persaud, Bhagwant

    2014-09-01

    Crash modification factors (CMFs) for road safety treatments are developed as multiplicative factors that are used to reflect the expected changes in safety performance associated with changes in highway design and/or the traffic control features. However, current CMFs have methodological drawbacks. For example, variability with application circumstance is not well understood, and, as important, correlation is not addressed when several CMFs are applied multiplicatively. These issues can be addressed by developing safety performance functions (SPFs) with components of crash modification functions (CM-Functions), an approach that includes all CMF related variables, along with others, while capturing quantitative and other effects of factors and accounting for cross-factor correlations. CM-Functions can capture the safety impact of factors through a continuous and quantitative approach, avoiding the problematic categorical analysis that is often used to capture CMF variability. There are two formulations to develop such SPFs with CM-Function components - fully specified models and hierarchical models. Based on sample datasets from two Canadian cities, both approaches are investigated in this paper. While both model formulations yielded promising results and reasonable CM-Functions, the hierarchical model was found to be more suitable in retaining homogeneity of first-level SPFs, while addressing CM-Functions in sub-level modeling. In addition, hierarchical models better capture the correlations between different impact factors. PMID:24727204

  9. Differential Item Functioning Assessment in Cognitive Diagnostic Modeling: Application of the Wald Test to Investigate DIF in the DINA Model

    ERIC Educational Resources Information Center

    Hou, Likun; de la Torre, Jimmy; Nandakumar, Ratna

    2014-01-01

    Analyzing examinees' responses using cognitive diagnostic models (CDMs) has the advantage of providing diagnostic information. To ensure the validity of the results from these models, differential item functioning (DIF) in CDMs needs to be investigated. In this article, the Wald test is proposed to examine DIF in the context of CDMs. This…

  10. Integrating computational modeling and functional assays to decipher the structure-function relationship of influenza virus PB1 protein

    PubMed Central

    Li, Chunfeng; Wu, Aiping; Peng, Yousong; Wang, Jingfeng; Guo, Yang; Chen, Zhigao; Zhang, Hong; Wang, Yongqiang; Dong, Jiuhong; Wang, Lulan; Qin, F. Xiao-Feng; Cheng, Genhong; Deng, Tao; Jiang, Taijiao

    2014-01-01

    The influenza virus PB1 protein is the core subunit of the heterotrimeric polymerase complex (PA, PB1 and PB2) in which PB1 is responsible for catalyzing RNA polymerization and binding to the viral RNA promoter. Among the three subunits, PB1 is the least known subunit so far in terms of its structural information. In this work, by integrating template-based structural modeling approach with all known sequence and functional information about the PB1 protein, we constructed a modeled structure of PB1. Based on this model, we performed mutagenesis analysis for the key residues that constitute the RNA template binding and catalytic (TBC) channel in an RNP reconstitution system. The results correlated well with the model and further identified new residues of PB1 that are critical for RNA synthesis. Moreover, we derived 5 peptides from the sequence of PB1 that form the TBC channel and 4 of them can inhibit the viral RNA polymerase activity. Interestingly, we found that one of them named PB1(491–515) can inhibit influenza virus replication by disrupting viral RNA promoter binding activity of polymerase. Therefore, this study has not only deepened our understanding of structure-function relationship of PB1, but also promoted the development of novel therapeutics against influenza virus. PMID:25424584

  11. Predicting predation through prey ontogeny using size-dependent functional response models.

    PubMed

    McCoy, Michael W; Bolker, Benjamin M; Warkentin, Karen M; Vonesh, James R

    2011-06-01

    The functional response is a critical link between consumer and resource dynamics, describing how a consumer's feeding rate varies with prey density. Functional response models often assume homogenous prey size and size-independent feeding rates. However, variation in prey size due to ontogeny and competition is ubiquitous, and predation rates are often size dependent. Thus, functional responses that ignore prey size may not effectively predict predation rates through ontogeny or in heterogeneous populations. Here, we use short-term response-surface experiments and statistical modeling to develop and test prey size-dependent functional responses for water bugs and dragonfly larvae feeding on red-eyed treefrog tadpoles. We then extend these models through simulations to predict mortality through time for growing prey. Both conventional and size-dependent functional response models predicted average overall mortality in short-term mixed-cohort experiments, but only the size-dependent models accurately captured how mortality was spread across sizes. As a result, simulations that extrapolated these results through prey ontogeny showed that differences in size-specific mortality are compounded as prey grow, causing predictions from conventional and size-dependent functional response models to diverge dramatically through time. Our results highlight the importance of incorporating prey size when modeling consumer-prey dynamics in size-structured, growing prey populations. PMID:21597252

  12. Expanding the Range of Plant Functional Diversity Represented in Global Vegetation Models: Towards Lineage-based Plant Functional Types

    NASA Astrophysics Data System (ADS)

    Still, C. J.; Griffith, D.; Edwards, E.; Forrestel, E.; Lehmann, C.; Anderson, M.; Craine, J.; Pau, S.; Osborne, C.

    2014-12-01

    Variation in plant species traits, such as photosynthetic and hydraulic properties, can indicate vulnerability or resilience to climate change, and feed back to broad-scale spatial and temporal patterns in biogeochemistry, demographics, and biogeography. Yet, predicting how vegetation will respond to future environmental changes is severely limited by the inability of our models to represent species-level trait variation in processes and properties, as current generation process-based models are mostly based on the generalized and abstracted concept of plant functional types (PFTs) which were originally developed for hydrological modeling. For example, there are close to 11,000 grass species, but most vegetation models have only a single C4 grass and one or two C3 grass PFTs. However, while species trait databases are expanding rapidly, they have been produced mostly from unstructured research, with a focus on easily researched traits that are not necessarily the most important for determining plant function. Additionally, implementing realistic species-level trait variation in models is challenging. Combining related and ecologically similar species in these models might ameliorate this limitation. Here we argue for an intermediate, lineage-based approach to PFTs, which draws upon recent advances in gene sequencing and phylogenetic modeling, and where trait complex variations and anatomical features are constrained by a shared evolutionary history. We provide an example of this approach with grass lineages that vary in photosynthetic pathway (C3 or C4) and other functional and structural traits. We use machine learning approaches and geospatial databases to infer the most important environmental controls and climate niche variation for the distribution of grass lineages, and utilize a rapidly expanding grass trait database to demonstrate examples of lineage-based grass PFTs. For example, grasses in the Andropogoneae are typically tall species that dominate wet and

  13. A functional PCA model for the study of time series of pressure maps.

    PubMed

    Chicote, Juan C; Durá, Juan V; Belda, Juan M; Poveda, Rakel

    2013-04-01

    Principal component analysis and functional regression are combined in a model to analyze a time series of pressure maps. The model is tested measuring the pressures over a chair seat while a subject performs a combination of simple movements. A sampling rate of 3 Hz is adequate for applying the model in sitting postures. The model is able to detect patterns of movement over time, although more variables are necessary if the movements produce similar pressure distributions. PMID:23645485

  14. The Use of Haemoglobin as a Model for Teaching the Relationship Between Structure and Function

    ERIC Educational Resources Information Center

    Diggins, F. W. E.

    1974-01-01

    Presents information about an atomic model of haemoglobin and describes the oxygenation mechanism as a teaching principle to illustrate the relationship between structure and function at the molecular level. (Author/PEB)

  15. An Approach toward the Development of a Functional Encoding Model of Short Term Memory during Reading.

    ERIC Educational Resources Information Center

    Herndon, Mary Anne

    1978-01-01

    In a model of the functioning of short term memory, the encoding of information for subsequent storage in long term memory is simulated. In the encoding process, semantically equivalent paragraphs are detected for recombination into a macro information unit. (HOD)

  16. Memory Effects and Sensory Integration: An Examination of Sensory Modality Translation Models of Intersensory Functioning.

    ERIC Educational Resources Information Center

    Marcell, Michael M.; Allen, Terry W.

    1978-01-01

    The sensory modality of a task and the modality of a retroactive interfering activity were systematically covaried in order to test two models of intersensory functioning. Subjects were 40 ten-year-old boys and girls. (BD)

  17. On the Fitting of Non-Linear, Empirical Functions for the Fitting of Model Crater Ages

    NASA Astrophysics Data System (ADS)

    Weaver, B. P.; Hilbe, J. M.; Robbins, S. J.; Plesko, C. S.; Riggs, J. D.

    2015-05-01

    Fitting model crater production functions to observed crater data is considered an "art" by many, and there is no standard in the field for how best to do it. We will discuss mathematical techniques' pros and cons and make recommendations.

  18. Semi-analytical modeling and parameterization of particulates-in-water phase function for forward angles.

    PubMed

    Sahu, Sanjay Kumar; Shanmugam, Palanisamy

    2015-08-24

    A model based on Mie theory is described for predicting scattering phase functions at forward angles (0.1°-90°) with particle size distribution (PSD) slope and bulk refractive index as input parameters. The PSD slope 'ξ ' is calculated from the hyperbolic slope of the particle attenuation spectrum measured in different waters. The bulk refractive index 'n' is evaluated by an inversion model, using measured backscattering ratio (Bp) and PSD slope values. For predicting the desired phase function in a certain water type, in situ measurements of the coefficients of particulate backscattering, scattering and beam attenuation are needed. These parameters are easily measurable using commercially available instruments which provide data with high sampling rates. Thus numerical calculation of the volume scattering function is carried out extensively by varying the optical characteristics of particulates in water. The entire range of forward scattering angles (0.1°-90°) is divided into two subsets, i.e., 0.1° to 5° and 5° to 90°. The particulates-in-water phase function is then modeled for both the ranges. Results of the present model are evaluated based on the well-established Petzold average particle phase function and by comparison with those predicted by other phase function models. For validation, the backscattering ratio is modeled as a function of the bulk refractive index and PSD slope, which is subsequently inverted to give a methodology to estimate the bulk refractive index from easily measurable optical parameters. The new phase function model which is based on the exact numerical solution obtained through Mie theory is mathematically less complex and predicts forward scattering phase functions within the desired accuracy. PMID:26368201

  19. Binder model system to be used for determination of prepolymer functionality

    NASA Technical Reports Server (NTRS)

    Martinelli, F. J.; Hodgkin, J. H.

    1971-01-01

    Development of a method for determining the functionality distribution of prepolymers used for rocket binders is discussed. Research has been concerned with accurately determining the gel point of a model polyester system containing a single trifunctional crosslinker, and the application of these methods to more complicated model systems containing a second trifunctional crosslinker, monofunctional ingredients, or a higher functionality crosslinker. Correlations of observed with theoretical gel points for these systems would allow the methods to be applied directly to prepolymers.

  20. Modeling free molecular plume flow and impingement by an ellipsoidal distribution function

    NASA Astrophysics Data System (ADS)

    Legge, Hubert

    Modeling frozen plume flow is outlined using a freezing surface and an ellipsoidal distribution function beyond a freezing surface. Formulas are given for the number flux, pressure, shear stress, and heat-transfer on a surface element in free molecular flow with an ellipsoidal distribution function. To demonstrate the accuracy of the modeling, the method is applied to the totally frozen Knudsen effusion, for which the flow quantities are given. For the given example, the accuracy is better than 2.5 percent.

  1. LETTER: The partition function of the trigonometric SOS model with a reflecting end

    NASA Astrophysics Data System (ADS)

    Filali, G.; Kitanine, N.

    2010-06-01

    We compute the partition function of the trigonometric SOS model with one reflecting end and domain wall type boundary conditions. We show that in this case, instead of the sum of determinants obtained by Rosengren for the SOS model on a square lattice without reflection, the partition function can be represented as a single Izergin determinant. This result is crucial for the study of the Bethe vectors of the spin chains with non-diagonal boundary terms.

  2. A model for the two-point velocity correlation function in turbulent channel flow

    SciTech Connect

    Sahay, A.; Sreenivasan, K.R.

    1996-06-01

    A relatively simple analytical expression is presented to approximate the equal-time, two-point, double-velocity correlation function in turbulent channel flow. To assess the accuracy of the model, we perform the spectral decomposition of the integral operator having the model correlation function as its kernel. Comparisons of the empirical eigenvalues and eigenfunctions with those constructed from direct numerical simulations data show good agreement. {copyright} {ital 1996 American Institute of Physics.}

  3. A Conceptual Analysis of Differential Item Functioning in Terms of a Multidimensional Item Response Model.

    ERIC Educational Resources Information Center

    Camilli, Gregory

    1992-01-01

    A mathematical model is proposed to describe how group differences in distributions of abilities, which are distinct from the target ability, influence the probability of a correct item response. In the multidimensional approach, differential item functioning is considered a function of the educational histories of the examinees. (SLD)

  4. An Examination of Family Communication within the Core and Balance Model of Family Leisure Functioning

    ERIC Educational Resources Information Center

    Smith, Kevin M.; Freeman, Patti A.; Zabriskie, Ramon B.

    2009-01-01

    The purpose of this study was to examine family communication within the core and balance model of family leisure functioning. The study was conducted from a youth perspective of family leisure and family functioning. The sample consisted of youth (N= 95) aged 11 - 17 from 25 different states in the United States. Path analyses indicated that…

  5. A model distribution function for relativistic bi-Maxwellian with drift

    SciTech Connect

    Naito, O.

    2013-04-15

    A model distribution function for relativistic bi-Maxwellian with drift is proposed, based on the maximum entropy principle and the relativistic canonical transformation. Since the obtained expression is compatible with the existing distribution functions and has a relatively simple form as well as smoothness, it might serve as a useful tool in the research fields of space or high temperature fusion plasmas.

  6. Grid digital elevation model based algorithms for determination of hillslope width functions through flow distance transforms

    NASA Astrophysics Data System (ADS)

    Liu, Jintao; Chen, Xi; Zhang, Xingnan; Hoagland, Kyle D.

    2012-04-01

    Recently developed hillslope storage dynamics theory can represent the essential physical behavior of a natural system by accounting explicitly for the plan shape of a hillslope in an elegant and simple way. As a result, this theory is promising for improving catchment-scale hydrologic modeling. In this study, grid digital elevation model (DEM) based algorithms for determination of hillslope geometric characteristics (e.g., hillslope units and width functions in hillslope storage dynamics models) are presented. This study further develops a method for hillslope partitioning, established by Fan and Bras (1998), by applying it on a grid network. On the basis of hillslope unit derivation, a flow distance transforms method (TD∞) is suggested in order to decrease the systematic error of grid DEM-based flow distance calculation caused by flow direction approximation to streamlines. Hillslope width transfer functions are then derived to convert the probability density functions of flow distance into hillslope width functions. These algorithms are applied and evaluated on five abstract hillslopes, and detailed tests and analyses are carried out by comparing the derivation results with theoretical width functions. The results demonstrate that the TD∞ improves estimations of the flow distance and thus hillslope width function. As the proposed procedures are further applied in a natural catchment, we find that the natural hillslope width function can be well fitted by the Gaussian function. This finding is very important for applying the newly developed hillslope storage dynamics models in a real catchment.

  7. Applications of the Functional Writing Model in Technical and Professional Writing.

    ERIC Educational Resources Information Center

    Brostoff, Anita

    The functional writing model is a method by which students learn to devise and organize a written argument. Salient features of functional writing include the organizing idea (a component that logically unifies a paragraph or sequence of paragraphs), the reader's frame of reference, forecasting (prediction of the sequence by which the organizing…

  8. Plant parameters for plant functional groups of western rangelands to enable process-based simulation modeling

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Regional environmental assessments with process-based models require realistic estimates of plant parameters for the primary plant functional groups in the region. “Functional group” in this context is an operational term, based on similarities in plant type and in plant parameter values. Likewise...

  9. Selection Strategies for Univariate Loglinear Smoothing Models and Their Effect on Equating Function Accuracy

    ERIC Educational Resources Information Center

    Moses, Tim; Holland, Paul W.

    2009-01-01

    In this study, we compared 12 statistical strategies proposed for selecting loglinear models for smoothing univariate test score distributions and for enhancing the stability of equipercentile equating functions. The major focus was on evaluating the effects of the selection strategies on equating function accuracy. Selection strategies' influence…

  10. Understanding Complex Natural Systems by Articulating Structure-Behavior-Function Models

    ERIC Educational Resources Information Center

    Vattam, Swaroop S.; Goel, Ashok K.; Rugaber, Spencer; Hmelo-Silver, Cindy E.; Jordan, Rebecca; Gray, Steven; Sinha, Suparna

    2011-01-01

    Artificial intelligence research on creative design has led to Structure-Behavior-Function (SBF) models that emphasize functions as abstractions for organizing understanding of physical systems. Empirical studies on understanding complex systems suggest that novice understanding is shallow, typically focusing on their visible structures and…

  11. General atomistic approach for modeling metal-semiconductor interfaces using density functional theory and nonequilibrium Green's function

    NASA Astrophysics Data System (ADS)

    Stradi, Daniele; Martinez, Umberto; Blom, Anders; Brandbyge, Mads; Stokbro, Kurt

    2016-04-01

    Metal-semiconductor contacts are a pillar of modern semiconductor technology. Historically, their microscopic understanding has been hampered by the inability of traditional analytical and numerical methods to fully capture the complex physics governing their operating principles. Here we introduce an atomistic approach based on density functional theory and nonequilibrium Green's function, which includes all the relevant ingredients required to model realistic metal-semiconductor interfaces and allows for a direct comparison between theory and experiments via I -Vbias curve simulations. We apply this method to characterize an Ag/Si interface relevant for photovoltaic applications and study the rectifying-to-Ohmic transition as a function of the semiconductor doping. We also demonstrate that the standard "activation energy" method for the analysis of I -Vbias data might be inaccurate for nonideal interfaces as it neglects electron tunneling, and that finite-size atomistic models have problems in describing these interfaces in the presence of doping due to a poor representation of space-charge effects. Conversely, the present method deals effectively with both issues, thus representing a valid alternative to conventional procedures for the accurate characterization of metal-semiconductor interfaces.

  12. A comparison of two predator-prey models with Holling's type I functional response.

    PubMed

    Seo, Gunog; Kot, Mark

    2008-04-01

    In this paper, we analyze a laissez-faire predator-prey model and a Leslie-type predator-prey model with type I functional responses. We study the stability of the equilibrium where the predator and prey coexist by both performing a linearized stability analysis and by constructing a Lyapunov function. For the Leslie-type model, we use a generalized Jacobian to determine how eigenvalues jump at the corner of the functional response. We show, numerically, that our two models can both possess two limit cycles that surround a stable equilibrium and that these cycles arise through global cyclic-fold bifurcations. The Leslie-type model may also exhibit super-critical and discontinuous Hopf bifurcations. We then present and analyze a new functional response, built around the arctangent, that smoothes the sharp corner in a type I functional response. For this new functional response, both models undergo Hopf, cyclic-fold, and Bautin bifurcations. We use our analyses to characterize predator-prey systems that may exhibit bistability. PMID:18346761

  13. Application of scaling model to investigate solvent quality and functionality in star polymers

    NASA Astrophysics Data System (ADS)

    Rai, Durgesh; Beaucage, Gregory; Ramachandran, Ramanth; Ratkanthwar, Kedar; Hadjichristidis, Nikos; Kunlun, Hong; Uhrig, David; Tsou, Andy

    2014-03-01

    Symmetric star polymers serve as model systems to understand branching effects in long chain macromolecules. Generally, the solution properties of stars have been modeled based on ideal Gaussian statistics or using empirical approaches that incorporate fractal scaling neither of which provide satisfactory complete understanding of thermodynamic or structural details across different solvent quality and temperature ranges. A coupling of the unified scattering function with the RPA equation and Benoit's approach to model inter-arm and intra-arm interactions is proposed to analytically quantify thermodynamic effects along with topological variations using the proposed scaling model. Detailed topological quantification of star polymers systems have been able to describe both, good and theta solvent conditions along with effects of functionalities, as well as resolve deviations in chain conformations due to steric interactions between star arms. The scaling model quantifies the distinction between invariant topological features for star polymers and chain tortuosity, which changes with functionality as well as goodness of solvent and steric interactions.

  14. Evolutionary model of flexible exponential function to characterize decay pattern of OCT signal in turbid tissues

    NASA Astrophysics Data System (ADS)

    Chen, Bingling; Guo, Zhouyi

    2008-12-01

    Conventional analyses of OCT signal measurements resolve the signal decay profile in terms of single discrete exponential function with distinct exponential model. In symmetrical medium, mono-exponential decay function can appear to provide a well fit to OCT signal decay data, but the assuption of symmetrical components is essentially arbitrary and is often erroneous. Actually, the real biological samples such as tissue contained more complex components and are more heterogeneous. To avoid the shortages of mono-exponential decay function fitting to OCT signal decay data from heterogeneous biological tissues, a novel model of flexible exponential function has been developed. The main idea of the flexible exponential function modle is based on the assuption that heterogeneous biological tissue can be considered as a multi-layered tissue. Each layer is symmetric and the OCT signal decay profile in each layer obeies to a distinct single exponential function. If we can find out all the distinct single exponential function for each layer, the total flexible exponential function is determined by summing up all the single exponential functions. As pilot studies on the practical application of flexibleexponential decay model for monitoring and quantifying the diffusion of different analytes in turbid biological tissues in vivo by using OCT system, we demonstrate an experiment of monitoring of glucose diffusion in agar gel. In addition, the flexible-exponential decay model can provide a direct measure of the heterogeneity of the sample, and the analysis of turbid tissues OCT map using the flexible-exponential decay model can reveal subtle tissue differences that other models fail to show.

  15. Evaluation of a functional model for simulating boron transport in soil

    SciTech Connect

    Corwin, D.L.; Goldberg, S.; David, A.

    1999-10-01

    There has been renewed interest in the application of functional models to the transport of nonpoint source pollutants at polypedon and watershed scales because of the ease of their coupling to a geographic information system and to the accepted organizational hierarchy of pedogenetic modeling approaches. However, very little work has been done to evaluate the performance of a functional transient-state model for the transport of a reactive solute over an extensive study period. Subsequently, the functional model TETrans (Trace Element Transport) was evaluated for model performance with boron (B) transport data collected from a meso-scale soil lysimeter column over a 1,000-day study period. Because the ability to simulate water flow has been evaluated previously for TETrans, the focus of this evaluation centered around the performance of various functional models of B adsorption used as subroutines within the TETrans model, including the (1) Freundlich, (2) kinetic Freundlich, (3) Langmuir, (4) temperature-dependent Langmuir, and (5) pH-dependent Keren adsorption isotherm equations. Model performance was evaluated with statistical functions, specifically the Average Absolute Prediction Error, the Root Mean Square Error, the Reduced Error Estimate and the Coefficient of Residual Mass, and graphic displays of observed and predicted B concentration profiles. Even though no single adsorption isotherm equation, when coupled to TETrans, could be considered poor in its performance, results indicated that the order of model performance was the pH-dependent Keren equation first, followed by the temperature-dependent Langmuir and kinetic Freundlich equations, the Freundlich equation, and, finally, the Langmuir equation. Overall, the TETrans model was able to simulate the transport of B with deviations because no functional adsorption equation incorporated all the influences of pH, ionic strength, temperature, and kinetic effects into a single equation. The inability to

  16. Evolution of a Foundational Model of Physiology: symbolic representation for functional bioinformatics.

    PubMed

    Cook, Daniel L; Mejino, Jose L V; Rosse, Cornelius

    2004-01-01

    We describe the need for a Foundational Model of Physiology (FMP) as a reference ontology for "functional bioinformatics". The FMP is intended to support symbolic lookup, logical inference and mathematical analysis by integrating descriptive, qualitative and quantitative functional knowledge. The FMP will serve as a symbolic representation of biological functions initially pertaining to human physiology and ultimately extensible to other species. We describe the evolving architecture of the FMP, which is based on the ontological principles of the BioD biological description language and the Foundational Model of Anatomy (FMA). PMID:15360830

  17. Alternative Measurement Paradigms for Measuring Executive Functions: SEM (Formative and Reflective Models) and IRT (Rasch Models)

    ERIC Educational Resources Information Center

    Engelhard, George, Jr.; Wang, Jue

    2014-01-01

    The authors of the Focus article pose important questions regarding whether or not performance-based tasks related to executive functioning are best viewed as reflective or formative indicators. Miyake and Friedman (2012) define executive functioning (EF) as "a set of general-purpose control mechanisms, often linked to the prefrontal cortex…

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

    PubMed Central

    Ben-Tal, Alona

    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 compartmentalise 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 multi-circuit 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. PMID:24591490

  19. Functional Fault Modeling of a Cryogenic System for Real-Time Fault Detection and Isolation

    NASA Technical Reports Server (NTRS)

    Ferrell, Bob; Lewis, Mark; Oostdyk, Rebecca; Perotti, Jose

    2009-01-01

    When setting out to model and/or simulate a complex mechanical or electrical system, a modeler is faced with a vast array of tools, software, equations, algorithms and techniques that may individually or in concert aid in the development of the model. Mature requirements and a well understood purpose for the model may considerably shrink the field of possible tools and algorithms that will suit the modeling solution. Is the model intended to be used in an offline fashion or in real-time? On what platform does it need to execute? How long will the model be allowed to run before it outputs the desired parameters? What resolution is desired? Do the parameters need to be qualitative or quantitative? Is it more important to capture the physics or the function of the system in the model? Does the model need to produce simulated data? All these questions and more will drive the selection of the appropriate tools and algorithms, but the modeler must be diligent to bear in mind the final application throughout the modeling process to ensure the model meets its requirements without needless iterations of the design. The purpose of this paper is to describe the considerations and techniques used in the process of creating a functional fault model of a liquid hydrogen (LH2) system that will be used in a real-time environment to automatically detect and isolate failures.

  20. Modeling of the effective work function instability in metal/high-κ dielectric stacks

    NASA Astrophysics Data System (ADS)

    Fet, A.; Häublein, V.; Bauer, A. J.; Ryssel, H.; Frey, L.

    2010-06-01

    This paper discusses the effective work function instability in high-κ-based MOS gate stacks, which occurs after high temperature (1070 °C) processing. Theories which have been put forward to explain this effect are discussed and unified to a consistent phenomenological model. The Vfb roll-off effect is also discussed and can be described by the model.

  1. Origami: A Versatile Modeling System for Visualising Chemical Structure and Exploring Molecular Function

    ERIC Educational Resources Information Center

    Davis, James; Leslie, Ray; Billington, Susan; Slater, Peter R.

    2010-01-01

    The use of "Origami" is presented as an accessible and transferable modeling system through which to convey the intricacies of molecular shape and highlight structure-function relationships. The implementation of origami has been found to be a versatile alternative to conventional ball-and-stick models, possessing the key advantages of being both…

  2. Detecting and Analyzing Differential Item Functioning in an Essay Test Using the Partial Credit Model.

    ERIC Educational Resources Information Center

    Ferrara, Steven; Walker-Bartnick, Leslie

    A procedure was developed to detect differential item functioning (DIF) in a standardized essay test using the Partial Credit Model, the general polychotomous form of the Rasch model. Using a panel of experts in the writing process, hypothesized explanations for DIF at some score points were developed. Data for the study included averaged…

  3. Transverse momentum dependent distribution functions in a covariant parton model approach with quark orbital motion

    SciTech Connect

    Efremov, A. V.; Teryaev, O. V.; Schweitzer, P.; Zavada, P.

    2009-07-01

    Transverse parton momentum dependent distribution functions (TMDs) of the nucleon are studied in a covariant model, which describes the intrinsic motion of partons in terms of a covariant momentum distribution. The consistency of the approach is demonstrated, and model relations among TMDs are studied. As a by-product it is shown how the approach allows to formulate the nonrelativistic limit.

  4. Evaluation of a Digital Library by Means of Quality Function Deployment (QFD) and the Kano Model

    ERIC Educational Resources Information Center

    Garibay, Cecilia; Gutierrez, Humberto; Figueroa, Arturo

    2010-01-01

    This paper proposes utilizing a combination of the Quality Function Deployment (QFD)-Kano model as a useful tool to evaluate service quality. The digital library of the University of Guadalajara (Mexico) is presented as a case study. Data to feed the QFD-Kano model was gathered by an online questionnaire that was made available to users on the…

  5. Testing for Nonuniform Differential Item Functioning with Multiple Indicator Multiple Cause Models

    ERIC Educational Resources Information Center

    Woods, Carol M.; Grimm, Kevin J.

    2011-01-01

    In extant literature, multiple indicator multiple cause (MIMIC) models have been presented for identifying items that display uniform differential item functioning (DIF) only, not nonuniform DIF. This article addresses, for apparently the first time, the use of MIMIC models for testing both uniform and nonuniform DIF with categorical indicators. A…

  6. A Functional Model of Quality Assurance for Psychiatric Hospitals and Corresponding Staffing Requirements.

    ERIC Educational Resources Information Center

    Kamis-Gould, Edna; And Others

    1991-01-01

    A model for quality assurance (QA) in psychiatric hospitals is described. Its functions (general QA, utilization review, clinical records, evaluation, management information systems, risk management, and infection control), subfunctions, and corresponding staffing requirements are reviewed. This model was designed to foster standardization in QA…

  7. Item Purification in Differential Item Functioning Using Generalized Linear Mixed Models

    ERIC Educational Resources Information Center

    Liu, Qian

    2011-01-01

    For this dissertation, four item purification procedures were implemented onto the generalized linear mixed model for differential item functioning (DIF) analysis, and the performance of these item purification procedures was investigated through a series of simulations. Among the four procedures, forward and generalized linear mixed model (GLMM)…

  8. A Functional Model of the Digital Extensor Mechanism: Demonstrating Biomechanics with Hair Bands

    ERIC Educational Resources Information Center

    Cloud, Beth A.; Youdas, James W.; Hellyer, Nathan J.; Krause, David A.

    2010-01-01

    The action of muscles about joints can be explained through analysis of their spatial relationship. A functional model of these relationships can be valuable in learning and understanding the muscular action about a joint. A model can be particularly helpful when examining complex actions across multiple joints such as in the digital extensor…

  9. Poor Vision, Functioning, and Depressive Symptoms: A Test of the Activity Restriction Model

    ERIC Educational Resources Information Center

    Bookwala, Jamila; Lawson, Brendan

    2011-01-01

    Purpose: This study tested the applicability of the activity restriction model of depressed affect to the context of poor vision in late life. This model hypothesizes that late-life stressors contribute to poorer mental health not only directly but also indirectly by restricting routine everyday functioning. Method: We used data from a national…

  10. A Model of Marital Functioning Based on an Attraction Paradigm and Social-Penetration Dimensions.

    ERIC Educational Resources Information Center

    Honeycutt, James

    1986-01-01

    Tested structural equation model of marital functioning based on an attraction paradigm and social-penetration variables. The model posited that the attraction paradigm factors of being satisfied with marital issues and of perceived attitudinal similarity would have an impact upon marital happiness as well as perceived partner understanding, which…

  11. Model-based metrics of human-automation function allocation in complex work environments

    NASA Astrophysics Data System (ADS)

    Kim, So Young

    Function allocation is the design decision which assigns work functions to all agents in a team, both human and automated. Efforts to guide function allocation systematically has been studied in many fields such as engineering, human factors, team and organization design, management science, and cognitive systems engineering. Each field focuses on certain aspects of function allocation, but not all; thus, an independent discussion of each does not address all necessary issues with function allocation. Four distinctive perspectives emerged from a review of these fields: technology-centered, human-centered, team-oriented, and work-oriented. Each perspective focuses on different aspects of function allocation: capabilities and characteristics of agents (automation or human), team structure and processes, and work structure and the work environment. Together, these perspectives identify the following eight issues with function allocation: 1) Workload, 2) Incoherency in function allocations, 3) Mismatches between responsibility and authority, 4) Interruptive automation, 5) Automation boundary conditions, 6) Function allocation preventing human adaptation to context, 7) Function allocation destabilizing the humans' work environment, and 8) Mission Performance. Addressing these issues systematically requires formal models and simulations that include all necessary aspects of human-automation function allocation: the work environment, the dynamics inherent to the work, agents, and relationships among them. Also, addressing these issues requires not only a (static) model, but also a (dynamic) simulation that captures temporal aspects of work such as the timing of actions and their impact on the agent's work. Therefore, with properly modeled work as described by the work environment, the dynamics inherent to the work, agents, and relationships among them, a modeling framework developed by this thesis, which includes static work models and dynamic simulation, can capture the

  12. Modeling fracture toughness of functionally graded steels in crack divider configuration

    NASA Astrophysics Data System (ADS)

    Aghazadeh Mohandesi, J.; Nazari, A.; Vishkasogheh, Mehdi Hamid; Abedi, Mohammad

    2010-10-01

    Fracture toughness of functionally graded steels in crack divider configuration has been modeled. By utilizing plain carbon and austenitic stainless steel slices with various thicknesses and arrangements as electroslag remelting electrodes, functionally graded steels were produced. The fracture toughness of the functionally graded steels was found to depend on the type, volume fraction and position of the phases present. According to the area under the stress-strain curve of each layer in the functionally graded composites, a mathematical model has been presented for fracture toughness prediction using the rule of mixtures. In addition, the fracture toughness of the composites has been simulated by the 3D dynamic finite element method. There is good agreement between experimental results and those acquired from the numerical and mathematical models.

  13. Inferring Functional Interaction and Transition Patterns via Dynamic Bayesian Variable Partition Models

    PubMed Central

    Zhang, Jing; Li, Xiang; Li, Cong; Lian, Zhichao; Huang, Xiu; Zhong, Guocheng; Zhu, Dajiang; Li, Kaiming; Jin, Changfeng; Hu, Xintao; Han, Junwei; Guo, Lei; Hu, Xiaoping; Li, Lingjiang; Liu, Tianming

    2014-01-01

    Multivariate connectivity and functional dynamics have been of wide interest in the neuroimaging field, and a variety of methods have been developed to study functional interactions and dynamics. In contrast, the temporal dynamic transitions of multivariate functional interactions among brain networks, in particular, in resting state, have been much less explored. This paper presents a novel dynamic Bayesian variable partition model (DBVPM) that simultaneously considers and models multivariate functional interactions and their dynamics via a unified Bayesian framework. The basic idea is to detect the temporal boundaries of piecewise quasi-stable functional interaction patterns, which are then modeled by representative signature patterns and whose temporal transitions are characterized by finite-state transition machines. Results on both simulated and experimental datasets demonstrated the effectiveness and accuracy of the DBVPM in dividing temporally transiting functional interaction patterns. The application of DBVPM on a post-traumatic stress disorder (PTSD) dataset revealed substantially different multivariate functional interaction signatures and temporal transitions in the default mode and emotion networks of PTSD patients, in comparison with those in healthy controls. This result demonstrated the utility of DBVPM in elucidating salient features that cannot be revealed by static pair-wise functional connectivity analysis. PMID:24222313

  14. FUNCTIONALITY OF AN INTEGRATED EMISSION PREPROCESSING SYSTEM FOR AIR QUALITY MODELING: THE MODELS-3 EMISSION PREPROCESSOR

    EPA Science Inventory

    Conventional preparation of emission inventories for air quality modeling is typically an extended process using computer routines to reformat, quality check, chemically speciate, and temporally and spatially allocate data. rocessing of emission inventories for regional modeling ...

  15. A numerical study of the string function using a primitive equation ocean model

    NASA Astrophysics Data System (ADS)

    Tyler, R. H.; Käse, R.

    We use results from a primitive-equation ocean numerical model (SCRUM) to test a theoretical 'string function' formulation put forward by Tyler and Käse in another article in this issue. The string function acts as a stream function for the large-scale potential energy flow under the combined beta and topographic effects. The model results verify that large-scale anomalies propagate along the string function contours with a speed correctly given by the cross-string gradient. For anomalies having a scale similar to the Rossby radius, material rates of change in the layer mass following the string velocity are balanced by material rates of change in relative vorticity following the flow velocity. It is shown that large-amplitude anomalies can be generated when wind stress is resonant with the string function configuration.

  16. Dannie Heineman Prize for Mathematical Physics Prize Lecture: Correlation Functions in Integrable Models: Ising Model and Monodromy Preserving Deformation

    NASA Astrophysics Data System (ADS)

    Miwa, Tetsuji

    2013-03-01

    Studies on integrable models in statistical mechanics and quantum field theory originated in the works of Bethe on the one-dimensional quantum spin chain and the work of Onsager on the two-dimensional Ising model. I will talk on the discovery in 1977 of the link between quantum field theory in the scaling limit of the two-dimensional Ising model and the theory of monodromy preserving linear ordinary differential equations. This work was the staring point of our journey with Michio Jimbo in integrable models, the journey which finally led us to the exact results on the correlation functions of quantum spin chains in 1992.

  17. The application of a mathematical model linking structural and functional connectomes in severe brain injury

    PubMed Central

    Kuceyeski, A.; Shah, S.; Dyke, J.P.; Bickel, S.; Abdelnour, F.; Schiff, N.D.; Voss, H.U.; Raj, A.

    2016-01-01

    Following severe injuries that result in disorders of consciousness, recovery can occur over many months or years post-injury. While post-injury synaptogenesis, axonal sprouting and functional reorganization are known to occur, the network-level processes underlying recovery are poorly understood. Here, we test a network-level functional rerouting hypothesis in recovery of patients with disorders of consciousness following severe brain injury. This hypothesis states that the brain recovers from injury by restoring normal functional connections via alternate structural pathways that circumvent impaired white matter connections. The so-called network diffusion model, which relates an individual's structural and functional connectomes by assuming that functional activation diffuses along structural pathways, is used here to capture this functional rerouting. We jointly examined functional and structural connectomes extracted from MRIs of 12 healthy and 16 brain-injured subjects. Connectome properties were quantified via graph theoretic measures and network diffusion model parameters. While a few graph metrics showed groupwise differences, they did not correlate with patients' level of consciousness as measured by the Coma Recovery Scale — Revised. There was, however, a strong and significant partial Pearson's correlation (accounting for age and years post-injury) between level of consciousness and network diffusion model propagation time (r = 0.76, p < 0.05, corrected), i.e. the time functional activation spends traversing the structural network. We concluded that functional rerouting via alternate (and less efficient) pathways leads to increases in network diffusion model propagation time. Simulations of injury and recovery in healthy connectomes confirmed these results. This work establishes the feasibility for using the network diffusion model to capture network-level mechanisms in recovery of consciousness after severe brain injury. PMID:27200264

  18. Aircraft/Air Traffic Management Functional Analysis Model: Technical Description. 2.0

    NASA Technical Reports Server (NTRS)

    Etheridge, Melvin; Plugge, Joana; Retina, Nusrat

    1998-01-01

    The Aircraft/Air Traffic Management Functional Analysis Model, Version 2.0 (FAM 2.0), is a discrete event simulation model designed to support analysis of alternative concepts in air traffic management and control. FAM 2.0 was developed by the Logistics Management Institute (LMI) under a National Aeronautics and Space Administration (NASA) contract. This document provides a technical description of FAM 2.0 and its computer files to enable the modeler and programmer to make enhancements or modifications to the model. Those interested in a guide for using the model in analysis should consult the companion document, Aircraft/Air Traffic Management Functional Analysis Model, Version 2.0 Users Manual.

  19. Modeling heterogeneous and fractured reservoirs with inverse methods based on iterated function systems

    SciTech Connect

    Long, J.C.S.; Doughty, C.; Hestir, K.; Martel, S.

    1992-05-01

    Fractured and heterogeneous reservoirs are complex and difficult to characterize. In many cases, the modeling approaches used for making predictions of behavior in such reservoirs have been unsatisfactory. In this paper we describe a new modeling approach which results in a model that has fractal-like qualities. This is an inverse approach which uses observations of reservoir behavior to create a model that can reproduce observed behavior. The model is described by an iterated function system (IFS) that creates a fractal-like object that can be mapped into a conductivity distribution. It may be possible to identify subclasses of Iterated Function Systems which describe geological facies. By limiting the behavior-based search for an IFS to the geologic subclasses, we can condition the reservoir model on geologic information. This technique is under development, but several examples provide encouragement for eventual application to reservoir prediction.

  20. A prototype symbolic model of canonical functional neuroanatomy of the motor system.

    PubMed

    Talos, Ion-Florin; Rubin, Daniel L; Halle, Michael; Musen, Mark; Kikinis, Ron

    2008-04-01

    Recent advances in bioinformatics have opened entire new avenues for organizing, integrating and retrieving neuroscientific data, in a digital, machine-processable format, which can be at the same time understood by humans, using ontological, symbolic data representations. Declarative information stored in ontological format can be perused and maintained by domain experts, interpreted by machines, and serve as basis for a multitude of decision support, computerized simulation, data mining, and teaching applications. We have developed a prototype symbolic model of canonical neuroanatomy of the motor system. Our symbolic model is intended to support symbolic look up, logical inference and mathematical modeling by integrating descriptive, qualitative and quantitative functional neuroanatomical knowledge. Furthermore, we show how our approach can be extended to modeling impaired brain connectivity in disease states, such as common movement disorders. In developing our ontology, we adopted a disciplined modeling approach, relying on a set of declared principles, a high-level schema, Aristotelian definitions, and a frame-based authoring system. These features, along with the use of the Unified Medical Language System (UMLS) vocabulary, enable the alignment of our functional ontology with an existing comprehensive ontology of human anatomy, and thus allow for combining the structural and functional views of neuroanatomy for clinical decision support and neuroanatomy teaching applications. Although the scope of our current prototype ontology is limited to a particular functional system in the brain, it may be possible to adapt this approach for modeling other brain functional systems as well. PMID:18164666

  1. Modeling the Pulse Signal by Wave-Shape Function and Analyzing by Synchrosqueezing Transform.

    PubMed

    Wu, Hau-Tieng; Wu, Han-Kuei; Wang, Chun-Li; Yang, Yueh-Lung; Wu, Wen-Hsiang; Tsai, Tung-Hu; Chang, Hen-Hong

    2016-01-01

    We apply the recently developed adaptive non-harmonic model based on the wave-shape function, as well as the time-frequency analysis tool called synchrosqueezing transform (SST) to model and analyze oscillatory physiological signals. To demonstrate how the model and algorithm work, we apply them to study the pulse wave signal. By extracting features called the spectral pulse signature, and based on functional regression, we characterize the hemodynamics from the radial pulse wave signals recorded by the sphygmomanometer. Analysis results suggest the potential of the proposed signal processing approach to extract health-related hemodynamics features. PMID:27304979

  2. Modeling the Pulse Signal by Wave-Shape Function and Analyzing by Synchrosqueezing Transform

    PubMed Central

    Wang, Chun-Li; Yang, Yueh-Lung; Wu, Wen-Hsiang; Tsai, Tung-Hu; Chang, Hen-Hong

    2016-01-01

    We apply the recently developed adaptive non-harmonic model based on the wave-shape function, as well as the time-frequency analysis tool called synchrosqueezing transform (SST) to model and analyze oscillatory physiological signals. To demonstrate how the model and algorithm work, we apply them to study the pulse wave signal. By extracting features called the spectral pulse signature, and based on functional regression, we characterize the hemodynamics from the radial pulse wave signals recorded by the sphygmomanometer. Analysis results suggest the potential of the proposed signal processing approach to extract health-related hemodynamics features. PMID:27304979

  3. Region-Based Association Test for Familial Data under Functional Linear Models.

    PubMed

    Svishcheva, Gulnara R; Belonogova, Nadezhda M; Axenovich, Tatiana I

    2015-01-01

    Region-based association analysis is a more powerful tool for gene mapping than testing of individual genetic variants, particularly for rare genetic variants. The most powerful methods for regional mapping are based on the functional data analysis approach, which assumes that the regional genome of an individual may be considered as a continuous stochastic function that contains information about both linkage and linkage disequilibrium. Here, we extend this powerful approach, earlier applied only to independent samples, to the samples of related individuals. To this end, we additionally include a random polygene effects in functional linear model used for testing association between quantitative traits and multiple genetic variants in the region. We compare the statistical power of different methods using Genetic Analysis Workshop 17 mini-exome family data and a wide range of simulation scenarios. Our method increases the power of regional association analysis of quantitative traits compared with burden-based and kernel-based methods for the majority of the scenarios. In addition, we estimate the statistical power of our method using regions with small number of genetic variants, and show that our method retains its advantage over burden-based and kernel-based methods in this case as well. The new method is implemented as the R-function 'famFLM' using two types of basis functions: the B-spline and Fourier bases. We compare the properties of the new method using models that differ from each other in the type of their function basis. The models based on the Fourier basis functions have an advantage in terms of speed and power over the models that use the B-spline basis functions and those that combine B-spline and Fourier basis functions. The 'famFLM' function is distributed under GPLv3 license and is freely available at http://mga.bionet.nsc.ru/soft/famFLM/. PMID:26111046

  4. A dual change model of life satisfaction and functioning for individuals with schizophrenia.

    PubMed

    Edmondson, Melissa; Pahwa, Rohini; Lee, Karen Kyeunghae; Hoe, Maanse; Brekke, John S

    2012-08-01

    Despite the notion that increases in functioning should be associated with increases in life satisfaction in schizophrenia, research has often found no association between the two. Dual change models of global and domain-specific life satisfaction and functioning were examined in 145 individuals with schizophrenia receiving community-based services over 12 months. Functioning and satisfaction were measured using the Role Functioning Scale and Satisfaction with Life Scale. Data were analyzed using latent growth curve modeling. Improvement in global life satisfaction was associated with improvement in overall functioning over time. Satisfaction with living situation also improved as independent functioning improved. Work satisfaction did not improve as work functioning improved. Although social functioning improved, satisfaction with social relationships did not. The link between overall functioning and global life satisfaction provides support for a recovery-based orientation to community based psychosocial rehabilitation services. When examining sub-domains, the link between outcomes and subjective experience suggests a more complex picture than previously found. These findings are crucial to interventions and programs aimed at improving functioning and the subjective experiences of consumers recovering from mental illness. Interventions that show improvements in functional outcomes can assume that they will show concurrent improvements in global life satisfaction as well and in satisfaction with independent living. Interventions geared toward improving social functioning will need to consider the complexity of social relationships and how they affect satisfaction associated with personal relationships. Interventions geared towards improving work functioning will need to consider how the quality and level of work affect satisfaction with employment. PMID:22591780

  5. Probabilistic model-based functional parcellation reveals a robust, fine-grained subdivision of the striatum.

    PubMed

    Janssen, R J; Jylänki, P; Kessels, R P C; van Gerven, M A J

    2015-10-01

    The striatum is involved in many different aspects of behaviour, reflected by the variety of cortical areas that provide input to this structure. This input is topographically organized and is likely to result in functionally specific signals. Such specificity can be examined using functional clustering approaches. Here, we propose a Bayesian model-based functional clustering approach applied solely to resting state striatal functional MRI timecourses to identify intrinsic striatal functional modules. Data from two sets of ten participants were used to obtain parcellations and examine their robustness. This stable clustering was used to initialize a more constrained model in order to obtain individualized parcellations in 57 additional participants. Resulting cluster time courses were used to examine functional connectivity between clusters and related to the rest of the brain in a GLM analysis. We find six distinct clusters in each hemisphere, with clear inter-hemispheric correspondence and functional relevance. These clusters exhibit functional connectivity profiles that further underscore their homologous nature and are consistent with existing notions on segregation and integration in parallel cortico-basal ganglia loops. Our findings suggest that multiple territories within both the affective and motor regions can be distinguished solely using resting state functional MRI from these regions. PMID:26163800

  6. Parameter estimation in a human operator describing function model for a two-dimensional tracking task

    NASA Technical Reports Server (NTRS)

    Vanlunteren, A.

    1977-01-01

    A previously described parameter estimation program was applied to a number of control tasks, each involving a human operator model consisting of more than one describing function. One of these experiments is treated in more detail. It consisted of a two dimensional tracking task with identical controlled elements. The tracking errors were presented on one display as two vertically moving horizontal lines. Each loop had its own manipulator. The two forcing functions were mutually independent and consisted each of 9 sine waves. A human operator model was chosen consisting of 4 describing functions, thus taking into account possible linear cross couplings. From the Fourier coefficients of the relevant signals the model parameters were estimated after alignment, averaging over a number of runs and decoupling. The results show that for the elements in the main loops the crossover model applies. A weak linear cross coupling existed with the same dynamics as the elements in the main loops but with a negative sign.

  7. A phenotypic in vitro model for the main determinants of human whole heart function.

    PubMed

    Stancescu, Maria; Molnar, Peter; McAleer, Christopher W; McLamb, William; Long, Christopher J; Oleaga, Carlota; Prot, Jean-Matthieu; Hickman, James J

    2015-08-01

    This article details the construction and testing of a phenotypic assay system that models in vivo cardiac function in a parallel in vitro environment with human stem cell derived cardiomyocytes. The major determinants of human whole-heart function were experimentally modeled by integrating separate 2D cellular systems with BioMicroelectromechanical Systems (BioMEMS) constructs. The model features a serum-free defined medium to enable both acute and chronic evaluation of drugs and toxins. The integration of data from both systems produced biologically relevant predictions of cardiac function in response to varying concentrations of selected drugs. Sotalol, norepinephrine and verapamil were shown to affect the measured parameters according to their specific mechanism of action, in agreement with clinical data. This system is applicable for cardiac side effect assessment, general toxicology, efficacy studies, and evaluation of in vitro cellular disease models in body-on-a-chip systems. PMID:25978005

  8. Simulation of Preterm Neonatal Brain Metabolism During Functional Neuronal Activation Using a Computational Model.

    PubMed

    Hapuarachchi, T; Scholkmann, F; Caldwell, M; Hagmann, C; Kleiser, S; Metz, A J; Pastewski, M; Wolf, M; Tachtsidis, I

    2016-01-01

    We present a computational model of metabolism in the preterm neonatal brain. The model has the capacity to mimic haemodynamic and metabolic changes during functional activation and simulate functional near-infrared spectroscopy (fNIRS) data. As an initial test of the model's efficacy, we simulate data obtained from published studies investigating functional activity in preterm neonates. In addition we simulated recently collected data from preterm neonates during visual activation. The model is well able to predict the haemodynamic and metabolic changes from these observations. In particular, we found that changes in cerebral blood flow and blood pressure may account for the observed variability of the magnitude and sign of stimulus-evoked haemodynamic changes reported in preterm infants. PMID:26782202

  9. A phenotypic in vitro model for the main determinants of human whole heart function

    PubMed Central

    Stancescu, Maria; Molnar, Peter; McAleer, Christopher W.; McLamb, William; Long, Christopher J.; Oleaga, Carlota; Prot, Jean-Matthieu; Hickman, James J.

    2015-01-01

    This article details the construction and testing of a phenotypic assay system that models in vivo cardiac function in a parallel in vitro environment with human stem cell derived cardiomyocytes. The major determinants of human whole-heart function were experimentally modeled by integrating separate 2D cellular systems with BioMicroelectromechanical Systems (BioMEMS) constructs. The model featured a serum-free defined medium to enable both acute and chronic evaluation of drugs and toxins. The integration of data from both systems produced biologically relevant predictions of cardiac function in response to varying concentrations of selected drugs. Sotalol, norepinephrine and verapamil were shown to affect the measured parameters according to their specific mechanism of action, in agreement with clinical data. This system is applicable for cardiac side effect assessment, general toxicology, efficacy studies, and evaluation of in vitro cellular disease models in body-on-a-chip systems. PMID:25978005

  10. [Mathematic concept model of accumulation of functional disorders associated with environmental factors].

    PubMed

    Zaĭtseva, N V; Trusov, P V; Kir'ianov, D A

    2012-01-01

    The mathematic concept model presented describes accumulation of functional disorders associated with environmental factors, plays predictive role and is designed for assessments of possible effects caused by heterogenous factors with variable exposures. Considering exposure changes with self-restoration process opens prospects of using the model to evaluate, analyse and manage occupational risks. To develop current theoretic approaches, the authors suggested a model considering age-related body peculiarities, systemic interactions of organs, including neuro-humoral regulation, accumulation of functional disorders due to external factors, rehabilitation of functions during treatment. General objective setting covers defining over a hundred unknow coefficients that characterize speed of various processes within the body. To solve this problem, the authors used iteration approach, successive identification, that starts from the certain primary approximation of the model parameters and processes subsequent updating on the basis of new theoretic and empirical knowledge. PMID:23461190

  11. Generalized Constitutive-Based Theoretical and Empirical Models for Hot Working Behavior of Functionally Graded Steels

    NASA Astrophysics Data System (ADS)

    Vanini, Seyed Ali Sadough; Abolghasemzadeh, Mohammad; Assadi, Abbas

    2013-07-01

    Functionally graded steels with graded ferritic and austenitic regions including bainite and martensite intermediate layers produced by electroslag remelting have attracted much attention in recent years. In this article, an empirical model based on the Zener-Hollomon (Z-H) constitutive equation with generalized material constants is presented to investigate the effects of temperature and strain rate on the hot working behavior of functionally graded steels. Next, a theoretical model, generalized by strain compensation, is developed for the flow stress estimation of functionally graded steels under hot compression based on the phase mixture rule and boundary layer characteristics. The model is used for different strains and grading configurations. Specifically, the results for αβγMγ steels from empirical and theoretical models showed excellent agreement with those of experiments of other references within acceptable error.

  12. A model function for ocean radar cross sections at 14.6 GHz

    NASA Technical Reports Server (NTRS)

    Wentz, F. J.; Thomas, L. A.; Peteherych, S.

    1984-01-01

    The relationship between the ocean's normalized radar cross section (NRCS) at 14.6 GHz and the surface wind vector is derived using the 3 months of Seasat microwave scatterometer (SASS) measurements. The derivation is based on the statistics of the SASS observations, and no in situ measurements are required, other than a mean global wind speed, which comes from climatology. The frequency distribution of the global wind vectors observed by SASS is assumed to be a bivariate normal probability function. A NRCS model function is found that maps the assumed wind vector statistics into the observed SASS NRCS statistics. This function is compared with a NRCS model coming from the Joint Air Sea Interaction Experiment (JASIN) and with aircraft scatterometer measurements. The results indicate that the statistically derived NRCS model is an improvement over the JASIN model, which was based on a limited number of in situ anemometer measurements.

  13. Modeling and Testing Differential Item Functioning in Unidimensional Binary Item Response Models with a Single Continuous Covariate: A Functional Data Analysis Approach.

    PubMed

    Liu, Yang; Magnus, Brooke E; Thissen, David

    2016-06-01

    Differential item functioning (DIF), referring to between-group variation in item characteristics above and beyond the group-level disparity in the latent variable of interest, has long been regarded as an important item-level diagnostic. The presence of DIF impairs the fit of the single-group item response model being used, and calls for either model modification or item deletion in practice, depending on the mode of analysis. Methods for testing DIF with continuous covariates, rather than categorical grouping variables, have been developed; however, they are restrictive in parametric forms, and thus are not sufficiently flexible to describe complex interaction among latent variables and covariates. In the current study, we formulate the probability of endorsing each test item as a general bivariate function of a unidimensional latent trait and a single covariate, which is then approximated by a two-dimensional smoothing spline. The accuracy and precision of the proposed procedure is evaluated via Monte Carlo simulations. If anchor items are available, we proposed an extended model that simultaneously estimates item characteristic functions (ICFs) for anchor items, ICFs conditional on the covariate for non-anchor items, and the latent variable density conditional on the covariate-all using regression splines. A permutation DIF test is developed, and its performance is compared to the conventional parametric approach in a simulation study. We also illustrate the proposed semiparametric DIF testing procedure with an empirical example. PMID:26155757

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

    PubMed

    Park, Hahnbeom; Lee, Gyu Rie; Heo, Lim; Seok, Chaok

    2014-01-01

    Protein loop modeling is a tool for predicting protein local structures of particular interest, providing opportunities for applications involving protein structure prediction and de novo protein design. Until recently, the majority of loop modeling methods have been developed and tested by reconstructing loops in frameworks of experimentally resolved structures. In many practical applications, however, the protein loops to be modeled are located in inaccurate structural environments. These include loops in model structures, low-resolution experimental structures, or experimental structures of different functional forms. Accordingly, discrepancies in the accuracy of the structural environment assumed in development of the method and that in practical applications present additional challenges to modern loop modeling methods. This study demonstrates a new strategy for employing a hybrid energy function combining physics-based and knowledge-based components to help tackle this challenge. The hybrid energy function is designed to combine the strengths of each energy component, simultaneously maintaining accurate loop structure prediction in a high-resolution framework structure and tolerating minor environmental errors in low-resolution structures. A loop modeling method based on global optimization of this new energy function is tested on loop targets situated in different levels of environmental errors, ranging from experimental structures to structures perturbed in backbone as well as side chains and template-based model structures. The new method performs comparably to force field-based approaches in loop reconstruction in crystal structures and better in loop prediction in inaccurate framework structures. This result suggests that higher-accuracy predictions would be possible for a broader range of applications. The web server for this method is available at http://galaxy.seoklab.org/loop with the PS2 option for the scoring function. PMID:25419655

  15. Constitutive Modeling of Skeletal Muscle Tissue with an Explicit Strain-Energy Function

    PubMed Central

    Odegard, G.M.; Donahue, T.L. Haut; Morrow, D.A.; Kaufman, K.R.

    2010-01-01

    While much work has previously been done in the modeling of skeletal muscle, no model has, to date, been developed that describes the mechanical behavior with an explicit strain-energy function associated with the active response of skeletal muscle tissue. A model is presented herein that has been developed to accommodate this design consideration using a robust dynamical approach. The model shows excellent agreement with a previously published model of both the active and passive length-tension properties of skeletal muscle. PMID:19045546

  16. A functional-dynamic reflection on participatory processes in modeling projects.

    PubMed

    Seidl, Roman

    2015-12-01

    The participation of nonscientists in modeling projects/studies is increasingly employed to fulfill different functions. However, it is not well investigated if and how explicitly these functions and the dynamics of a participatory process are reflected by modeling projects in particular. In this review study, I explore participatory modeling projects from a functional-dynamic process perspective. The main differences among projects relate to the functions of participation-most often, more than one per project can be identified, along with the degree of explicit reflection (i.e., awareness and anticipation) on the dynamic process perspective. Moreover, two main approaches are revealed: participatory modeling covering diverse approaches and companion modeling. It becomes apparent that the degree of reflection on the participatory process itself is not always explicit and perfectly visible in the descriptions of the modeling projects. Thus, the use of common protocols or templates is discussed to facilitate project planning, as well as the publication of project results. A generic template may help, not in providing details of a project or model development, but in explicitly reflecting on the participatory process. It can serve to systematize the particular project's approach to stakeholder collaboration, and thus quality management. PMID:25999270

  17. Takagi-Sugeno fuzzy models in the framework of orthonormal basis functions.

    PubMed

    Machado, Jeremias B; Campello, Ricardo J G B; Amaral, Wagner Caradori

    2013-06-01

    An approach to obtain Takagi-Sugeno (TS) fuzzy models of nonlinear dynamic systems using the framework of orthonormal basis functions (OBFs) is presented in this paper. This approach is based on an architecture in which local linear models with ladder-structured generalized OBFs (GOBFs) constitute the fuzzy rule consequents and the outputs of the corresponding GOBF filters are input variables for the rule antecedents. The resulting GOBF-TS model is characterized by having only real-valued parameters that do not depend on any user specification about particular types of functions to be used in the orthonormal basis. The fuzzy rules of the model are initially obtained by means of a well-known technique based on fuzzy clustering and least squares. Those rules are then simplified, and the model parameters (GOBF poles, GOBF expansion coefficients, and fuzzy membership functions) are subsequently adjusted by using a nonlinear optimization algorithm. The exact gradients of an error functional with respect to the parameters to be optimized are computed analytically. Those gradients provide exact search directions for the optimization process, which relies solely on input-output data measured from the system to be modeled. An example is presented to illustrate the performance of this approach in the modeling of a complex nonlinear dynamic system. PMID:23096073

  18. Model selection using multivariate functional data analysis for fast uncertainty quantification in subsurface reservoir forecasting

    NASA Astrophysics Data System (ADS)

    Grujic, O.; Caers, J.

    2014-12-01

    Modern approaches to uncertainty quantification in the subsurface rely on complex procedures of geological modeling combined with numerical simulation of flow & transport. This approach requires long computational times rendering any full Monte Carlo simulation infeasible, in particular solving the flow & transport problem takes hours of computing time in real field problems. This motivated the development of model selection methods aiming to identify a small subset of models that capture important statistics of a larger ensemble of geological model realization. A recent method, based on model selection in metric space, termed distance-kernel method (DKM) allows selecting representative models though kernel k-medoid clustering. The distance defining the metric space is usually based on some approximate flow model. However, the output of an approximate flow model can be multi-variate (reporting heads/pressures, saturation, rates). In addition, the modeler may have information from several other approximate models (e.g. upscaled models) or summary statistical information about geological heterogeneity that could allow for a more accurate selection. In an effort to perform model selection based on multivariate attributes, we rely on functional data analysis which allows for an exploitation of covariances between time-varying multivariate numerical simulation output. Based on mixed functional principal component analysis, we construct a lower dimensional space in which kernel k-medoid clustering is used for model selection. In this work we demonstrate the functional approach on a complex compositional flow problem where the geological uncertainty consists of channels with uncertain spatial distribution of facies, proportions, orientations and geometries. We illustrate that using multivariate attributes and multiple approximate models provides accuracy improvement over using a single attribute.

  19. Testing a full-range soil-water retention function in modeling water potential and temperature

    USGS Publications Warehouse

    Andraski, B.J.; Jacobson, E.A.

    2000-01-01

    Recent work has emphasized development of full-range water-retention functions that are applicable under both wet and dry soil conditions, but evaluation of such functions in numerical modeling has been limited. Here we show that simulations using the Rossi-Nimmo (RN) full-range function compared favorably with those using the common Brooks-Corey function and that the RN function can improve prediction of water potentials in near-surface soil, particularly under dry conditions. Simulations using the RN function also improved prediction of temperatures throughout the soil profile. Such improvements could be important for calculations of liquid and vapor flow in near-surface soils and in deep unsaturated zones of arid and semiarid regions.

  20. Cosmogenic nuclide production rates as a function of latitude and altitude calculated via a physics based model and excitation functions

    NASA Astrophysics Data System (ADS)

    Argento, D.; Reedy, R. C.; Stone, J. O.

    2012-12-01

    Cosmogenic nuclides have been used to develop a set of tools critical to the quantification of a wide range of geomorphic and climatic processes and events (Dunai 2010). Having reliable absolute measurement methods has had great impact on research constraining ice age extents as well as providing important climatic data via well constrained erosion rates, etc. Continuing to improve CN methods is critical for these sciences. While significant progress has been made in the last two decades to reduce uncertainties (Dunai 2010; Gosse & Phillips 2001), numerous aspects still need to be refined in order to achieve the analytic resolution desired by glaciologists and geomorphologists. In order to investigate the finer details of the radiation responsible for cosmogenic nuclide production, we have developed a physics based model which models the radiation cascade of primary and secondary cosmic-rays through the atmosphere. In this study, a Monte Carlo method radiation transport code, MCNPX, is used to model the galactic cosmic-ray (GCR) radiation impinging on the upper atmosphere. Beginning with a spectrum of high energy protons and alpha particles at the top of the atmosphere, the code tracks the primary and resulting secondary particles through a model of the Earth's atmosphere and into the lithosphere. Folding the neutron and proton flux results with energy dependent cross sections for nuclide production provides production rates for key cosmogenic nuclides (Argento et al. 2012, in press; Reedy 2012, in press). Our initial study for high latitude shows that nuclides scale at different rates for each nuclide (Argento 2012, in press). Furthermore, the attenuation length for each of these nuclide production rates increases with altitude, and again, they increase at different rates. This has the consequence of changing the production rate ratio as a function of altitude. The earth's geomagnetic field differentially filters low energy cosmic-rays by deflecting them away

  1. An engineering time-domain model for curve squeal: Tangential point-contact model and Green's functions approach

    NASA Astrophysics Data System (ADS)

    Zenzerovic, I.; Kropp, W.; Pieringer, A.

    2016-08-01

    Curve squeal is a strong tonal sound that may arise when a railway vehicle negotiates a tight curve. In contrast to frequency-domain models, time-domain models are able to capture the nonlinear and transient nature of curve squeal. However, these models are computationally expensive due to requirements for fine spatial and time discretization. In this paper, a computationally efficient engineering model for curve squeal in the time-domain is proposed. It is based on a steady-state point-contact model for the tangential wheel/rail contact and a Green's functions approach for wheel and rail dynamics. The squeal model also includes a simple model of sound radiation from the railway wheel from the literature. A validation of the tangential point-contact model against Kalker's transient variational contact model reveals that the point-contact model performs well within the squeal model up to at least 5 kHz. The proposed squeal model is applied to investigate the influence of lateral creepage, friction and wheel/rail contact position on squeal occurrence and amplitude. The study indicates a significant influence of the wheel/rail contact position on squeal frequencies and amplitudes. Friction and lateral creepage show an influence on squeal occurrence and amplitudes, but this is only secondary to the influence of the contact position.

  2. Wavelet-based functional linear mixed models: an application to measurement error–corrected distributed lag models

    PubMed Central

    Malloy, Elizabeth J.; Morris, Jeffrey S.; Adar, Sara D.; Suh, Helen; Gold, Diane R.; Coull, Brent A.

    2010-01-01

    Frequently, exposure data are measured over time on a grid of discrete values that collectively define a functional observation. In many applications, researchers are interested in using these measurements as covariates to predict a scalar response in a regression setting, with interest focusing on the most biologically relevant time window of exposure. One example is in panel studies of the health effects of particulate matter (PM), where particle levels are measured over time. In such studies, there are many more values of the functional data than observations in the data set so that regularization of the corresponding functional regression coefficient is necessary for estimation. Additional issues in this setting are the possibility of exposure measurement error and the need to incorporate additional potential confounders, such as meteorological or co-pollutant measures, that themselves may have effects that vary over time. To accommodate all these features, we develop wavelet-based linear mixed distributed lag models that incorporate repeated measures of functional data as covariates into a linear mixed model. A Bayesian approach to model fitting uses wavelet shrinkage to regularize functional coefficients. We show that, as long as the exposure error induces fine-scale variability in the functional exposure profile and the distributed lag function representing the exposure effect varies smoothly in time, the model corrects for the exposure measurement error without further adjustment. Both these conditions are likely to hold in the environmental applications we consider. We examine properties of the method using simulations and apply the method to data from a study examining the association between PM, measured as hourly averages for 1–7 days, and markers of acute systemic inflammation. We use the method to fully control for the effects of confounding by other time-varying predictors, such as temperature and co-pollutants. PMID:20156988

  3. Influence of objective function selection on modeling high and low flows in a changing climate

    NASA Astrophysics Data System (ADS)

    Vaze, J.; Petheram, C.; Chiew, F. H.; Teng, J.; Wang, B.; Post, D. A.

    2012-12-01

    This study evaluates the ability of commonly used hydrological models at simulating streamflow under variable climate conditions for different streamflow characteristics. The models are calibrated using three objective functions that weight high and low flow characteristics differently. The models are calibrated using data from ten unregulated catchments in southeast Australia. The results show that when the GR4J model is calibrated against low flows, it performs better in simulating low flows over an independent period compared to the simulation when using a high-flow objective function but this improvement in simulating low flows comes at the cost of poor simulations of high flows. The simulation results for the Sacramento model are different to GR4J and show that the Sacramento model calibrated specifically against low flows does not necessarily perform better in simulating low flows for an independent period not used in model calibration. The results for the two models also show that a model calibrated specifically against low flows does not necessarily perform better in simulating the bias of the lower 30% of fdc for an independent period not used in model calibration. The simulation results for both of the models indicate that model parameters calibrated using an objective function which gives more weight to high and medium flows are suitable for simulating streamflow for an independent period with reasonably high daily NSE values. The results also show that objective functions which puts more weight on low flows or similar weight to all flows is not suitable for simulating streamflow for an independent period if the metric of interest is daily NSE. The simulation-bias results indicate that there is no clear under or overestimation of flows when model parameters calibrated against wet or dry periods are used to simulate streamflow for an independent dry or wet period. The overall results from this study indicate that there is no single objective function that

  4. Modelling of the functioning of karst aquifers with a reservoir model: Application to Fontaine de Vaucluse (South of France)

    NASA Astrophysics Data System (ADS)

    Fleury, Perrine; Plagnes, Valérie; Bakalowicz, Michel

    2007-10-01

    SummaryThis work deals with a rainfall-discharge model applied to a well known karst aquifer. A new approach is developed in order to minimize the fitting parameters: here, some of the model parameters do not result from a simple fitting, as it was the case with earlier models, i.e., some of them were assessed from the hydrograph analysis. The conceptual model of the functioning is based on a production function based on a simple calculation of effective rainfall and a transfer function consisting of two reservoirs. A slow discharge reservoir transfers the low flow and a rapid discharge reservoir feeds the high flow. The model has three fitted parameters plus one for its initialisation. Three parameters are deduced from the hydrograph analysis over the entire time series. For example, the recession coefficient of the slow discharge reservoir is determined from the hydrodynamic analysis of the recession [Mangin, A., 1975. Contribution à l'étude hydrodynamique des aquifères karstiques. 3ème partie. Constitution et fonctionnement des aquifères karstiques. Annales de Spéléologie, 30 (1), 210-124]. This model was tested over a ten years period on the Fontaine de Vaucluse French karst system. The first hydrological year is used for fitting the model; the nine other cycles validate the modelling. The good quality of the model is proved by the Nash criterion of 92.3% on the validation period. Moreover, the simulation results were validated by a statistical analysis of measured and simulated time series. The model successfully simulates both the high and low flow at the same time. Also it estimates the water volumes available in the different parts of the aquifer and it proposes a management tool capable of predicting the evolution of the discharge in different climate conditions.

  5. An efficient modeling methodology of structural systems containing viscoelastic dampers based on frequency response function substructuring

    NASA Astrophysics Data System (ADS)

    de Lima, A. M. G.; Rade, D. A.; Lépore Neto, F. P.

    2009-05-01

    In this paper it is suggested a modeling methodology of structural systems supported by translational and rotational viscoelastic mounts or joints based on a frequency response function coupling technique. Such strategy enables to predict the dynamic behaviour of the composite systems given a set of frequency response functions of the main structure and a driving point frequency response function of the viscoelastic support. These frequency response functions can be obtained either experimentally or by finite element modeling. Both cases are considered in the study. After presenting the underlying theoretical aspects, the results of numerical simulations of two-dimensional structures are presented, emphasizing the procedure conceived to compute the frequency response functions of the viscoelastic mounts or joints from a detailed finite element model using commercial packages and material properties provided by manufacturers. The dependency of the viscoelastic behaviour on frequency and temperature is accounted for by using the complex modulus approach and the concepts of reduced frequency and shift factor. An investigation using experimentally acquired frequency response functions of a frame structure with a translational viscoelastic damper is presented. Based on the obtained results, the main features of the modeling methodology are highlighted.

  6. Verifying the functional ability of microstructured surfaces by model-based testing

    NASA Astrophysics Data System (ADS)

    Hartmann, Wito; Weckenmann, Albert

    2014-09-01

    Micro- and nanotechnology enables the use of new product features such as improved light absorption, self-cleaning or protection, which are based, on the one hand, on the size of functional nanostructures and the other hand, on material-specific properties. With the need to reliably measure progressively smaller geometric features, coordinate and surface-measuring instruments have been refined and now allow high-resolution topography and structure measurements down to the sub-nanometre range. Nevertheless, in many cases it is not possible to make a clear statement about the functional ability of the workpiece or its topography because conventional concepts of dimensioning and tolerancing are solely geometry oriented and standardized surface parameters are not sufficient to consider interaction with non-geometric parameters, which are dominant for functions such as sliding, wetting, sealing and optical reflection. To verify the functional ability of microstructured surfaces, a method was developed based on a parameterized mathematical-physical model of the function. From this model, function-related properties can be identified and geometric parameters can be derived, which may be different for the manufacturing and verification processes. With this method it is possible to optimize the definition of the shape of the workpiece regarding the intended function by applying theoretical and experimental knowledge, as well as modelling and simulation. Advantages of this approach will be discussed and demonstrated by the example of a microstructured inking roll.

  7. Predicting Functional Cortical ROIs via DTI-Derived Fiber Shape Models

    PubMed Central

    Zhang, Tuo; Guo, Lei; Li, Kaiming; Jing, Changfeng; Yin, Yan; Zhu, Dajiang; Cui, Guangbin; Li, Lingjiang

    2012-01-01

    Studying structural and functional connectivities of human cerebral cortex has drawn significant interest and effort recently. A fundamental and challenging problem arises when attempting to measure the structural and/or functional connectivities of specific cortical networks: how to identify and localize the best possible regions of interests (ROIs) on the cortex? In our view, the major challenges come from uncertainties in ROI boundary definition, the remarkable structural and functional variability across individuals and high nonlinearities within and around ROIs. In this paper, we present a novel ROI prediction framework that localizes ROIs in individual brains based on their learned fiber shape models from multimodal task-based functional magnetic resonance imaging (fMRI) and diffusion tensor imaging (DTI) data. In the training stage, shape models of white matter fibers are learnt from those emanating from the functional ROIs, which are activated brain regions detected from task-based fMRI data. In the prediction stage, functional ROIs are predicted in individual brains based only on DTI data. Our experiment results show that the average ROI prediction error is around 3.94 mm, in comparison with benchmark data provided by working memory and visual task-based fMRI. Our work demonstrated that fiber bundle shape models derived from DTI data are good predictors of functional cortical ROIs. PMID:21705394

  8. SPARSE GENERALIZED FUNCTIONAL LINEAR MODEL FOR PREDICTING REMISSION STATUS OF DEPRESSION PATIENTS

    PubMed Central

    Liu, Yashu; Nie, Zhi; Zhou, Jiayu; Farnum, Michael; Narayan, Vaibhav A; Wittenberg, Gayle; Ye, Jieping

    2014-01-01

    Complex diseases such as major depression affect people over time in complicated patterns. Longitudinal data analysis is thus crucial for understanding and prognosis of such diseases and has received considerable attention in the biomedical research community. Traditional classification and regression methods have been commonly applied in a simple (controlled) clinical setting with a small number of time points. However, these methods cannot be easily extended to the more general setting for longitudinal analysis, as they are not inherently built for time-dependent data. Functional regression, in contrast, is capable of identifying the relationship between features and outcomes along with time information by assuming features and/or outcomes as random functions over time rather than independent random variables. In this paper, we propose a novel sparse generalized functional linear model for the prediction of treatment remission status of the depression participants with longitudinal features. Compared to traditional functional regression models, our model enables high-dimensional learning, smoothness of functional coefficients, longitudinal feature selection and interpretable estimation of functional coefficients. Extensive experiments have been conducted on the Sequenced Treatment Alternatives to Relieve Depression (STAR*D) data set and the results show that the proposed sparse functional regression method achieves significantly higher prediction power than existing approaches. PMID:24297562

  9. Drosophila as a Model for MECP2 Gain of Function in Neurons

    PubMed Central

    Vonhoff, Fernando; Williams, Alison; Ryglewski, Stefanie; Duch, Carsten

    2012-01-01

    Methyl-CpG-binding protein 2 (MECP2) is a multi-functional regulator of gene expression. In humans loss of MECP2 function causes classic Rett syndrome, but gain of MECP2 function also causes mental retardation. Although mouse models provide valuable insight into Mecp2 gain and loss of function, the identification of MECP2 genetic targets and interactors remains time intensive and complicated. This study takes a step toward utilizing Drosophila as a model to identify genetic targets and cellular consequences of MECP2 gain-of function mutations in neurons, the principle cell type affected in patients with Rett-related mental retardation. We show that heterologous expression of human MECP2 in Drosophila motoneurons causes distinct defects in dendritic structure and motor behavior, as reported with MECP2 gain of function in humans and mice. Multiple lines of evidence suggest that these defects arise from specific MECP2 function. First, neurons with MECP2-induced dendrite loss show normal membrane currents. Second, dendritic phenotypes require an intact methyl-CpG-binding domain. Third, dendritic defects are amended by reducing the dose of the chromatin remodeling protein, osa, indicating that MECP2 may act via chromatin remodeling in Drosophila. MECP2-induced motoneuron dendritic defects cause specific motor behavior defects that are easy to score in genetic screening. In sum, our data show that some aspects of MECP2 function can be studied in the Drosophila model, thus expanding the repertoire of genetic reagents that can be used to unravel specific neural functions of MECP2. However, additional genes and signaling pathways identified through such approaches in Drosophila will require careful validation in the mouse model. PMID:22363746

  10. Development and validation of an evaporation duct model. Part II: Evaluation and improvement of stability functions

    NASA Astrophysics Data System (ADS)

    Ding, Juli; Fei, Jianfang; Huang, Xiaogang; Cheng, Xiaoping; Hu, Xiaohua; Ji, Liang

    2015-06-01

    This study aims to validate and improve the universal evaporation duct (UED) model through a further analysis of the stability function ( ψ). A large number of hydrometeorological observations obtained from a tower platform near Xisha Island of the South China Sea are employed, together with the latest variations in ψ function. Applicability of different ψ functions for specific sea areas and stratification conditions is investigated based on three objective criteria. The results show that, under unstable conditions, ψ function of Fairall et al. (1996) (i.e., Fairall96, similar for abbreviations of other function names) in general offers the best performance. However, strictly speaking, this holds true only for the stability (represented by bulk Richardson number R iB) range -2.6 ⩽ R iB < -0.1; when conditions become weakly unstable (-0.1 ⩽ R iB < -0.01), Fairall96 offers the second best performance after Hu and Zhang (1992) (HYQ92). Conversely, for near-neutral but slightly unstable conditions (-0.01 ⩽ R iB < 0.0), the effects of Edson04, Fairall03, Grachev00, and Fairall96 are similar, with Edson04 being the best function but offering only a weak advantage. Under stable conditions, HYQ92 is the optimal and offers a pronounced advantage, followed by the newly introduced SHEBA07 (by Grachev et al., 2007) function. Accordingly, the most favorable functions, i.e., Fairall96 and HYQ92, are incorporated into the UED model to obtain an improved version of the model. With the new functions, the mean root-mean-square (rms) errors of the modified refractivity ( M), 0-5-m M slope, 5-40-m M slope, and the rms errors of evaporation duct height (EDH) are reduced by 21.65%, 9.12%, 38.79%, and 59.06%, respectively, compared to the classical Naval Postgraduate School model.

  11. Physical models have gender-specific effects on student understanding of protein structure-function relationships

    PubMed Central

    Harris, Michelle A.; Chang, Wesley S.; Dent, Erik W.; Nordheim, Erik V.; Franzen, Margaret A.

    2016-01-01

    Understanding how basic structural units influence function is identified as a foundational/core concept for undergraduate biological and biochemical literacy. It is essential for students to understand this concept at all size scales, but it is often more difficult for students to understand structure-function relationships at the molecular level, which they cannot as effectively visualize. Students need to develop accurate, 3-dimensional (3D) mental models of biomolecules to understand how biomolecular structure affects cellular functions at the molecular level, yet most traditional curricular tools such as textbooks include only 2-dimensional (2D) representations. We used a controlled, backwards design approach to investigate how hand-held physical molecular model use affected students’ ability to logically predict structure-function relationships. Brief (one class period) physical model use increased quiz score for females, whereas there was no significant increase in score for males using physical models. Females also self-reported higher learning gains in their understanding of context-specific protein function. Gender differences in spatial visualization may explain the gender-specific benefits of physical model use observed. PMID:26923186

  12. Executive functions, impulsivity, and inhibitory control in adolescents: A structural equation model.

    PubMed

    Fino, Emanuele; Melogno, Sergio; Iliceto, Paolo; D'Aliesio, Sara; Pinto, Maria Antonietta; Candilera, Gabriella; Sabatello, Ugo

    2014-01-01

    Background. Adolescence represents a critical period for brain development, addressed by neurodevelopmental models to frontal, subcortical-limbic, and striatal activation, a pattern associated with rise of impulsivity and deficits in inhibitory control. The present study aimed at studying the association between self-report measures of impulsivity and inhibitory control with executive function in adolescents, employing structural equation modeling. Method. Tests were administered to 434 high school students. Acting without thinking was measured through the Barratt Impulsiveness Scale and the Dickman Impulsivity Inventory, reward sensitivity through the Behavioral Activation System, and sensation seeking through the Zuckerman-Kuhlman-Aluja Personali- ty Questionnaire. Inhibitory control was assessed through the Behavioral Inhibition System. The performance at the Wisconsin Card Sorting Task indicated executive function. Three models were specified using Sample Covariance Matrix, and the estimated parameters using Maximum Likelihood. Results. In the final model, impulsivity and inhibitory control predicted executive function, but sensation seeking did not. The fit of the model to data was excellent. Conclusions. The hypothesis that inhibitory control and impulsivity are predictors of executive function was supported. Our results appear informative of the validity of self-report measures to examine the relation between impulsivity traits rather than others to regulatory function of cognition and behavior. PMID:25157298

  13. Physical models have gender-specific effects on student understanding of protein structure-function relationships.

    PubMed

    Forbes-Lorman, Robin M; Harris, Michelle A; Chang, Wesley S; Dent, Erik W; Nordheim, Erik V; Franzen, Margaret A

    2016-07-01

    Understanding how basic structural units influence function is identified as a foundational/core concept for undergraduate biological and biochemical literacy. It is essential for students to understand this concept at all size scales, but it is often more difficult for students to understand structure-function relationships at the molecular level, which they cannot as effectively visualize. Students need to develop accurate, 3-dimensional mental models of biomolecules to understand how biomolecular structure affects cellular functions at the molecular level, yet most traditional curricular tools such as textbooks include only 2-dimensional representations. We used a controlled, backward design approach to investigate how hand-held physical molecular model use affected students' ability to logically predict structure-function relationships. Brief (one class period) physical model use increased quiz score for females, whereas there was no significant increase in score for males using physical models. Females also self-reported higher learning gains in their understanding of context-specific protein function. Gender differences in spatial visualization may explain the gender-specific benefits of physical model use observed. © 2016 The Authors Biochemistry and Molecular Biology Education published by Wiley Periodicals, Inc. on behalf of International Union of Biochemistry and Molecular Biology, 44(4):326-335, 2016. PMID:26923186

  14. A new approach for determining fully empirical altimeter wind speed model functions

    NASA Astrophysics Data System (ADS)

    Freilich, Michael H.; Challenor, Peter G.

    1994-12-01

    A statistical technique is developed for determining fully empirical model functions relating altimeter radar backscatter (σ0) measurements to near-surface neutral stability wind speed. By assuming that σ0 varies monotonically and uniquely with wind speed, the method requires knowledge only of the separate, rather than joint, distribution functions of σ0 and wind speed. Analytic simplifications result from using a Weibull distribution to approximate the global ocean wind speed distribution; several different wind data sets are used to demonstrate the validity of the Weibull approximation. The technique has been applied to 1 year of Geosat data. Validation of the new and historical model functions using an independent buoy data set demonstrates that the present model function not only has small overall bias and RMS errors, but yields smaller systematic error trends with wind speed and pseudowave age than previously published models. The present analysis suggests that generally accurate altimeter model functions can be derived without the use of collocated measurements, nor is additional significant wave height information measured by the altimeter necessary.

  15. Functional test of pedotransfer functions to predict water flow and solute transport with the dual-permeability model MACRO

    NASA Astrophysics Data System (ADS)

    Moeys, J.; Larsbo, M.; Bergström, L.; Brown, C. D.; Coquet, Y.; Jarvis, N. J.

    2012-07-01

    Estimating pesticide leaching risks at the regional scale requires the ability to completely parameterise a pesticide fate model using only survey data, such as soil and land-use maps. Such parameterisations usually rely on a set of lookup tables and (pedo)transfer functions, relating elementary soil and site properties to model parameters. The aim of this paper is to describe and test a complete set of parameter estimation algorithms developed for the pesticide fate model MACRO, which accounts for preferential flow in soil macropores. We used tracer monitoring data from 16 lysimeter studies, carried out in three European countries, to evaluate the ability of MACRO and this "blind parameterisation" scheme to reproduce measured solute leaching at the base of each lysimeter. We focused on the prediction of early tracer breakthrough due to preferential flow, because this is critical for pesticide leaching. We then calibrated a selected number of parameters in order to assess to what extent the prediction of water and solute leaching could be improved. Our results show that water flow was generally reasonably well predicted (median model efficiency, ME, of 0.42). Although the general pattern of solute leaching was reproduced well by the model, the overall model efficiency was low (median ME = -0.26) due to errors in the timing and magnitude of some peaks. Preferential solute leaching at early pore volumes was also systematically underestimated. Nonetheless, the ranking of soils according to solute loads at early pore volumes was reasonably well estimated (concordance correlation coefficient, CCC, between 0.54 and 0.72). Moreover, we also found that ignoring macropore flow leads to a significant deterioration in the ability of the model to reproduce the observed leaching pattern, and especially the early breakthrough in some soils. Finally, the calibration procedure showed that improving the estimation of solute transport parameters is probably more important than the

  16. Functional test of pedotransfer functions to predict water flow and solute transport with the dual-permeability model MACRO

    NASA Astrophysics Data System (ADS)

    Moeys, J.; Larsbo, M.; Bergström, L.; Brown, C. D.; Coquet, Y.; Jarvis, N. J.

    2012-02-01

    Estimating pesticide leaching risks at the regional scale requires the ability to completely parameterise a pesticide fate model using only survey data, such as soil and land-use maps. Such parameterisation usually rely on a set of lookup tables and (pedo)transfer functions, relating elementary soil and site properties to model parameters. The aim of this paper is to describe and test a complete set of parameter estimation algorithms developed for the pesticide fate model MACRO, which accounts for preferential flow in soil macropores. We used tracer monitoring data from 16 lysimeter studies, carried out in three European countries, to evaluate the ability of MACRO and this "blind parameterisation" scheme to reproduce measured solute leaching at the base of each lysimeter. We focused on the prediction of early tracer breakthrough due to preferential flow, because this is critical for pesticide leaching. We then calibrated a selected number of parameters in order to assess to what extent the prediction of water and solute leaching could be improved. Our results show that water flow was generally reasonably well predicted (median model efficiency, ME, of 0.42). Although the general pattern of solute leaching was reproduced well by the model, the overall model efficiency was low (median ME = -0.26) due to errors in the timing and magnitude of some peaks. Preferential solute leaching at early pore volumes was also systematically underestimated. Nonetheless, the ranking of soils according to solute loads at early pore volumes was reasonably well estimated (concordance correlation coefficient, CCC, between 0.54 and 0.72). Moreover, we also found that ignoring macropore flow leads to a significant deterioration in the ability of the model to reproduce the observed leaching pattern, and especially the early breakthrough in some soils. Finally, the calibration procedure showed that improving the estimation of solute transport parameters is probably more important than the

  17. Functional relationships for the estimation of van Genuchten parameter values in landfill processes models.

    PubMed

    White, Jim; Zardava, Kiriaki; Nayagum, Dharumarajen; Powrie, William

    2015-04-01

    Numerical models of landfill processes need to be able to estimate the capillary pressure and relative permeability of waste as a function of moisture content using analytical equations such as the van Genuchten equations. The paper identifies the range of van Genuchten parameter values for use in models and proposes a formulaic relationship between these parameter values and saturated moisture content. The concept of porous material, its behaviour under unsaturated conditions and Mualem's integral transform equation that estimates relative permeability from capillary pressure are reviewed. The application of the algebraic form of the capillary pressure function proposed by van Genuchten and its application using Mualem's transform to obtain the van Genuchten algebraic functions for relative permeability are discussed. Functional relationships are identified between saturated moisture content and the van Genuchten parameters using a database of results from other sources. These relationships may be used in numerical modelling of unsaturated flow in landfilled waste where the saturated moisture content varies significantly as the result of compression, settlement and degradation. A 2D numerical model simulation of leachate recirculation is used to investigate the sensitivity of the simulation to the introduction of these functional relationships. It is found that the transient liquid and gas flows across the model boundaries appear to be insensitive to whether or not the functions are incorporated into the model algorithm. However it is observed that using the relationships does have some impact on the distribution of the degree of saturation throughout the model and on the transient behaviour of the way in which the recirculation recharges the waste. However it is not thought that this impact would be sufficient to influence the design of a leachate recirculation system. PMID:25573738

  18. Identification of Functional Differences in Metabolic Networks Using Comparative Genomics and Constraint-Based Models

    PubMed Central

    Hamilton, Joshua J.; Reed, Jennifer L.

    2012-01-01

    Genome-scale network reconstructions are useful tools for understanding cellular metabolism, and comparisons of such reconstructions can provide insight into metabolic differences between organisms. Recent efforts toward comparing genome-scale models have focused primarily on aligning metabolic networks at the reaction level and then looking at differences and similarities in reaction and gene content. However, these reaction comparison approaches are time-consuming and do not identify the effect network differences have on the functional states of the network. We have developed a bilevel mixed-integer programming approach, CONGA, to identify functional differences between metabolic networks by comparing network reconstructions aligned at the gene level. We first identify orthologous genes across two reconstructions and then use CONGA to identify conditions under which differences in gene content give rise to differences in metabolic capabilities. By seeking genes whose deletion in one or both models disproportionately changes flux through a selected reaction (e.g., growth or by-product secretion) in one model over another, we are able to identify structural metabolic network differences enabling unique metabolic capabilities. Using CONGA, we explore functional differences between two metabolic reconstructions of Escherichia coli and identify a set of reactions responsible for chemical production differences between the two models. We also use this approach to aid in the development of a genome-scale model of Synechococcus sp. PCC 7002. Finally, we propose potential antimicrobial targets in Mycobacterium tuberculosis and Staphylococcus aureus based on differences in their metabolic capabilities. Through these examples, we demonstrate that a gene-centric approach to comparing metabolic networks allows for a rapid comparison of metabolic models at a functional level. Using CONGA, we can identify differences in reaction and gene content which give rise to different

  19. Functional MRI and neural responses in a rat model of Alzheimer’s disease

    PubMed Central

    Sanganahalli, Basavaraju G.; Herman, Peter; Behar, Kevin L.; Blumenfeld, Hal; Rothman, Douglas L.; Hyder, Fahmeed

    2013-01-01

    Based on the hypothesis that brain plaques and tangles can affect cortical functions in Alzheimer's disease (AD) and thus modify functional activity, we investigated functional responses in an AD rat model (called the Samaritan Alzheimer’s rat achieved by ventricular infusion of amyloid peptide) and age-matched healthy control. High-field functional magnetic resonance imaging (fMRI) and extracellular neural activity measurements were applied to characterize sensory-evoked responses. Electrical stimulation of the forepaw led to BOLD and neural responses in the contralateral somatosensory cortex and thalamus. In AD brain we noted much smaller BOLD activation patterns in the somatosensory cortex (i.e., about 50% less activated voxels compared to normal brain). While magnitudes of BOLD and neural responses in the cerebral cortex were markedly attenuated in AD rats compared to normal rats (by about 50%), the dynamic coupling between the BOLD and neural responses in the cerebral cortex, as assessed by transfer function analysis, remained unaltered between the groups. However thalamic BOLD and neural responses were unaltered in AD brain compared to controls. Thus cortical responses in the AD model were indeed diminished compared to controls, but the thalamic responses in the AD and control rats were quite similar. Therefore these results suggest that Alzheimer’s disease may affect cortical function more than subcortical function, which may have implications for interpreting altered human brain functional responses in fMRI studies of Alzheimer’s disease. PMID:23648961

  20. Asymptotic behaviour of two-point functions in multi-species models

    NASA Astrophysics Data System (ADS)

    Kozlowski, Karol K.; Ragoucy, Eric

    2016-05-01

    We extract the long-distance asymptotic behaviour of two-point correlation functions in massless quantum integrable models containing multi-species excitations. For such a purpose, we extend to these models the method of a large-distance regime re-summation of the form factor expansion of correlation functions. The key feature of our analysis is a technical hypothesis on the large-volume behaviour of the form factors of local operators in such models. We check the validity of this hypothesis on the example of the SU (3)-invariant XXX magnet by means of the determinant representations for the form factors of local operators in this model. Our approach confirms the structure of the critical exponents obtained previously for numerous models solvable by the nested Bethe Ansatz.

  1. A Probabilistic Model of Functional Brain Connectivity Network for Discovering Novel Biomarkers

    PubMed Central

    Bian, Jiang; Xie, Mengjun; Topaloglu, Umit; Cisler, Josh M.

    2013-01-01

    Graph theoretical analyses of functional brain connectivity networks have been limited to a static view of brain activities over the entire timeseries. In this paper, we propose a new probabilistic model of the functional brain connectivity network, the strong-edge model, which incorporates the temporal fluctuation of neurodynamics. We also introduce a systematic approach to identifying biomarkers based on network characteristics that quantitatively describe the organization of the brain network. The evaluation results of the proposed strong-edge network model is quite promising. The biomarkers derived from the strong-edge model have achieved much higher prediction accuracy of 89% (ROCAUC: 0.96) in distinguishing depression subjects from healthy controls in comparison with the conventional network model (accuracy: 76%, ROC-AUC: 0.87). These novel biomarkers have the high potential of being applied clinically in diagnosing neurological and psychiatric brain diseases with noninvasive neuroimaging technologies. PMID:24303289

  2. Rabbit-Specific Ventricular Model of Cardiac Electrophysiological Function including Specialized Conduction System

    PubMed Central

    Bordas, R.; Gillow, K.; Lou, Q.; Efimov, I. R.; Gavaghan, D.; Kohl, P.; Grau, V.; Rodriguez, B.

    2011-01-01

    The function of the ventricular specialized conduction system in the heart is to ensure the coordinated electrical activation of the ventricles. It is therefore critical to the overall function of the heart, and has also been implicated as an important player in various diseases, including lethal ventricular arrhythmias such as ventricular fibrillation and drug-induced torsades de pointes. However, current ventricular models of electrophysiology usually ignore, or include highly simplified representations of the specialized conduction system. Here, we describe the development of a image-based, species-consistent, anatomically-detailed model of rabbit ventricular electrophysiology that incorporates a detailed description of the free-running part of the specialized conduction system. Techniques used for the construction of the geometrical model of the specialized conduction system from a magnetic resonance dataset and integration of the system model into a ventricular anatomical model, developed from the same dataset, are described. Computer simulations of rabbit ventricular electrophysiology are conducted using the novel anatomical model and rabbit-specific membrane kinetics to investigate the importance of the components and properties of the conduction system in determining ventricular function under physiological conditions. Simulation results are compared to panoramic optical mapping experiments for model validation and results interpretation. Full access is provided to the anatomical models developed in this study. PMID:21672547

  3. Memory for places: a navigational model in support of Marr's theory of hippocampal function.

    PubMed

    Recce, M; Harris, K D

    1996-01-01

    In this report we describe a model that applies Marr's theory of hippocampal function to the problem of map-based navigation. Like many others we attribute a spatial memory function to the hippocampus, but we suggest that the additional functional components required for map-based navigation are located elsewhere in the brain. One of the key functional components in this model is an egocentric map of space, located in the neocortex, that is continuously updated using ideothetic (self-motion) information. The hippocampus stores snapshots of this egocentric map. The modeled activity pattern of head direction cells is used to set the best egocentric map rotation to match the snapshots stored in the hippocampus, resulting in place cells with a nondirectional firing pattern. We describe an evaluation of this model using a mobile robot and demonstrate that with this model the robot can recognize an environment and find a hidden goal. This model is discussed in the context of prior experiments that were designed to discover the map-based spatial processing of animals. We also predict the results of further experiments. PMID:9034859

  4. Weaving Authentication and Authorization Requirements into the Functional Model of a System Using Z Promotion

    NASA Astrophysics Data System (ADS)

    Haidar, Ali Nasrat; Abdallah, Ali E.

    The use of Z in software development has focused on specifying the functionality of a system. However, when developing secure system, it is important to address fundamental security aspects, such as authentication, authorization, and auditing. In this paper, we show an approach for building systems from generic and modular security components using promotion technique in Z. The approach focuses on weaving security component into the functionality of a system using promotion technique in Z. For each component, Z notation is used to construct its state-based model and the relevant operations. Once a component is introduced, the defined local operations are promoted to work on the global state. We illustrate this approach on the development of a "secure" model for a conference management system. With this approach, it is possible to specify the core functionalities of a system independently from the security mechanisms. Authentication and authorization are viewed as components which are carefully integrated with the functional system.

  5. Alternate forms of the associated Legendre functions for use in geomagnetic modeling.

    USGS Publications Warehouse

    Alldredge, L.R.; Benton, E.R.

    1986-01-01

    An inconvenience attending traditional use of associated Legendre functions in global modeling is that the functions are not separable with respect to the 2 indices (order and degree). In 1973 Merilees suggested a way to avoid the problem by showing that associated Legendre functions of order m and degree m+k can be expressed in terms of elementary functions. This note calls attention to some possible gains in time savings and accuracy in geomagnetic modeling based upon this form. For this purpose, expansions of associated Legendre polynomials in terms of sines and cosines of multiple angles are displayed up to degree and order 10. Examples are also given explaining how some surface spherical harmonics can be transformed into true Fourier series for selected polar great circle paths. -from Authors

  6. The dependence of traction evolution on the earthquake source time function adopted in kinematic rupture models

    NASA Astrophysics Data System (ADS)

    Piatanesi, Alessio; Tinti, Elisa; Cocco, Massimo; Fukuyama, Eiichi

    2004-02-01

    We compute the temporal evolution of traction by solving the elasto-dynamic equation and by using the slip velocity history as a boundary condition on the fault plane. We use different source time functions to derive a suite of kinematic source models to image the spatial distribution of dynamic and breakdown stress drop, strength excess and critical slip weakening distance (Dc). Our results show that the source time functions, adopted in kinematic source models, affect the inferred dynamic parameters. The critical slip weakening distance, characterizing the constitutive relation, ranges between 30% and 80% of the total slip. The ratio between Dc and total slip depends on the adopted source time functions and, in these applications, is nearly constant over the fault. We propose that source time functions compatible with earthquake dynamics should be used to infer the traction time history.

  7. Sivers and Boer-Mulders functions in Light-Cone Quark Models

    SciTech Connect

    Pasquini, Barbara; Yuan, Feng

    2010-01-29

    Results for the naive-time-reversal-odd quark distributions in a light-cone quark model are presented. The final-state interaction effects are generated via single-gluon exchange mechanism. The formalism of light-cone wave functions is used to derive general expressions in terms of overlap of wave-function amplitudes describing the different orbital angular momentum components of the nucleon. In particular, the model predictions show a dominant contribution from S- and P-wave interference in the Sivers function and a significant contribution also from the interference of P and D waves in the Boer-Mulders function. The favourable comparison with existing phenomenological parametrizations motivates further applications to describe azimuthal asymmetries in hadronic reactions.

  8. The GRB luminosity function: prediction of the internal shock model and comparison to observations

    SciTech Connect

    Zitouni, H.; Daigne, F.; Mochkovitch, R.

    2008-05-22

    We compute the expected GRB luminosity function in the internal shock model. We find that if the population of GRB central engines produces all kind of relativistic outflows, from very smooth to highly variable, the luminosity function has to branchs: at low luminosity, the distribution is dominated by low efficiency GRBs and is close to a power law of slope -0.5, whereas at high luminosity, the luminosity function follows the distribution of injected kinetic power. Using Monte Carlo simulations and several observational constrains (BATSE logN-logP diagram, peak energy distribution of bright BATSE bursts, fraction of XRFs in the HETE2 sample), we show that it is currently impossible to distinguish between a single power law or a broken power law luminosity function. However, when the second case is considered, the low-luminosity slope is found to be -0.6{+-}0.2, which is compatible with the prediction of the internal shock model.

  9. Determinants of functioning and well-being among individuals with schizophrenia: An integrated model

    PubMed Central

    Yanos, P.T.; Moos, R.H.

    2006-01-01

    Outcomes for health conditions are typically the result of multiple factors; however, studies tend to focus on a narrow class of variables. Functioning and well-being outcomes for schizophrenia are diverse and have resisted simple explanation; however, prior research has not offered an integrated understanding of the relative contributions of enduring and episodic environmental factors, personal resources and psychiatric factors, and cognitive appraisal and coping, on functioning and well-being outcomes in schizophrenia. The present article sets out an integrated model of the determinants of functioning and well-being among individuals with schizophrenia. To examine evidence that bears on the model, literature on hypothesized relationships is reviewed to identify areas for which there is strong evidence and areas where more research is needed. The article suggests areas for further research, and directs researchers and practitioners toward areas of intervention that can enhance functioning and well-being for persons diagnosed with schizophrenia. PMID:16480804

  10. An overview of multiphase cartilage mechanical modelling and its role in understanding function and pathology.

    PubMed

    Klika, Václav; Gaffney, Eamonn A; Chen, Ying-Chun; Brown, Cameron P

    2016-09-01

    There is a long history of mathematical and computational modelling with the objective of understanding the mechanisms governing cartilage׳s remarkable mechanical performance. Nonetheless, despite sophisticated modelling development, simulations of cartilage have consistently lagged behind structural knowledge and thus the relationship between structure and function in cartilage is not fully understood. However, in the most recent generation of studies, there is an emerging confluence between our structural knowledge and the structure represented in cartilage modelling. This raises the prospect of further refinement in our understanding of cartilage function and also the initiation of an engineering-level understanding for how structural degradation and ageing relates to cartilage dysfunction and pathology, as well as informing the potential design of prospective interventions. Aimed at researchers entering the field of cartilage modelling, we thus review the basic principles of cartilage models, discussing the underlying physics and assumptions in relatively simple settings, whilst presenting the derivation of relatively parsimonious multiphase cartilage models consistent with our discussions. We proceed to consider modern developments that start aligning the structure captured in the models with observed complexities. This emphasises the challenges associated with constitutive relations, boundary conditions, parameter estimation and validation in cartilage modelling programmes. Consequently, we further detail how both experimental interrogations and modelling developments can be utilised to investigate and reduce such difficulties before summarising how cartilage modelling initiatives may improve our understanding of cartilage ageing, pathology and intervention. PMID:27195911

  11. Evaluating Different Model Structures for Representing Watershed Functions through the use of Signature Measures

    NASA Astrophysics Data System (ADS)

    Mendoza, P. A.; Clark, M. P.; Rajagopalan, B.

    2012-12-01

    The increasing availability of hydrometeorological data and computational resources has allowed the evolution of hydrological models from lumped, conceptual to fully distributed. However, principal catchment behavioral functions are poorly understood, mainly because model evaluation has been typically based on the comparison of simulated and observed time series of model outputs (e.g., streamflow), ignoring the possibility that we may be getting the right results because of a compensation of errors in model structure, parameters and data. In recent years the hydrological community has redirected its efforts to look for a better understanding of hydrological models from a functional point of view (e.g. water balance, vertical redistribution of soil moisture and redistribution of runoff in time, among others). In this research, we evaluate the ability of three hydrological models (PRMS, VIC and Noah-MP) to skillfully reproduce relevant watershed processes in the Animas River basin, which is a sub-basin of the Colorado River Basin. A suite of signature measures that have diagnostic power of model behaviors is developed and analyzed in order to diagnose the model deficiency. All model simulations were run with the same spatial discretization and forcing data to enable fair comparison of model structures

  12. Bayesian inference in an item response theory model with a generalized student t link function

    NASA Astrophysics Data System (ADS)

    Azevedo, Caio L. N.; Migon, Helio S.

    2012-10-01

    In this paper we introduce a new item response theory (IRT) model with a generalized Student t-link function with unknown degrees of freedom (df), named generalized t-link (GtL) IRT model. In this model we consider only the difficulty parameter in the item response function. GtL is an alternative to the two parameter logit and probit models, since the degrees of freedom (df) play a similar role to the discrimination parameter. However, the behavior of the curves of the GtL is different from those of the two parameter models and the usual Student t link, since in GtL the curve obtained from different df's can cross the probit curves in more than one latent trait level. The GtL model has similar proprieties to the generalized linear mixed models, such as the existence of sufficient statistics and easy parameter interpretation. Also, many techniques of parameter estimation, model fit assessment and residual analysis developed for that models can be used for the GtL model. We develop fully Bayesian estimation and model fit assessment tools through a Metropolis-Hastings step within Gibbs sampling algorithm. We consider a prior sensitivity choice concerning the degrees of freedom. The simulation study indicates that the algorithm recovers all parameters properly. In addition, some Bayesian model fit assessment tools are considered. Finally, a real data set is analyzed using our approach and other usual models. The results indicate that our model fits the data better than the two parameter models.

  13. Pleiades luminosity function: fine structure and new Pre-MS models

    NASA Astrophysics Data System (ADS)

    Belikov, A. N.; Piskunov, A. E.; Schilbach, E.

    In order to study a model-dependence of the results achieved in the previous investigations of the Pleiades luminosity function using D'Antona and Mazzitelli (1994) evolutionary tracks, we repeated the computations with the new track system by D'Antona and Mazzitelli (1997). T h e following main conclusions can be drawn: the new models agree better with observations; the helium abundance needed to fit the Hipparcos distance modulus is reduced to a more reasonable value of Y=0.31; the cluster age becomes slightly higher and the slope of the initial mass function somewhat lower. The conclusions on the fine structure of the luminosity function do not change significantly due to the application of the new models.

  14. Bifactor Modeling of the Behavior Rating Inventory of Executive Function (BRIEF) in a Chilean Sample.

    PubMed

    Pérez-Salas, Claudia Paz; Ramos, Carlos; Oliva, Karen; Ortega, Alonso

    2016-06-01

    The Behavior Rating Inventory of Executive Functions evaluates executive functioning through the observation of students' performance in real contexts. Most psychometric studies of the scale have only tested the first-order structure, despite the hierarchical configuration of its theoretical model. A bifactor model was conducted on a normative sample of 5- to 18-year-old Chileans (M age = 11.3 years, SD = 3.7) to test a hierarchical structure of three first-order factors and an independent second-order factor. Bifactor analyses showed best fit for the proposed hierarchical structure. Findings supported a method to evaluate executive functioning models that provides a general global factor score that may complement existing indices and thus help clinicians to make better inferences. PMID:27216945

  15. Calculations of longitudinal and transverse velocity structure functions using a vortex model of isotropic turbulence

    SciTech Connect

    He, G.; Doolen, G.D.; Chen, S.

    1999-12-01

    The longitudinal structure function (LSF) and the transverse structure function (TSF) in isotropic turbulence are calculated using a vortex model. The vortex model is composed of the Rankine and Burgers vortices which have the exponential distributions in the vortex Reynolds number and vortex radii. This model exhibits a power law in the inertial range and satisfies the minimal condition of isotropy that the second-order exponent of the LSF in the inertial range is equal to that of the TSF. Also observed are differences between longitudinal and transverse structure functions caused by intermittency. These differences are related to their scaling differences which have been previously observed in experiments and numerical simulations. {copyright} {ital 1999 American Institute of Physics.}

  16. STRONG GRAVITATIONAL LENS MODELING WITH SPATIALLY VARIANT POINT-SPREAD FUNCTIONS

    SciTech Connect

    Rogers, Adam; Fiege, Jason D.

    2011-12-10

    Astronomical instruments generally possess spatially variant point-spread functions, which determine the amount by which an image pixel is blurred as a function of position. Several techniques have been devised to handle this variability in the context of the standard image deconvolution problem. We have developed an iterative gravitational lens modeling code called Mirage that determines the parameters of pixelated source intensity distributions for a given lens model. We are able to include the effects of spatially variant point-spread functions using the iterative procedures in this lensing code. In this paper, we discuss the methods to include spatially variant blurring effects and test the results of the algorithm in the context of gravitational lens modeling problems.

  17. Correlations between statistical models of robotically collected kinematics and clinical measures of upper extremity function.

    PubMed

    Rohafza, Maryam; Fluet, Gerard G; Qiu, Qinyin; Adamovich, Sergei

    2012-01-01

    One of the obstacles in the development of rehabilitation robotics has been inadequacy in the measurement of treatment effects due to interventions. A measurement tool that will efficiently produce a large reliable sample of measurements collected during a single session that can also produce a rich set of data which reflects a subject's ability to perform meaningful functional activities has not been developed. This paper presents three linear regression models generated from seven kinematic measures collected during the performance of virtually simulated rehabilitation activities that were integrated with haptic robots by 19 persons with upper extremity hemiparesis due to chronic stroke. One of these models demonstrated a statistically significant correlation with the subjects' scores on the Jebsen Test of Hand Function (JTHF), a battery of six standardized upper extremity functional activities. The second and third models demonstrated a statistically significant correlation with the subjects' change scores on the JTHF. PMID:23366834

  18. Strong Gravitational Lens Modeling with Spatially Variant Point-spread Functions

    NASA Astrophysics Data System (ADS)

    Rogers, Adam; Fiege, Jason D.

    2011-12-01

    Astronomical instruments generally possess spatially variant point-spread functions, which determine the amount by which an image pixel is blurred as a function of position. Several techniques have been devised to handle this variability in the context of the standard image deconvolution problem. We have developed an iterative gravitational lens modeling code called Mirage that determines the parameters of pixelated source intensity distributions for a given lens model. We are able to include the effects of spatially variant point-spread functions using the iterative procedures in this lensing code. In this paper, we discuss the methods to include spatially variant blurring effects and test the results of the algorithm in the context of gravitational lens modeling problems.

  19. Natural convection flow in a square cavity revisited: Laminar and turbulent models with wall functions

    NASA Astrophysics Data System (ADS)

    Barakos, G.; Mitsoulis, E.; Assimacopoulos, D.

    1994-04-01

    Numerical simulations have been undertaken for the benchmark problem of natural convection flow in a square cavity. The control volume method is used to solve the conservation equations for laminar and turbulent flows for a series of Rayleigh numbers (Ra) reaching values up to 10(exp 10). The k-epsilon model has been used for turbulence modelling with and without logarithmic wall functions. Uniform and non-uniform (stretched) grids have been employed with increasing density to guarantee accurate solutions, especially near the walls for high Ra-values. ADI and SIP solvers are implemented to accelerate convergence. Excellent agreement is obtained with previous numerical solutions, while some discrepancies with others for high Ra-values may be due to a possibly different implementation of the wall functions. Comparisons with experimental data for heat transfer (Nusselt number) clearly demonstrates the limitations of the standard k-epsilon model with logarithmic wall functions, which gives significant overpredictions.

  20. Measurement and modeling of transfer functions for lightning coupling into the Sago mine.

    SciTech Connect

    Morris, Marvin E.; Higgins, Matthew B.

    2007-04-01

    This report documents measurements and analytical modeling of electromagnetic transfer functions to quantify the ability of cloud-to-ground lightning strokes (including horizontal arc-channel components) to couple electromagnetic energy into the Sago mine located near Buckhannon, WV. Two coupling mechanisms were measured: direct and indirect drive. These transfer functions are then used to predict electric fields within the mine and induced voltages on conductors that were left abandoned in the sealed area of the Sago mine.