WorldWideScience

Sample records for coarse temporal structure

  1. Downscaling of coarse resolution LAI products to achieve both high spatial and temporal resolution for regions of interest

    KAUST Repository

    Houborg, Rasmus; McCabe, Matthew; Gao, Feng

    2015-01-01

    This paper presents a flexible tool for spatio-temporal enhancement of coarse resolution leaf area index (LAI) products, which is readily adaptable to different land cover types, landscape heterogeneities and cloud cover conditions. The framework integrates a rule-based regression tree approach for estimating Landsat-scale LAI from existing 1 km resolution LAI products, and the Spatial and Temporal Adaptive Reflectance Fusion Model (STARFM) to intelligently interpolate the downscaled LAI between Landsat acquisitions. Comparisons against in-situ records of LAI measured over corn and soybean highlights its utility for resolving sub-field LAI dynamics occurring over a range of plant development stages.

  2. Downscaling of coarse resolution LAI products to achieve both high spatial and temporal resolution for regions of interest

    KAUST Repository

    Houborg, Rasmus

    2015-11-12

    This paper presents a flexible tool for spatio-temporal enhancement of coarse resolution leaf area index (LAI) products, which is readily adaptable to different land cover types, landscape heterogeneities and cloud cover conditions. The framework integrates a rule-based regression tree approach for estimating Landsat-scale LAI from existing 1 km resolution LAI products, and the Spatial and Temporal Adaptive Reflectance Fusion Model (STARFM) to intelligently interpolate the downscaled LAI between Landsat acquisitions. Comparisons against in-situ records of LAI measured over corn and soybean highlights its utility for resolving sub-field LAI dynamics occurring over a range of plant development stages.

  3. Systematic and simulation-free coarse graining of homopolymer melts: A structure-based study

    International Nuclear Information System (INIS)

    Yang, Delian; Wang, Qiang

    2015-01-01

    We propose a systematic and simulation-free strategy for coarse graining of homopolymer melts, where each chain of N m monomers is uniformly divided into N segments, with the spatial position of each segment corresponding to the center-of-mass of its monomers. We use integral-equation theories suitable for the study of equilibrium properties of polymers, instead of many-chain molecular simulations, to obtain the structural and thermodynamic properties of both original and coarse-grained (CG) systems, and quantitatively examine how the effective pair potentials between CG segments and the thermodynamic properties of CG systems vary with N. Our systematic and simulation-free strategy is much faster than those using many-chain simulations, thus effectively solving the transferability problem in coarse graining, and provides the quantitative basis for choosing the appropriate N-values. It also avoids the problems caused by finite-size effects and statistical uncertainties in many-chain simulations. Taking the simple hard-core Gaussian thread model [K. S. Schweizer and J. G. Curro, Chem. Phys. 149, 105 (1990)] as the original system, we demonstrate our strategy applied to structure-based coarse graining, which is quite general and versatile, and compare in detail the various integral-equation theories and closures for coarse graining. Our numerical results show that the effective CG potentials for various N and closures can be collapsed approximately onto the same curve, and that structure-based coarse graining cannot give thermodynamic consistency between original and CG systems at any N < N m

  4. Lectures on coarse geometry

    CERN Document Server

    Roe, John

    2003-01-01

    Coarse geometry is the study of spaces (particularly metric spaces) from a 'large scale' point of view, so that two spaces that look the same from a great distance are actually equivalent. This point of view is effective because it is often true that the relevant geometric properties of metric spaces are determined by their coarse geometry. Two examples of important uses of coarse geometry are Gromov's beautiful notion of a hyperbolic group and Mostow's proof of his famous rigidity theorem. The first few chapters of the book provide a general perspective on coarse structures. Even when only metric coarse structures are in view, the abstract framework brings the same simplification as does the passage from epsilons and deltas to open sets when speaking of continuity. The middle section reviews notions of negative curvature and rigidity. Modern interest in large scale geometry derives in large part from Mostow's rigidity theorem and from Gromov's subsequent 'large scale' rendition of the crucial properties of n...

  5. Assessing Temporal Stability for Coarse Scale Satellite Moisture Validation in the Maqu Area, Tibet

    Science.gov (United States)

    Bhatti, Haris Akram; Rientjes, Tom; Verhoef, Wouter; Yaseen, Muhammad

    2013-01-01

    This study evaluates if the temporal stability concept is applicable to a time series of satellite soil moisture images so to extend the common procedure of satellite image validation. The area of study is the Maqu area, which is located in the northeastern part of the Tibetan plateau. The network serves validation purposes of coarse scale (25–50 km) satellite soil moisture products and comprises 20 stations with probes installed at depths of 5, 10, 20, 40, 80 cm. The study period is 2009. The temporal stability concept is applied to all five depths of the soil moisture measuring network and to a time series of satellite-based moisture products from the Advance Microwave Scanning Radiometer (AMSR-E). The in-situ network is also assessed by Pearsons's correlation analysis. Assessments by the temporal stability concept proved to be useful and results suggest that probe measurements at 10 cm depth best match to the satellite observations. The Mean Relative Difference plot for satellite pixels shows that a RMSM pixel can be identified but in our case this pixel does not overlay any in-situ station. Also, the RMSM pixel does not overlay any of the Representative Mean Soil Moisture (RMSM) stations of the five probe depths. Pearson's correlation analysis on in-situ measurements suggests that moisture patterns over time are more persistent than over space. Since this study presents first results on the application of the temporal stability concept to a series of satellite images, we recommend further tests to become more conclusive on effectiveness to broaden the procedure of satellite validation. PMID:23959237

  6. Generalized coarse-grained Becker-Doering equations

    International Nuclear Information System (INIS)

    Bolton, Colin D; Wattis, Jonathan A D

    2003-01-01

    We present and apply a generalized coarse-graining method of reducing the Becker-Doering model; originally formulated to describe the stepwise aggregation and fragmentation of clusters during nucleation. Previous formulations of the coarse-graining procedure have allowed a temporal rescaling of the coarse-grained reaction rates; this is generalized to allow the rescaling to depend on cluster size. The form of this factor is derived for general reaction rates and general mesh function so that the steady-state solution is preserved; in the case of an even mesh function the kinetics can also be accurately reproduced. With a size-dependent mesh function the equilibrium solution and the form of convergence to this state are matched for a specific example. Finally we consider reaction rates relevant to the classical nucleation theory of spherical cluster growth, and numerically compare solutions of the full system to the generalized coarse-grained system in both constant monomer and constant mass formulations, demonstrating the accuracy of the method

  7. Flow structure of coarse-grained slurry in a horizontal pipe

    Czech Academy of Sciences Publication Activity Database

    Vlasák, Pavel; Kysela, Bohuš; Chára, Zdeněk

    2012-01-01

    Roč. 60, č. 2 (2012), s. 115-124 ISSN 0042-790X R&D Projects: GA ČR GAP105/10/1574 Institutional research plan: CEZ:AV0Z20600510 Keywords : coarse-grained slurry * turbulent flow * pressure drop * velocity distribution * flow structure * concentration effect Subject RIV: BK - Fluid Dynamics Impact factor: 0.653, year: 2012

  8. The Andatza coarse-grained turbidite system (westernmost Pyrenees: Stratigraphy, sedimentology and structural control

    Directory of Open Access Journals (Sweden)

    A. Bodego

    2017-06-01

    Full Text Available This is a field-based work that describes the stratigraphy and sedimentology of the Andatza Conglomerate Formation. Based on facies analysis three facies associations of a coarse-grained turbidite system and the related slope have been identified: (1 an inner fan of a turbidite system (or canyon and (2 a low- and (3 a high-gradient muddy slope respectively. The spatial distribution of the facies associations and the palaeocurrent analysis allow to interpret a depositional model for the Andatza Conglomerates consisting of an L-shaped, coarse-grained turbidite system, whose morphology was structurally controlled by synsedimentary basement-involved normal faults. The coarse-grained character of the turbidite system indicates the proximity of the source area, with the presence of a narrow shelf that fed the turbidite canyon from the north.

  9. Alignment-free comparative genomic screen for structured RNAs using coarse-grained secondary structure dot plots

    DEFF Research Database (Denmark)

    Kato, Yuki; Gorodkin, Jan; Havgaard, Jakob Hull

    2017-01-01

    . Methods: Here we present a fast and efficient method, DotcodeR, for detecting structurally similar RNAs in genomic sequences by comparing their corresponding coarse-grained secondary structure dot plots at string level. This allows us to perform an all-against-all scan of all window pairs from two genomes...... without alignment. Results: Our computational experiments with simulated data and real chromosomes demonstrate that the presented method has good sensitivity. Conclusions: DotcodeR can be useful as a pre-filter in a genomic comparative scan for structured RNAs....

  10. The Voronoi spatio-temporal data structure

    Science.gov (United States)

    Mioc, Darka

    2002-04-01

    Current GIS models cannot integrate the temporal dimension of spatial data easily. Indeed, current GISs do not support incremental (local) addition and deletion of spatial objects, and they can not support the temporal evolution of spatial data. Spatio-temporal facilities would be very useful in many GIS applications: harvesting and forest planning, cadastre, urban and regional planning, and emergency planning. The spatio-temporal model that can overcome these problems is based on a topological model---the Voronoi data structure. Voronoi diagrams are irregular tessellations of space, that adapt to spatial objects and therefore they are a synthesis of raster and vector spatial data models. The main advantage of the Voronoi data structure is its local and sequential map updates, which allows us to automatically record each event and performed map updates within the system. These map updates are executed through map construction commands that are composed of atomic actions (geometric algorithms for addition, deletion, and motion of spatial objects) on the dynamic Voronoi data structure. The formalization of map commands led to the development of a spatial language comprising a set of atomic operations or constructs on spatial primitives (points and lines), powerful enough to define the complex operations. This resulted in a new formal model for spatio-temporal change representation, where each update is uniquely characterized by the numbers of newly created and inactivated Voronoi regions. This is used for the extension of the model towards the hierarchical Voronoi data structure. In this model, spatio-temporal changes induced by map updates are preserved in a hierarchical data structure that combines events and corresponding changes in topology. This hierarchical Voronoi data structure has an implicit time ordering of events visible through changes in topology, and it is equivalent to an event structure that can support temporal data without precise temporal

  11. Coarse-grained description of cosmic structure from Szekeres models

    International Nuclear Information System (INIS)

    Sussman, Roberto A.; Gaspar, I. Delgado; Hidalgo, Juan Carlos

    2016-01-01

    We show that the full dynamical freedom of the well known Szekeres models allows for the description of elaborated 3-dimensional networks of cold dark matter structures (over-densities and/or density voids) undergoing ''pancake'' collapse. By reducing Einstein's field equations to a set of evolution equations, which themselves reduce in the linear limit to evolution equations for linear perturbations, we determine the dynamics of such structures, with the spatial comoving location of each structure uniquely specified by standard early Universe initial conditions. By means of a representative example we examine in detail the density contrast, the Hubble flow and peculiar velocities of structures that evolved, from linear initial data at the last scattering surface, to fully non-linear 10–20 Mpc scale configurations today. To motivate further research, we provide a qualitative discussion on the connection of Szekeres models with linear perturbations and the pancake collapse of the Zeldovich approximation. This type of structure modelling provides a coarse grained—but fully relativistic non-linear and non-perturbative —description of evolving large scale cosmic structures before their virialisation, and as such it has an enormous potential for applications in cosmological research

  12. Quantum theory of multiscale coarse-graining.

    Science.gov (United States)

    Han, Yining; Jin, Jaehyeok; Wagner, Jacob W; Voth, Gregory A

    2018-03-14

    Coarse-grained (CG) models serve as a powerful tool to simulate molecular systems at much longer temporal and spatial scales. Previously, CG models and methods have been built upon classical statistical mechanics. The present paper develops a theory and numerical methodology for coarse-graining in quantum statistical mechanics, by generalizing the multiscale coarse-graining (MS-CG) method to quantum Boltzmann statistics. A rigorous derivation of the sufficient thermodynamic consistency condition is first presented via imaginary time Feynman path integrals. It identifies the optimal choice of CG action functional and effective quantum CG (qCG) force field to generate a quantum MS-CG (qMS-CG) description of the equilibrium system that is consistent with the quantum fine-grained model projected onto the CG variables. A variational principle then provides a class of algorithms for optimally approximating the qMS-CG force fields. Specifically, a variational method based on force matching, which was also adopted in the classical MS-CG theory, is generalized to quantum Boltzmann statistics. The qMS-CG numerical algorithms and practical issues in implementing this variational minimization procedure are also discussed. Then, two numerical examples are presented to demonstrate the method. Finally, as an alternative strategy, a quasi-classical approximation for the thermal density matrix expressed in the CG variables is derived. This approach provides an interesting physical picture for coarse-graining in quantum Boltzmann statistical mechanics in which the consistency with the quantum particle delocalization is obviously manifest, and it opens up an avenue for using path integral centroid-based effective classical force fields in a coarse-graining methodology.

  13. Quantum theory of multiscale coarse-graining

    Science.gov (United States)

    Han, Yining; Jin, Jaehyeok; Wagner, Jacob W.; Voth, Gregory A.

    2018-03-01

    Coarse-grained (CG) models serve as a powerful tool to simulate molecular systems at much longer temporal and spatial scales. Previously, CG models and methods have been built upon classical statistical mechanics. The present paper develops a theory and numerical methodology for coarse-graining in quantum statistical mechanics, by generalizing the multiscale coarse-graining (MS-CG) method to quantum Boltzmann statistics. A rigorous derivation of the sufficient thermodynamic consistency condition is first presented via imaginary time Feynman path integrals. It identifies the optimal choice of CG action functional and effective quantum CG (qCG) force field to generate a quantum MS-CG (qMS-CG) description of the equilibrium system that is consistent with the quantum fine-grained model projected onto the CG variables. A variational principle then provides a class of algorithms for optimally approximating the qMS-CG force fields. Specifically, a variational method based on force matching, which was also adopted in the classical MS-CG theory, is generalized to quantum Boltzmann statistics. The qMS-CG numerical algorithms and practical issues in implementing this variational minimization procedure are also discussed. Then, two numerical examples are presented to demonstrate the method. Finally, as an alternative strategy, a quasi-classical approximation for the thermal density matrix expressed in the CG variables is derived. This approach provides an interesting physical picture for coarse-graining in quantum Boltzmann statistical mechanics in which the consistency with the quantum particle delocalization is obviously manifest, and it opens up an avenue for using path integral centroid-based effective classical force fields in a coarse-graining methodology.

  14. Role of short-time acoustic temporal fine structure cues in sentence recognition for normal-hearing listeners.

    Science.gov (United States)

    Hou, Limin; Xu, Li

    2018-02-01

    Short-time processing was employed to manipulate the amplitude, bandwidth, and temporal fine structure (TFS) in sentences. Fifty-two native-English-speaking, normal-hearing listeners participated in four sentence-recognition experiments. Results showed that recovered envelope (E) played an important role in speech recognition when the bandwidth was > 1 equivalent rectangular bandwidth. Removing TFS drastically reduced sentence recognition. Preserving TFS greatly improved sentence recognition when amplitude information was available at a rate ≥ 10 Hz (i.e., time segment ≤ 100 ms). Therefore, the short-time TFS facilitates speech perception together with the recovered E and works with the coarse amplitude cues to provide useful information for speech recognition.

  15. UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics.

    Science.gov (United States)

    Czaplewski, Cezary; Karczynska, Agnieszka; Sieradzan, Adam K; Liwo, Adam

    2018-04-30

    A server implementation of the UNRES package (http://www.unres.pl) for coarse-grained simulations of protein structures with the physics-based UNRES model, coined a name UNRES server, is presented. In contrast to most of the protein coarse-grained models, owing to its physics-based origin, the UNRES force field can be used in simulations, including those aimed at protein-structure prediction, without ancillary information from structural databases; however, the implementation includes the possibility of using restraints. Local energy minimization, canonical molecular dynamics simulations, replica exchange and multiplexed replica exchange molecular dynamics simulations can be run with the current UNRES server; the latter are suitable for protein-structure prediction. The user-supplied input includes protein sequence and, optionally, restraints from secondary-structure prediction or small x-ray scattering data, and simulation type and parameters which are selected or typed in. Oligomeric proteins, as well as those containing D-amino-acid residues and disulfide links can be treated. The output is displayed graphically (minimized structures, trajectories, final models, analysis of trajectory/ensembles); however, all output files can be downloaded by the user. The UNRES server can be freely accessed at http://unres-server.chem.ug.edu.pl.

  16. Combining an Elastic Network With a Coarse-Grained Molecular Force Field : Structure, Dynamics, and Intermolecular Recognition

    NARCIS (Netherlands)

    Periole, Xavier; Cavalli, Marco; Marrink, Siewert-Jan; Ceruso, Marco A.

    Structure-based and physics-based coarse-grained molecular force fields have become attractive approaches to gain mechanistic insight into the function of large biomolecular assemblies. Here, we study how both approaches can be combined into a single representation, that we term ELNEDIN. In this

  17. GARN2: coarse-grained prediction of 3D structure of large RNA molecules by regret minimization.

    Science.gov (United States)

    Boudard, Mélanie; Barth, Dominique; Bernauer, Julie; Denise, Alain; Cohen, Johanne

    2017-08-15

    Predicting the 3D structure of RNA molecules is a key feature towards predicting their functions. Methods which work at atomic or nucleotide level are not suitable for large molecules. In these cases, coarse-grained prediction methods aim to predict a shape which could be refined later by using more precise methods on smaller parts of the molecule. We developed a complete method for sampling 3D RNA structure at a coarse-grained model, taking a secondary structure as input. One of the novelties of our method is that a second step extracts two best possible structures close to the native, from a set of possible structures. Although our method benefits from the first version of GARN, some of the main features on GARN2 are very different. GARN2 is much faster than the previous version and than the well-known methods of the state-of-art. Our experiments show that GARN2 can also provide better structures than the other state-of-the-art methods. GARN2 is written in Java. It is freely distributed and available at http://garn.lri.fr/. melanie.boudard@lri.fr or johanne.cohen@lri.fr. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  18. Temporal structures in shell models

    DEFF Research Database (Denmark)

    Okkels, F.

    2001-01-01

    The intermittent dynamics of the turbulent Gledzer, Ohkitani, and Yamada shell-model is completely characterized by a single type of burstlike structure, which moves through the shells like a front. This temporal structure is described by the dynamics of the instantaneous configuration of the shell...

  19. Fundamental Study on the Development of Structural Lightweight Concrete by Using Normal Coarse Aggregate and Foaming Agent

    Science.gov (United States)

    Lee, Han-Seung; Ismail, Mohamed A.; Woo, Young-Je; Min, Tae-Beom; Choi, Hyun-Kook

    2014-01-01

    Structural lightweight concrete (SLWC) has superior properties that allow the optimization of super tall structure systems for the process of design. Because of the limited supply of lightweight aggregates in Korea, the development of structural lightweight concrete without lightweight aggregates is needed. The physical and mechanical properties of specimens that were cast using normal coarse aggregates and different mixing ratios of foaming agent to evaluate the possibility of creating structural lightweight concrete were investigated. The results show that the density of SLWC decreases as the dosage of foaming agent increases up to a dosage of 0.6%, as observed by SEM. It was also observed that the foaming agent induced well separated pores, and that the size of the pores ranged from 50 to 100 μm. Based on the porosity of concrete specimens with foaming agent, compressive strength values of structural lightweight foam concrete (SLWFC) were obtained. It was also found that the estimated values from proposed equations for compressive strength and modulus of elasticity of SLWFC, and values obtained by actual measurements were in good agreement. Thus, this study confirms that new structural lightweight concrete using normal coarse aggregates and foaming agent can be developed successfully. PMID:28788691

  20. Modeling Temporal Evolution and Multiscale Structure in Networks

    DEFF Research Database (Denmark)

    Herlau, Tue; Mørup, Morten; Schmidt, Mikkel Nørgaard

    2013-01-01

    Many real-world networks exhibit both temporal evolution and multiscale structure. We propose a model for temporally correlated multifurcating hierarchies in complex networks which jointly capture both effects. We use the Gibbs fragmentation tree as prior over multifurcating trees and a change......-point model to account for the temporal evolution of each vertex. We demonstrate that our model is able to infer time-varying multiscale structure in synthetic as well as three real world time-evolving complex networks. Our modeling of the temporal evolution of hierarchies brings new insights...

  1. Effects of creating two forest structures and using prescribed fire on coarse woody debris in northeastern California, USA

    Science.gov (United States)

    Fabian C. C. Uzoh; Carl N. Skinner

    2009-01-01

    Little is known about the dynamics of coarse woody debris (CWD) in forests that were originally characterized by frequent, low-moderate intensity fires. We investigated effects of prescribed burning at the Blacks Mountain Experimental Forest in northeastern California following creation of two stand structure conditions: 1) high structural diversity (HiD) that included...

  2. Sensitivity to Temporal Reward Structure in Amygdala Neurons

    OpenAIRE

    Bermudez, Maria A.; Göbel, Carl; Schultz, Wolfram

    2012-01-01

    Summary The time of reward and the temporal structure of reward occurrence fundamentally influence behavioral reinforcement and decision processes [1–11]. However, despite knowledge about timing in sensory and motor systems [12–17], we know little about temporal mechanisms of neuronal reward processing. In this experiment, visual stimuli predicted different instantaneous probabilities of reward occurrence that resulted in specific temporal reward structures. Licking behavior demonstrated that...

  3. Dynamics in coarse-grained models for oligomer-grafted silica nanoparticles

    KAUST Repository

    Hong, Bingbing

    2012-01-01

    Coarse-grained models of poly(ethylene oxide) oligomer-grafted nanoparticles are established by matching their structural distribution functions to atomistic simulation data. Coarse-grained force fields for bulk oligomer chains show excellent transferability with respect to chain lengths and temperature, but structure and dynamics of grafted nanoparticle systems exhibit a strong dependence on the core-core interactions. This leads to poor transferability of the core potential to conditions different from the state point at which the potential was optimized. Remarkably, coarse graining of grafted nanoparticles can either accelerate or slowdown the core motions, depending on the length of the grafted chains. This stands in sharp contrast to linear polymer systems, for which coarse graining always accelerates the dynamics. Diffusivity data suggest that the grafting topology is one cause of slower motions of the cores for short-chain oligomer-grafted nanoparticles; an estimation based on transition-state theory shows the coarse-grained core-core potential also has a slowing-down effect on the nanoparticle organic hybrid materials motions; both effects diminish as grafted chains become longer. © 2012 American Institute of Physics.

  4. The role of temporal structure in human vision.

    Science.gov (United States)

    Blake, Randolph; Lee, Sang-Hun

    2005-03-01

    Gestalt psychologists identified several stimulus properties thought to underlie visual grouping and figure/ground segmentation, and among those properties was common fate: the tendency to group together individual objects that move together in the same direction at the same speed. Recent years have witnessed an upsurge of interest in visual grouping based on other time-dependent sources of visual information, including synchronized changes in luminance, in motion direction, and in figure/ ground relations. These various sources of temporal grouping information can be subsumed under the rubric temporal structure. In this article, the authors review evidence bearing on the effectiveness of temporal structure in visual grouping. They start with an overview of evidence bearing on temporal acuity of human vision, covering studies dealing with temporal integration and temporal differentiation. They then summarize psychophysical studies dealing with figure/ground segregation based on temporal phase differences in deterministic and stochastic events. The authors conclude with a brief discussion of neurophysiological implications of these results.

  5. Temporal and Statistical Information in Causal Structure Learning

    Science.gov (United States)

    McCormack, Teresa; Frosch, Caren; Patrick, Fiona; Lagnado, David

    2015-01-01

    Three experiments examined children's and adults' abilities to use statistical and temporal information to distinguish between common cause and causal chain structures. In Experiment 1, participants were provided with conditional probability information and/or temporal information and asked to infer the causal structure of a 3-variable mechanical…

  6. An analytical coarse-graining method which preserves the free energy, structural correlations, and thermodynamic state of polymer melts from the atomistic to the mesoscale.

    Science.gov (United States)

    McCarty, J; Clark, A J; Copperman, J; Guenza, M G

    2014-05-28

    Structural and thermodynamic consistency of coarse-graining models across multiple length scales is essential for the predictive role of multi-scale modeling and molecular dynamic simulations that use mesoscale descriptions. Our approach is a coarse-grained model based on integral equation theory, which can represent polymer chains at variable levels of chemical details. The model is analytical and depends on molecular and thermodynamic parameters of the system under study, as well as on the direct correlation function in the k → 0 limit, c0. A numerical solution to the PRISM integral equations is used to determine c0, by adjusting the value of the effective hard sphere diameter, dHS, to agree with the predicted equation of state. This single quantity parameterizes the coarse-grained potential, which is used to perform mesoscale simulations that are directly compared with atomistic-level simulations of the same system. We test our coarse-graining formalism by comparing structural correlations, isothermal compressibility, equation of state, Helmholtz and Gibbs free energies, and potential energy and entropy using both united atom and coarse-grained descriptions. We find quantitative agreement between the analytical formalism for the thermodynamic properties, and the results of Molecular Dynamics simulations, independent of the chosen level of representation. In the mesoscale description, the potential energy of the soft-particle interaction becomes a free energy in the coarse-grained coordinates which preserves the excess free energy from an ideal gas across all levels of description. The structural consistency between the united-atom and mesoscale descriptions means the relative entropy between descriptions has been minimized without any variational optimization parameters. The approach is general and applicable to any polymeric system in different thermodynamic conditions.

  7. Action Recognition by Joint Spatial-Temporal Motion Feature

    Directory of Open Access Journals (Sweden)

    Weihua Zhang

    2013-01-01

    Full Text Available This paper introduces a method for human action recognition based on optical flow motion features extraction. Automatic spatial and temporal alignments are combined together in order to encourage the temporal consistence on each action by an enhanced dynamic time warping (DTW algorithm. At the same time, a fast method based on coarse-to-fine DTW constraint to improve computational performance without reducing accuracy is induced. The main contributions of this study include (1 a joint spatial-temporal multiresolution optical flow computation method which can keep encoding more informative motion information than recent proposed methods, (2 an enhanced DTW method to improve temporal consistence of motion in action recognition, and (3 coarse-to-fine DTW constraint on motion features pyramids to speed up recognition performance. Using this method, high recognition accuracy is achieved on different action databases like Weizmann database and KTH database.

  8. Recognition memory is improved by a structured temporal framework during encoding

    Directory of Open Access Journals (Sweden)

    Sathesan eThavabalasingam

    2016-01-01

    Full Text Available In order to function optimally within our environment, we continuously extract temporal patterns from our experiences and formulate expectations that facilitate adaptive behavior. Given that our memories are embedded within spatiotemporal contexts, an intriguing possibility is that mnemonic processes are sensitive to the temporal structure of events. To test this hypothesis, in a series of behavioral experiments we manipulated the regularity of interval durations at encoding to create temporally structured and unstructured frameworks. Our findings revealed enhanced recognition memory (d’ for stimuli that were explicitly encoded within a temporally structured versus unstructured framework. Encoding information within a temporally structured framework was also associated with a reduction in the negative effects of proactive interference and was linked to greater recollective recognition memory. Furthermore, rhythmic temporal structure was found to enhance recognition memory for incidentally encoded information. Collectively, these results support the possibility that we possess a greater capacity to learn and subsequently remember temporally structured information.

  9. Structural controllability and controlling centrality of temporal networks.

    Science.gov (United States)

    Pan, Yujian; Li, Xiang

    2014-01-01

    Temporal networks are such networks where nodes and interactions may appear and disappear at various time scales. With the evidence of ubiquity of temporal networks in our economy, nature and society, it's urgent and significant to focus on its structural controllability as well as the corresponding characteristics, which nowadays is still an untouched topic. We develop graphic tools to study the structural controllability as well as its characteristics, identifying the intrinsic mechanism of the ability of individuals in controlling a dynamic and large-scale temporal network. Classifying temporal trees of a temporal network into different types, we give (both upper and lower) analytical bounds of the controlling centrality, which are verified by numerical simulations of both artificial and empirical temporal networks. We find that the positive relationship between aggregated degree and controlling centrality as well as the scale-free distribution of node's controlling centrality are virtually independent of the time scale and types of datasets, meaning the inherent robustness and heterogeneity of the controlling centrality of nodes within temporal networks.

  10. Temporal Dependency and the Structure of Early Looking.

    Science.gov (United States)

    Messinger, Daniel S; Mattson, Whitney I; Todd, James Torrence; Gangi, Devon N; Myers, Nicholas D; Bahrick, Lorraine E

    2017-01-01

    Although looking time is used to assess infant perceptual and cognitive processing, little is known about the temporal structure of infant looking. To shed light on this temporal structure, 127 three-month-olds were assessed in an infant-controlled habituation procedure and presented with a pre-recorded display of a woman addressing the infant using infant-directed speech. Previous individual look durations positively predicted subsequent look durations over a six look window, suggesting a temporal dependency between successive infant looks. The previous look duration continued to predict the subsequent look duration after accounting for habituation-linked declines in look duration, and when looks were separated by an inter-trial interval in which no stimulus was displayed. Individual differences in temporal dependency, the strength of associations between consecutive look durations, are distinct from individual differences in mean infant look duration. Nevertheless, infants with stronger temporal dependency had briefer mean look durations, a potential index of stimulus processing. Temporal dependency was evident not only between individual infant looks but between the durations of successive habituation trials (total looking within a trial). Finally, temporal dependency was evident in associations between the last look at the habituation stimulus and the first look at a novel test stimulus. Thus temporal dependency was evident across multiple timescales (individual looks and trials comprised of multiple individual looks) and persisted across conditions including brief periods of no stimulus presentation and changes from a familiar to novel stimulus. Associations between consecutive look durations over multiple timescales and stimuli suggest a temporal structure of infant attention that has been largely ignored in previous work on infant looking.

  11. Predictive coarse-graining

    Energy Technology Data Exchange (ETDEWEB)

    Schöberl, Markus, E-mail: m.schoeberl@tum.de [Continuum Mechanics Group, Technical University of Munich, Boltzmannstraße 15, 85748 Garching (Germany); Zabaras, Nicholas [Institute for Advanced Study, Technical University of Munich, Lichtenbergstraße 2a, 85748 Garching (Germany); Department of Aerospace and Mechanical Engineering, University of Notre Dame, 365 Fitzpatrick Hall, Notre Dame, IN 46556 (United States); Koutsourelakis, Phaedon-Stelios [Continuum Mechanics Group, Technical University of Munich, Boltzmannstraße 15, 85748 Garching (Germany)

    2017-03-15

    We propose a data-driven, coarse-graining formulation in the context of equilibrium statistical mechanics. In contrast to existing techniques which are based on a fine-to-coarse map, we adopt the opposite strategy by prescribing a probabilistic coarse-to-fine map. This corresponds to a directed probabilistic model where the coarse variables play the role of latent generators of the fine scale (all-atom) data. From an information-theoretic perspective, the framework proposed provides an improvement upon the relative entropy method and is capable of quantifying the uncertainty due to the information loss that unavoidably takes place during the coarse-graining process. Furthermore, it can be readily extended to a fully Bayesian model where various sources of uncertainties are reflected in the posterior of the model parameters. The latter can be used to produce not only point estimates of fine-scale reconstructions or macroscopic observables, but more importantly, predictive posterior distributions on these quantities. Predictive posterior distributions reflect the confidence of the model as a function of the amount of data and the level of coarse-graining. The issues of model complexity and model selection are seamlessly addressed by employing a hierarchical prior that favors the discovery of sparse solutions, revealing the most prominent features in the coarse-grained model. A flexible and parallelizable Monte Carlo – Expectation–Maximization (MC-EM) scheme is proposed for carrying out inference and learning tasks. A comparative assessment of the proposed methodology is presented for a lattice spin system and the SPC/E water model.

  12. Temporal acceleration of spatially distributed kinetic Monte Carlo simulations

    International Nuclear Information System (INIS)

    Chatterjee, Abhijit; Vlachos, Dionisios G.

    2006-01-01

    The computational intensity of kinetic Monte Carlo (KMC) simulation is a major impediment in simulating large length and time scales. In recent work, an approximate method for KMC simulation of spatially uniform systems, termed the binomial τ-leap method, was introduced [A. Chatterjee, D.G. Vlachos, M.A. Katsoulakis, Binomial distribution based τ-leap accelerated stochastic simulation, J. Chem. Phys. 122 (2005) 024112], where molecular bundles instead of individual processes are executed over coarse-grained time increments. This temporal coarse-graining can lead to significant computational savings but its generalization to spatially lattice KMC simulation has not been realized yet. Here we extend the binomial τ-leap method to lattice KMC simulations by combining it with spatially adaptive coarse-graining. Absolute stability and computational speed-up analyses for spatial systems along with simulations provide insights into the conditions where accuracy and substantial acceleration of the new spatio-temporal coarse-graining method are ensured. Model systems demonstrate that the r-time increment criterion of Chatterjee et al. obeys the absolute stability limit for values of r up to near 1

  13. Horizontal Residual Mean Circulation: Evaluation of Spatial Correlations in Coarse Resolution Ocean Models

    Science.gov (United States)

    Li, Y.; McDougall, T. J.

    2016-02-01

    Coarse resolution ocean models lack knowledge of spatial correlations between variables on scales smaller than the grid scale. Some researchers have shown that these spatial correlations play a role in the poleward heat flux. In order to evaluate the poleward transport induced by the spatial correlations at a fixed horizontal position, an equation is obtained to calculate the approximate transport from velocity gradients. The equation involves two terms that can be added to the quasi-Stokes streamfunction (based on temporal correlations) to incorporate the contribution of spatial correlations. Moreover, these new terms do not need to be parameterized and is ready to be evaluated by using model data directly. In this study, data from a high resolution ocean model have been used to estimate the accuracy of this HRM approach for improving the horizontal property fluxes in coarse-resolution ocean models. A coarse grid is formed by sub-sampling and box-car averaging the fine grid scale. The transport calculated on the coarse grid is then compared to the transport on original high resolution grid scale accumulated over a corresponding number of grid boxes. The preliminary results have shown that the estimate on coarse resolution grids roughly match the corresponding transports on high resolution grids.

  14. A nucleobase-centered coarse-grained representation for structure prediction of RNA motifs.

    Science.gov (United States)

    Poblete, Simón; Bottaro, Sandro; Bussi, Giovanni

    2018-02-28

    We introduce the SPlit-and-conQueR (SPQR) model, a coarse-grained (CG) representation of RNA designed for structure prediction and refinement. In our approach, the representation of a nucleotide consists of a point particle for the phosphate group and an anisotropic particle for the nucleoside. The interactions are, in principle, knowledge-based potentials inspired by the $\\mathcal {E}$SCORE function, a base-centered scoring function. However, a special treatment is given to base-pairing interactions and certain geometrical conformations which are lost in a raw knowledge-based model. This results in a representation able to describe planar canonical and non-canonical base pairs and base-phosphate interactions and to distinguish sugar puckers and glycosidic torsion conformations. The model is applied to the folding of several structures, including duplexes with internal loops of non-canonical base pairs, tetraloops, junctions and a pseudoknot. For the majority of these systems, experimental structures are correctly predicted at the level of individual contacts. We also propose a method for efficiently reintroducing atomistic detail from the CG representation.

  15. Temporal variations of fine and coarse particulate matter sources in Jeddah, Saudi Arabia.

    Science.gov (United States)

    Lim, Chris C; Thurston, George D; Shamy, Magdy; Alghamdi, Mansour; Khoder, Mamdouh; Mohorjy, Abdullah M; Alkhalaf, Abdulrahman K; Brocato, Jason; Chen, Lung Chi; Costa, Max

    2018-02-01

    This study provides the first comprehensive analysis of the seasonal variations and weekday/weekend differences in fine (aerodynamic diameter Saudi Arabia. Air quality samples were collected over 1 yr, from June 2011 to May 2012 at a frequency of three times per week, and analyzed. The average mass concentrations of PM 2.5 (21.9 μg/m 3 ) and PM 10 (107.8 μg/m 3 ) during the sampling period exceeded the recommended annual average levels by the World Health Organization (WHO) for PM 2.5 (10 μg/m 3 ) and PM 10 (20 μg/m 3 ), respectively. Similar to other Middle Eastern locales, PM 2.5-10 is the prevailing mass component of atmospheric particulate matter at Jeddah, accounting for approximately 80% of the PM 10 mass. Considerations of enrichment factors, absolute principal component analysis (APCA), concentration roses, and backward trajectories identified the following source categories for both PM 2.5 and PM 2.5-10 : (1) soil/road dust, (2) incineration, and (3) traffic; and for PM 2.5 only, (4) residual oil burning. Soil/road dust accounted for a major portion of both the PM 2.5 (27%) and PM 2.5-10 (77%) mass, and the largest source contributor for PM 2.5 was from residual oil burning (63%). Temporal variations of PM 2.5-10 and PM 2.5 were observed, with the elevated concentration levels observed for mass during the spring (due to increased dust storm frequency) and on weekdays (due to increased traffic). The predominant role of windblown soil and road dust in both the PM 2.5 and PM 2.5-10 masses in this city may have implications regarding the toxicity of these particles versus those in the Western world where most PM health assessments have been made in the past. These results support the need for region-specific epidemiological investigations to be conducted and considered in future PM standard setting. Temporal variations of fine and coarse PM mass, elemental constituents, and sources were examined in Jeddah, Saudi Arabia, for the first time. The main source

  16. Balancing Structural and Temporal Constraints in Multitasking Contexts

    OpenAIRE

    Salvucci, Dario D.; Kujala, Tuomo

    2016-01-01

    Recent research has shown that when people multitask, both the subtask structure and the temporal constraints of the component tasks strongly influence people’s task-switching behavior. In this paper, we propose an integrated theoretical account and associated computational model that aims to quantify how people balance structural and temporal constraints in everyday multitasking. We validate the theory using data from an empirical study in which drivers performed a vi...

  17. Thermodynamic and structural signatures of water-driven methane-methane attraction in coarse-grained mW water.

    Science.gov (United States)

    Song, Bin; Molinero, Valeria

    2013-08-07

    Hydrophobic interactions are responsible for water-driven processes such as protein folding and self-assembly of biomolecules. Microscopic theories and molecular simulations have been used to study association of a pair of methanes in water, the paradigmatic example of hydrophobic attraction, and determined that entropy is the driving force for the association of the methane pair, while the enthalpy disfavors it. An open question is to which extent coarse-grained water models can still produce correct thermodynamic and structural signatures of hydrophobic interaction. In this work, we investigate the hydrophobic interaction between a methane pair in water at temperatures from 260 to 340 K through molecular dynamics simulations with the coarse-grained monatomic water model mW. We find that the coarse-grained model correctly represents the free energy of association of the methane pair, the temperature dependence of free energy, and the positive change in entropy and enthalpy upon association. We investigate the relationship between thermodynamic signatures and structural order of water through the analysis of the spatial distribution of the density, energy, and tetrahedral order parameter Qt of water. The simulations reveal an enhancement of tetrahedral order in the region between the first and second hydration shells of the methane molecules. The increase in tetrahedral order, however, is far from what would be expected for a clathrate-like or ice-like shell around the solutes. This work shows that the mW water model reproduces the key signatures of hydrophobic interaction without long ranged electrostatics or the need to be re-parameterized for different thermodynamic states. These characteristics, and its hundred-fold increase in efficiency with respect to atomistic models, make mW a promising water model for studying water-driven hydrophobic processes in more complex systems.

  18. Applying Ultrasonic Phased Array Technology to Examine Austenitic Coarse-Grained Structures for Light Water Reactor Piping

    International Nuclear Information System (INIS)

    Anderson, Michael T.; Cumblidge, Stephen E.; Doctor, Steven R.

    2003-01-01

    Pacific Northwest Laboratory is evaluating the capabilities and limitations of phased array (PA) technology to detect service-type flaws in coarse-grained austenitic piping structures. The work is being sponsored by the U.S. Nuclear Regulatory Commission, Office of Research. This paper presents initial work involving the use of PA technology to determine the effectiveness of detecting and accurately characterizing flaws on the far-side of austenitic piping welds

  19. Ceramic ware waste as coarse aggregate for structural concrete production.

    Science.gov (United States)

    García-González, Julia; Rodríguez-Robles, Desirée; Juan-Valdés, Andrés; Morán-Del Pozo, Julia M; Guerra-Romero, M Ignacio

    2015-01-01

    The manufacture of any kind of product inevitably entails the production of waste. The quantity of waste generated by the ceramic industry, a very important sector in Spain, is between 5% and 8% of the final output and it is therefore necessary to find an effective waste recovery method. The aim of the study reported in the present article was to seek a sustainable means of managing waste from the ceramic industry through the incorporation of this type of waste in the total replacement of conventional aggregate (gravel) used in structural concrete. Having verified that the recycled ceramic aggregates met all the technical requirements imposed by current Spanish legislation, established in the Code on Structural Concrete (EHE-08), then it is prepared a control concrete mix and the recycled concrete mix using 100% recycled ceramic aggregate instead of coarse natural aggregate. The concretes obtained were subjected to the appropriate tests in order to conduct a comparison of their mechanical properties. The results show that the concretes made using ceramic sanitary ware aggregate possessed the same mechanical properties as those made with conventional aggregate. It is therefore possible to conclude that the reuse of recycled ceramic aggregate to produce recycled concrete is a feasible alternative for the sustainable management of this waste.

  20. Functional connectivity between right and left mesial temporal structures.

    Science.gov (United States)

    Lacuey, Nuria; Zonjy, Bilal; Kahriman, Emine S; Kaffashi, Farhad; Miller, Jonathan; Lüders, Hans O

    2015-09-01

    The aim of this study is to investigate functional connectivity between right and left mesial temporal structures using cerebrocerebral evoked potentials. We studied seven patients with drug-resistant focal epilepsy who were explored with stereotactically implanted depth electrodes in bilateral hippocampi. In all patients cerebrocerebral evoked potentials evoked by stimulation of the fornix were evaluated as part of a research project assessing fornix stimulation for control of hippocampal seizures. Stimulation of the fornix elicited responses in the ipsilateral hippocampus in all patients with a mean latency of 4.6 ms (range 2-7 ms). Two patients (29 %) also had contralateral hippocampus responses with a mean latency of 7.5 ms (range 5-12 ms) and without involvement of the contralateral temporal neocortex or amygdala. This study confirms the existence of connections between bilateral mesial temporal structures in some patients and explains seizure discharge spreading between homotopic mesial temporal structures without neocortical involvement.

  1. Moving beyond Watson-Crick models of coarse grained DNA dynamics.

    Science.gov (United States)

    Linak, Margaret C; Tourdot, Richard; Dorfman, Kevin D

    2011-11-28

    DNA produces a wide range of structures in addition to the canonical B-form of double-stranded DNA. Some of these structures are stabilized by Hoogsteen bonds. We developed an experimentally parameterized, coarse-grained model that incorporates such bonds. The model reproduces many of the microscopic features of double-stranded DNA and captures the experimental melting curves for a number of short DNA hairpins, even when the open state forms complicated secondary structures. We demonstrate the utility of the model by simulating the folding of a thrombin aptamer, which contains G-quartets, and strand invasion during triplex formation. Our results highlight the importance of including Hoogsteen bonding in coarse-grained models of DNA.

  2. [The role of temporal fine structure in tone recognition and music perception].

    Science.gov (United States)

    Zhou, Q; Gu, X; Liu, B

    2017-11-07

    The sound signal can be decomposed into temporal envelope and temporal fine structure information. The temporal envelope information is crucial for speech perception in quiet environment, and the temporal fine structure information plays an important role in speech perception in noise, Mandarin tone recognition and music perception, especially the pitch and melody perception.

  3. Facile and tunable synthesis of hierarchical mesoporous silica materials ranging from flower structure with wrinkled edges to hollow structure with coarse surface

    Energy Technology Data Exchange (ETDEWEB)

    Hao, Nanjing, E-mail: nanjing.hao@dartmouth.edu [Dartmouth College, Thayer School of Engineering (United States); Li, Laifeng; Tang, Fangqiong, E-mail: tangfq@mail.ipc.ac.cn [Chinese Academy of Sciences, Technical Institute of Physics and Chemistry (China)

    2016-11-15

    Mesoporous silica materials have attracted great attention in many fields. However, facile and tunable synthesis of hierarchical mesoporous silica structures is still a big challenge, and thus the development of them still lags behind. Herein, well-defined mesoporous silica flower structure with wrinkled edges and mesoporous silica hollow structure with coarse surface were synthesized simply by using poly(vinylpyrrolidone) and hexadecylamine as cotemplates in different water/ethanol solvent systems. The shape evolution from flower to hollow can be easily realized by tuning the volume ratio of water to ethanol, and the yields of both materials can reach gram scale. The formation mechanisms of mesoporous silica flower and hollow structures were also experimentally investigated and discussed. These novel hierarchical structures having unique physicochemical properties may bring many interesting insights into scientific research and technological application.

  4. Optimal Design of Experiments by Combining Coarse and Fine Measurements

    Science.gov (United States)

    Lee, Alpha A.; Brenner, Michael P.; Colwell, Lucy J.

    2017-11-01

    In many contexts, it is extremely costly to perform enough high-quality experimental measurements to accurately parametrize a predictive quantitative model. However, it is often much easier to carry out large numbers of experiments that indicate whether each sample is above or below a given threshold. Can many such categorical or "coarse" measurements be combined with a much smaller number of high-resolution or "fine" measurements to yield accurate models? Here, we demonstrate an intuitive strategy, inspired by statistical physics, wherein the coarse measurements are used to identify the salient features of the data, while the fine measurements determine the relative importance of these features. A linear model is inferred from the fine measurements, augmented by a quadratic term that captures the correlation structure of the coarse data. We illustrate our strategy by considering the problems of predicting the antimalarial potency and aqueous solubility of small organic molecules from their 2D molecular structure.

  5. SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction.

    Science.gov (United States)

    Boniecki, Michal J; Lach, Grzegorz; Dawson, Wayne K; Tomala, Konrad; Lukasz, Pawel; Soltysinski, Tomasz; Rother, Kristian M; Bujnicki, Janusz M

    2016-04-20

    RNA molecules play fundamental roles in cellular processes. Their function and interactions with other biomolecules are dependent on the ability to form complex three-dimensional (3D) structures. However, experimental determination of RNA 3D structures is laborious and challenging, and therefore, the majority of known RNAs remain structurally uncharacterized. Here, we present SimRNA: a new method for computational RNA 3D structure prediction, which uses a coarse-grained representation, relies on the Monte Carlo method for sampling the conformational space, and employs a statistical potential to approximate the energy and identify conformations that correspond to biologically relevant structures. SimRNA can fold RNA molecules using only sequence information, and, on established test sequences, it recapitulates secondary structure with high accuracy, including correct prediction of pseudoknots. For modeling of complex 3D structures, it can use additional restraints, derived from experimental or computational analyses, including information about secondary structure and/or long-range contacts. SimRNA also can be used to analyze conformational landscapes and identify potential alternative structures. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  6. Brain activity related to working memory for temporal order and object information.

    Science.gov (United States)

    Roberts, Brooke M; Libby, Laura A; Inhoff, Marika C; Ranganath, Charan

    2017-06-08

    Maintaining items in an appropriate sequence is important for many daily activities; however, remarkably little is known about the neural basis of human temporal working memory. Prior work suggests that the prefrontal cortex (PFC) and medial temporal lobe (MTL), including the hippocampus, play a role in representing information about temporal order. The involvement of these areas in successful temporal working memory, however, is less clear. Additionally, it is unknown whether regions in the PFC and MTL support temporal working memory across different timescales, or at coarse or fine levels of temporal detail. To address these questions, participants were scanned while completing 3 working memory task conditions (Group, Position and Item) that were matched in terms of difficulty and the number of items to be actively maintained. Group and Position trials probed temporal working memory processes, requiring the maintenance of hierarchically organized coarse and fine temporal information, respectively. To isolate activation related to temporal working memory, Group and Position trials were contrasted against Item trials, which required detailed working memory maintenance of visual objects. Results revealed that working memory encoding and maintenance of temporal information relative to visual information was associated with increased activation in dorsolateral PFC (DLPFC), and perirhinal cortex (PRC). In contrast, maintenance of visual details relative to temporal information was characterized by greater activation of parahippocampal cortex (PHC), medial and anterior PFC, and retrosplenial cortex. In the hippocampus, a dissociation along the longitudinal axis was observed such that the anterior hippocampus was more active for working memory encoding and maintenance of visual detail information relative to temporal information, whereas the posterior hippocampus displayed the opposite effect. Posterior parietal cortex was the only region to show sensitivity to temporal

  7. Spatial and temporal patterns of beetles associated with coarse woody debris in managed bottomland hardwood forests.

    Energy Technology Data Exchange (ETDEWEB)

    Ulyshen, M., D.; Hanula, J., L.; Horn, S.; Kilgo, J., C.; Moorman, C., E.

    2004-05-13

    For. Ecol. and Mgt. 199:259-272. Malaise traps were used to sample beetles in artificial canopy gaps of different size (0.13 ha, 0.26 ha, and0.50 ha) and age in a South Carolina bottomland hardwood forest. Traps were placed at the center, edge, and in the surrounding forest of each gap. Young gaps (ý 1 year) had large amounts of coarse woody debris compared to the surrounding forest, while older gaps (ý 6 years) had virtually none. The total abundance and diversity of wood-dwelling beetles (Buprestidae, Cerambycidae, Brentidae, Bostrichidae, and Curculionidae (Scolytinae and Platypodinae)) was higher in the center of young gaps than in the center of old gaps. The abundance was higher in the center of young gaps than in the surrounding forest, while the forest surrounding old gaps and the edge of old gaps had a higher abundance and diversity of wood-dwelling beetles than did the center of old gaps. There was no difference in wood-dwelling beetle abundance between gaps of different size, but diversity was lower in 0.13 ha old gaps than in 0.26 ha or 0.50 ha old gaps. We suspect that gap size has more of an effect on woodborer abundance than indicated here because malaise traps sample a limited area. The predaceous beetle family Cleridae showed a very similar trend to that of the woodborers. Coarse woody debris is an important resource for many organisms, and our results lend further support to forest management practices that preserve coarse woody debris created during timber removal.

  8. Application of physical and numerical simulations for interpretation of peripheral coarse grain structure during hot extrusion of AA7020 aluminum alloy

    NARCIS (Netherlands)

    Eivani, A.R.; Zhou, J.

    2017-01-01

    In this research, hot compression test is used to simulate the metallurgical phenomena occurring in the peripheral part of AA7020 aluminum alloy extrudates during hot extrusion and leading to the formation of the peripheral coarse grain (PCG) structure. The temperature profiles at a tracking

  9. Second-order analysis of structured inhomogeneous spatio-temporal point processes

    DEFF Research Database (Denmark)

    Møller, Jesper; Ghorbani, Mohammad

    Statistical methodology for spatio-temporal point processes is in its infancy. We consider second-order analysis based on pair correlation functions and K-functions for first general inhomogeneous spatio-temporal point processes and second inhomogeneous spatio-temporal Cox processes. Assuming...... spatio-temporal separability of the intensity function, we clarify different meanings of second-order spatio-temporal separability. One is second-order spatio-temporal independence and relates e.g. to log-Gaussian Cox processes with an additive covariance structure of the underlying spatio......-temporal Gaussian process. Another concerns shot-noise Cox processes with a separable spatio-temporal covariance density. We propose diagnostic procedures for checking hypotheses of second-order spatio-temporal separability, which we apply on simulated and real data (the UK 2001 epidemic foot and mouth disease data)....

  10. Correlations of External Landmarks With Internal Structures of the Temporal Bone.

    Science.gov (United States)

    Piromchai, Patorn; Wijewickrema, Sudanthi; Smeds, Henrik; Kennedy, Gregor; O'Leary, Stephen

    2015-09-01

    The internal anatomy of a temporal bone could be inferred from external landmarks. Mastoid surgery is an important skill that ENT surgeons need to acquire. Surgeons commonly use CT scans as a guide to understanding anatomical variations before surgery. Conversely, in cases where CT scans are not available, or in the temporal bone laboratory where residents are usually not provided with CT scans, it would be beneficial if the internal anatomy of a temporal bone could be inferred from external landmarks. We explored correlations between internal anatomical variations and metrics established to quantify the position of external landmarks that are commonly exposed in the operating room, or the temporal bone laboratory, before commencement of drilling. Mathematical models were developed to predict internal anatomy based on external structures. From an operating room view, the distances between the following external landmarks were observed to have statistically significant correlations with the internal anatomy of a temporal bone: temporal line, external auditory canal, mastoid tip, occipitomastoid suture, and Henle's spine. These structures can be used to infer a low lying dura mater (p = 0.002), an anteriorly located sigmoid sinus (p = 0.006), and a more lateral course of the facial nerve (p external landmarks. The distances between these two landmarks and the operating view external structures were able to further infer the laterality of the facial nerve (p internal structures with a high level of accuracy: the distance from the sigmoid sinus to the posterior external auditory canal (p external landmarks found on the temporal bone. These relationships could be used as a guideline to predict challenges during drilling and choosing appropriate temporal bones for dissection.

  11. High speed true random number generator with a new structure of coarse-tuning PDL in FPGA

    Science.gov (United States)

    Fang, Hongzhen; Wang, Pengjun; Cheng, Xu; Zhou, Keji

    2018-03-01

    A metastability-based TRNG (true random number generator) is presented in this paper, and implemented in FPGA. The metastable state of a D flip-flop is tunable through a two-stage PDL (programmable delay line). With the proposed coarse-tuning PDL structure, the TRNG core does not require extra placement and routing to ensure its entropy. Furthermore, the core needs fewer stages of coarse-tuning PDL at higher operating frequency, and thus saves more resources in FPGA. The designed TRNG achieves 25 Mbps @ 100 MHz throughput after proper post-processing, which is several times higher than other previous TRNGs based on FPGA. Moreover, the robustness of the system is enhanced with the adoption of a feedback system. The quality of the designed TRNG is verified by NIST (National Institute of Standards and Technology) and also accepted by class P1 of the AIS-20/31 test suite. Project supported by the S&T Plan of Zhejiang Provincial Science and Technology Department (No. 2016C31078), the National Natural Science Foundation of China (Nos. 61574041, 61474068, 61234002), and the K.C. Wong Magna Fund in Ningbo University, China.

  12. NONLINEAR MULTIGRID SOLVER EXPLOITING AMGe COARSE SPACES WITH APPROXIMATION PROPERTIES

    Energy Technology Data Exchange (ETDEWEB)

    Christensen, Max La Cour [Technical Univ. of Denmark, Lyngby (Denmark); Villa, Umberto E. [Univ. of Texas, Austin, TX (United States); Engsig-Karup, Allan P. [Technical Univ. of Denmark, Lyngby (Denmark); Vassilevski, Panayot S. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2016-01-22

    The paper introduces a nonlinear multigrid solver for mixed nite element discretizations based on the Full Approximation Scheme (FAS) and element-based Algebraic Multigrid (AMGe). The main motivation to use FAS for unstruc- tured problems is the guaranteed approximation property of the AMGe coarse spaces that were developed recently at Lawrence Livermore National Laboratory. These give the ability to derive stable and accurate coarse nonlinear discretization problems. The previous attempts (including ones with the original AMGe method, [5, 11]), were less successful due to lack of such good approximation properties of the coarse spaces. With coarse spaces with approximation properties, our FAS approach on un- structured meshes should be as powerful/successful as FAS on geometrically re ned meshes. For comparison, Newton's method and Picard iterations with an inner state-of-the-art linear solver is compared to FAS on a nonlinear saddle point problem with applications to porous media ow. It is demonstrated that FAS is faster than Newton's method and Picard iterations for the experiments considered here. Due to the guaranteed approximation properties of our AMGe, the coarse spaces are very accurate, providing a solver with the potential for mesh-independent convergence on general unstructured meshes.

  13. Structure and dynamics of Ebola virus matrix protein VP40 by a coarse-grained Monte Carlo simulation

    Science.gov (United States)

    Pandey, Ras; Farmer, Barry

    Ebola virus matrix protein VP40 (consisting of 326 residues) plays a critical role in viral assembly and its functions such as regulation of viral transcription, packaging, and budding of mature virions into the plasma membrane of infected cells. How does the protein VP40 go through structural evolution during the viral life cycle remains an open question? Using a coarse-grained Monte Carlo simulation we investigate the structural evolution of VP40 as a function of temperature with the input of a knowledge-based residue-residue interaction. A number local and global physical quantities (e.g. mobility profile, contact map, radius of gyration, structure factor) are analyzed with our large-scale simulations. Our preliminary data show that the structure of the protein evolves through different state with well-defined morphologies which can be identified and quantified via a detailed analysis of structure factor.

  14. Detailed temporal structure of communication networks in groups of songbirds.

    Science.gov (United States)

    Stowell, Dan; Gill, Lisa; Clayton, David

    2016-06-01

    Animals in groups often exchange calls, in patterns whose temporal structure may be influenced by contextual factors such as physical location and the social network structure of the group. We introduce a model-based analysis for temporal patterns of animal call timing, originally developed for networks of firing neurons. This has advantages over cross-correlation analysis in that it can correctly handle common-cause confounds and provides a generative model of call patterns with explicit parameters for the influences between individuals. It also has advantages over standard Markovian analysis in that it incorporates detailed temporal interactions which affect timing as well as sequencing of calls. Further, a fitted model can be used to generate novel synthetic call sequences. We apply the method to calls recorded from groups of domesticated zebra finch (Taeniopygia guttata) individuals. We find that the communication network in these groups has stable structure that persists from one day to the next, and that 'kernels' reflecting the temporal range of influence have a characteristic structure for a calling individual's effect on itself, its partner and on others in the group. We further find characteristic patterns of influences by call type as well as by individual. © 2016 The Authors.

  15. Aspects of second-order analysis of structured inhomogeneous spatio-temporal processes

    DEFF Research Database (Denmark)

    Møller, Jesper; Ghorbani, Mohammad

    2012-01-01

    Statistical methodology for spatio-temporal point processes is in its infancy. We consider second-order analysis based on pair correlation functions and K-functions for general inhomogeneous spatio-temporal point processes and for inhomogeneous spatio-temporal Cox processes. Assuming spatio......-temporal separability of the intensity function, we clarify different meanings of second-order spatio-temporal separability. One is second-order spatio-temporal independence and relates to log-Gaussian Cox processes with an additive covariance structure of the underlying spatio-temporal Gaussian process. Another...... concerns shot-noise Cox processes with a separable spatio-temporal covariance density. We propose diagnostic procedures for checking hypotheses of second-order spatio-temporal separability, which we apply on simulated and real data....

  16. Martini Coarse-Grained Force Field : Extension to RNA

    NARCIS (Netherlands)

    Uusitalo, Jaakko J.; Ingolfsson, Helgi I.; Marrink, Siewert J.; Faustino, Ignacio

    2017-01-01

    RNA has an important role not only as the messenger of genetic information but also as a regulator of gene expression. Given its central role in cell biology, there is significant interest in studying the structural and dynamic behavior of RNA in relation to other biomolecules. Coarse-grain

  17. Introducing improved structural properties and salt dependence into a coarse-grained model of DNA

    Energy Technology Data Exchange (ETDEWEB)

    Snodin, Benedict E. K., E-mail: benedict.snodin@chem.ox.ac.uk; Mosayebi, Majid; Schreck, John S.; Romano, Flavio; Doye, Jonathan P. K., E-mail: jonathan.doye@chem.ox.ac.uk [Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ (United Kingdom); Randisi, Ferdinando [Life Sciences Interface Doctoral Training Center, South Parks Road, Oxford OX1 3QU (United Kingdom); Rudolf Peierls Centre for Theoretical Physics, 1 Keble Road, Oxford OX1 3NP (United Kingdom); Šulc, Petr [Center for Studies in Physics and Biology, The Rockefeller University, 1230 York Avenue, New York, New York 10065 (United States); Ouldridge, Thomas E. [Department of Mathematics, Imperial College, 180 Queen’s Gate, London SW7 2AZ (United Kingdom); Tsukanov, Roman; Nir, Eyal [Department of Chemistry and the Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva (Israel); Louis, Ard A. [Rudolf Peierls Centre for Theoretical Physics, 1 Keble Road, Oxford OX1 3NP (United Kingdom)

    2015-06-21

    We introduce an extended version of oxDNA, a coarse-grained model of deoxyribonucleic acid (DNA) designed to capture the thermodynamic, structural, and mechanical properties of single- and double-stranded DNA. By including explicit major and minor grooves and by slightly modifying the coaxial stacking and backbone-backbone interactions, we improve the ability of the model to treat large (kilobase-pair) structures, such as DNA origami, which are sensitive to these geometric features. Further, we extend the model, which was previously parameterised to just one salt concentration ([Na{sup +}] = 0.5M), so that it can be used for a range of salt concentrations including those corresponding to physiological conditions. Finally, we use new experimental data to parameterise the oxDNA potential so that consecutive adenine bases stack with a different strength to consecutive thymine bases, a feature which allows a more accurate treatment of systems where the flexibility of single-stranded regions is important. We illustrate the new possibilities opened up by the updated model, oxDNA2, by presenting results from simulations of the structure of large DNA objects and by using the model to investigate some salt-dependent properties of DNA.

  18. Introducing improved structural properties and salt dependence into a coarse-grained model of DNA

    International Nuclear Information System (INIS)

    Snodin, Benedict E. K.; Mosayebi, Majid; Schreck, John S.; Romano, Flavio; Doye, Jonathan P. K.; Randisi, Ferdinando; Šulc, Petr; Ouldridge, Thomas E.; Tsukanov, Roman; Nir, Eyal; Louis, Ard A.

    2015-01-01

    We introduce an extended version of oxDNA, a coarse-grained model of deoxyribonucleic acid (DNA) designed to capture the thermodynamic, structural, and mechanical properties of single- and double-stranded DNA. By including explicit major and minor grooves and by slightly modifying the coaxial stacking and backbone-backbone interactions, we improve the ability of the model to treat large (kilobase-pair) structures, such as DNA origami, which are sensitive to these geometric features. Further, we extend the model, which was previously parameterised to just one salt concentration ([Na + ] = 0.5M), so that it can be used for a range of salt concentrations including those corresponding to physiological conditions. Finally, we use new experimental data to parameterise the oxDNA potential so that consecutive adenine bases stack with a different strength to consecutive thymine bases, a feature which allows a more accurate treatment of systems where the flexibility of single-stranded regions is important. We illustrate the new possibilities opened up by the updated model, oxDNA2, by presenting results from simulations of the structure of large DNA objects and by using the model to investigate some salt-dependent properties of DNA

  19. Detecting settlement expansion using hyper-temporal SAR time-series

    CSIR Research Space (South Africa)

    Kleynhans, W

    2014-07-01

    Full Text Available The detection of new informal settlements in South Africa using time-series data derived from coarse resolution satellite imagery has recently been an active area of research. Most of the previous methods presented using hyper-temporal satellite...

  20. How coarse is too coarse for salmon spawning substrates?

    Science.gov (United States)

    Wooster, J. K.; Riebe, C. S.; Ligon, F. K.; Overstreet, B. T.

    2009-12-01

    Populations of Pacific salmon species have declined sharply in many rivers of the western US. Reversing these declines is a top priority and expense of many river restoration projects. To help restore salmon populations, managers often inject gravel into rivers, to supplement spawning habitat that has been depleted by gravel mining and the effects of dams—which block sediment and thus impair habitat downstream by coarsening the bed where salmon historically spawned. However, there is little quantitative understanding nor a methodology for determining when a river bed has become too coarse for salmon spawning. Hence there is little scientific basis for selecting sites that would optimize the restoration benefits of gravel injection (e.g., sites where flow velocities are suitable but bed materials are too coarse for spawning). To develop a quantitative understanding of what makes river beds too coarse for salmon spawning, we studied redds and spawning use in a series of California and Washington rivers where salmon spawning ability appears to be affected by coarse bed material. Our working hypothesis is that for a given flow condition, there is a maximum “threshold” particle size that a salmon of a given size is able to excavate and/or move as she builds her redd. A second, related hypothesis is that spawning use should decrease and eventually become impossible with increasing percent coverage by immovable particles. To test these hypotheses, we quantified the sizes and spatial distributions of immovably coarse particles in a series of salmon redds in each river during the peak of spawning. We also quantified spawning use and how it relates to percent coverage by immovable particles. Results from our studies of fall-run chinook salmon (Oncorhynchus tshawytsha) in the Feather River suggest that immovable particle size varies as a function of flow velocity over the redd, implying that faster water helps fish move bigger particles. Our Feather River study also

  1. Verbal memory after temporal lobe epilepsy surgery in children: Do only mesial structures matter?

    Science.gov (United States)

    Law, Nicole; Benifla, Mony; Rutka, James; Smith, Mary Lou

    2017-02-01

    Previous findings have been mixed regarding verbal memory outcome after left temporal lobectomy in children, and there are few studies comparing verbal memory change after lateral versus mesial temporal lobe resections. We compared verbal memory outcome associated with sparing or including the mesial structures in children who underwent left or right temporal lobe resection. We also investigated predictors of postsurgical verbal memory change. We retrospectively assessed verbal memory change approximately 1 year after unilateral temporal lobe epilepsy surgery using a list learning task. Participants included 23 children who underwent temporal lobe surgery with sparing of the mesial structures (13 left), and 40 children who had a temporal lobectomy that included resection of mesial structures (22 left). Children who underwent resection from the left lateral and mesial temporal lobe were the only group to show decline in verbal memory. Furthermore, when we considered language representation in the left temporal resection group, patients with left language representation and spared mesial structures showed essentially no change in verbal memory from preoperative to follow-up, whereas those with left language representation and excised mesial structures showed a decline. Postoperative seizure status had no effect on verbal memory change in children after left temporal lobe surgery. Finally, we found that patients with intact preoperative verbal memory experienced a significant decline compared to those with below average preoperative verbal memory. Our findings provide evidence of significant risk factors for verbal memory decline in children, specific to left mesial temporal lobe epilepsy. Children who undergo left temporal lobe surgery that includes mesial structures may be most vulnerable for verbal memory decline, especially when language representation is localized to the left hemisphere and when preoperative verbal memory is intact. Wiley Periodicals, Inc.

  2. Influence of grain structure on the deformation mechanism in martensitic shear reversion-induced Fe-16Cr-10Ni model austenitic alloy with low interstitial content: Coarse-grained versus nano-grained/ultrafine-grained structure

    Energy Technology Data Exchange (ETDEWEB)

    Challa, V.S.A. [Laboratory for Excellence in Advanced Steel Research, Department of Metallurgical, Materials Engineering, and Biomedical Engineering, University of Texas at El Paso, El Paso, TX 79968 (United States); Misra, R.D.K., E-mail: dmisra2@utep.edu [Laboratory for Excellence in Advanced Steel Research, Department of Metallurgical, Materials Engineering, and Biomedical Engineering, University of Texas at El Paso, El Paso, TX 79968 (United States); Somani, M.C. [Center for Advanced Steels Research, The University of Oulu, P.O. Box 4200, 90014 Oulu (Finland); Wang, Z.D. [State Key Laboratory for Rolling and Automation, Northeastern University, 3-11 Wenhua Road, Shenyang 110819 (China)

    2016-04-20

    Nanograined/ultrafine-grained (NG/UFG) materials characterized by high strength-high ductility combination are excellent vehicles to obtain an unambiguous understanding of deformation mechanisms vis-à-vis their coarse-grained counterparts. In this context, the innovative concept of phase reversion-induced NG/UFG structure enabled achieving high strength besides comparable ductility, for instance, in metastable austenitic stainless steels. In the phase reversion process, severe deformation of austenite at room temperature (typically ~60–80%) transforms face-centered cubic austenite (γ) to body centered cubic martensite (α′). Upon annealing, martensite reverts to austenite leading to extensive grain refinement. The objective of the present study to fundamentally understand the deformation mechanisms in NG/UFG structure in relation to that of the coarse-grained (CG) structure was accomplished by combining depth-sensing nanoscale experiments on an Fe-16Cr-10Ni model austenitic alloy conducted at different strain rates, followed by the study of structural evolution in the deformed zone using transmission electron microscopy (TEM). In the high strength NG/UFG steel (YS~585 MPa), stacking faults and nanotwins contributed to the enhanced ductility (El~35%), while in the case of low strength (YS~260 MPa) coarse-grained (CG) counterpart, ductility was also high (El~40%), but chiefly due to strain-induced martensite, which points to a clear case of grain size effect (and the corresponding level of strength). The distinct change in the deformation mechanism from stacking faults and twinning-induced plasticity (TWIP) in the NG structure to transformation-induced plasticity (TRIP) in the CG structure is elucidated in terms of austenite stability-strain energy relationship. The insights on the relationship between grain structure (and strength) and deformation mechanisms are envisaged to be important in providing a new direction for the futuristic design of high strength

  3. Calibration and validation of coarse-grained models of atomic systems: application to semiconductor manufacturing

    Science.gov (United States)

    Farrell, Kathryn; Oden, J. Tinsley

    2014-07-01

    methods through applications to representative atomic structures and we discuss extensions to the validation process for molecular models of polymer structures encountered in certain semiconductor nanomanufacturing processes. The powerful method of model plausibility as a means for selecting interaction potentials for coarse-grained models is discussed in connection with a coarse-grained hexane molecule. Discussions of how all-atom information is used to construct priors are contained in an appendix.

  4. Coarse-grained forms for equations describing the microscopic motion of particles in a fluid.

    Science.gov (United States)

    Das, Shankar P; Yoshimori, Akira

    2013-10-01

    Exact equations of motion for the microscopically defined collective density ρ(x,t) and the momentum density ĝ(x,t) of a fluid have been obtained in the past starting from the corresponding Langevin equations representing the dynamics of the fluid particles. In the present work we average these exact equations of microscopic dynamics over the local equilibrium distribution to obtain stochastic partial differential equations for the coarse-grained densities with smooth spatial and temporal dependence. In particular, we consider Dean's exact balance equation for the microscopic density of a system of interacting Brownian particles to obtain the basic equation of the dynamic density functional theory with noise. Our analysis demonstrates that on thermal averaging the dependence of the exact equations on the bare interaction potential is converted to dependence on the corresponding thermodynamic direct correlation functions in the coarse-grained equations.

  5. Vertical Subsurface Flow Mixing and Horizontal Anisotropy in Coarse Fluvial Aquifers: Structural Aspects

    Science.gov (United States)

    Huggenberger, P.; Huber, E.

    2014-12-01

    Detailed descriptions of the subsurface heterogeneities in coarse fluvial aquifer gravel often lack in concepts to distinguish between the essence and the noise of a permeability structure and the ability to extrapolate site specific hydraulic information at the tens to several hundred meters scale. At this scale the heterogeneity strongly influences the anisotropies of the flow field and the mixing processes in groundwater. However, in many hydrogeological models the complexity of natural systems is oversimplified. Understanding the link between the dynamics of the surface processes of braided-river systems and the resulting subsurface sedimentary structures is the key to characterizing the complexity of horizontal and vertical mixing processes in groundwater. From the different depositional elements of coarse braided-river systems, the largest permeability contrasts can be observed in the scour-fills. Other elements (e.g. different types of gravel sheets) show much smaller variabilities and could be considered as a kind of matrix. Field experiments on the river Tagliamento (Northeast Italy) based on morphological observation and ground-penetrating radar (GPR) surveys, as well as outcrop analyses of gravel pit exposures (Switzerland) allowed us to define the shape, sizes, spatial distribution and preservation potential of scour-fills. In vertical sections (e.g. 2D GPR data, vertical outcrop), the spatial density of remnant erosional bounding surfaces of scours is an indicator for the dynamics of the braided-river system (lateral mobility of the active floodplain, rate of sediment net deposition and spatial distribution of the confluence scours). In case of combined low aggradation rate and low lateral mobility the deposits may be dominated by a complex overprinting of scour-fills. The delineation of the erosional bounding surfaces, that are coherent over the survey area, is based on the identification of angular discontinuities of the reflectors. Fence diagrams

  6. FROM ATOMISTIC TO SYSTEMATIC COARSE-GRAINED MODELS FOR MOLECULAR SYSTEMS

    KAUST Repository

    Harmandaris, Vagelis

    2017-10-03

    The development of systematic (rigorous) coarse-grained mesoscopic models for complex molecular systems is an intense research area. Here we first give an overview of methods for obtaining optimal parametrized coarse-grained models, starting from detailed atomistic representation for high dimensional molecular systems. Different methods are described based on (a) structural properties (inverse Boltzmann approaches), (b) forces (force matching), and (c) path-space information (relative entropy). Next, we present a detailed investigation concerning the application of these methods in systems under equilibrium and non-equilibrium conditions. Finally, we present results from the application of these methods to model molecular systems.

  7. ASSIMILATION OF COARSE-SCALEDATAUSINGTHE ENSEMBLE KALMAN FILTER

    KAUST Repository

    Efendiev, Yalchin

    2011-01-01

    Reservoir data is usually scale dependent and exhibits multiscale features. In this paper we use the ensemble Kalman filter (EnKF) to integrate data at different spatial scales for estimating reservoir fine-scale characteristics. Relationships between the various scales is modeled via upscaling techniques. We propose two versions of the EnKF to assimilate the multiscale data, (i) where all the data are assimilated together and (ii) the data are assimilated sequentially in batches. Ensemble members obtained after assimilating one set of data are used as a prior to assimilate the next set of data. Both of these versions are easily implementable with any other upscaling which links the fine to the coarse scales. The numerical results with different methods are presented in a twin experiment setup using a two-dimensional, two-phase (oil and water) flow model. Results are shown with coarse-scale permeability and coarse-scale saturation data. They indicate that additional data provides better fine-scale estimates and fractional flow predictions. We observed that the two versions of the EnKF differed in their estimates when coarse-scale permeability is provided, whereas their results are similar when coarse-scale saturation is used. This behavior is thought to be due to the nonlinearity of the upscaling operator in the case of the former data. We also tested our procedures with various precisions of the coarse-scale data to account for the inexact relationship between the fine and coarse scale data. As expected, the results show that higher precision in the coarse-scale data yielded improved estimates. With better coarse-scale modeling and inversion techniques as more data at multiple coarse scales is made available, the proposed modification to the EnKF could be relevant in future studies.

  8. Measuring Crack Length in Coarse Grain Ceramics

    Science.gov (United States)

    Salem, Jonathan A.; Ghosn, Louis J.

    2010-01-01

    Due to a coarse grain structure, crack lengths in precracked spinel specimens could not be measured optically, so the crack lengths and fracture toughness were estimated by strain gage measurements. An expression was developed via finite element analysis to correlate the measured strain with crack length in four-point flexure. The fracture toughness estimated by the strain gaged samples and another standardized method were in agreement.

  9. Multiresolution Modeling of Semidilute Polymer Solutions: Coarse-Graining Using Wavelet-Accelerated Monte Carlo

    Directory of Open Access Journals (Sweden)

    Animesh Agarwal

    2017-09-01

    Full Text Available We present a hierarchical coarse-graining framework for modeling semidilute polymer solutions, based on the wavelet-accelerated Monte Carlo (WAMC method. This framework forms a hierarchy of resolutions to model polymers at length scales that cannot be reached via atomistic or even standard coarse-grained simulations. Previously, it was applied to simulations examining the structure of individual polymer chains in solution using up to four levels of coarse-graining (Ismail et al., J. Chem. Phys., 2005, 122, 234901 and Ismail et al., J. Chem. Phys., 2005, 122, 234902, recovering the correct scaling behavior in the coarse-grained representation. In the present work, we extend this method to the study of polymer solutions, deriving the bonded and non-bonded potentials between coarse-grained superatoms from the single chain statistics. A universal scaling function is obtained, which does not require recalculation of the potentials as the scale of the system is changed. To model semi-dilute polymer solutions, we assume the intermolecular potential between the coarse-grained beads to be equal to the non-bonded potential, which is a reasonable approximation in the case of semidilute systems. Thus, a minimal input of microscopic data is required for simulating the systems at the mesoscopic scale. We show that coarse-grained polymer solutions can reproduce results obtained from the more detailed atomistic system without a significant loss of accuracy.

  10. Characterizing protein conformations by correlation analysis of coarse-grained contact matrices

    Science.gov (United States)

    Lindsay, Richard J.; Siess, Jan; Lohry, David P.; McGee, Trevor S.; Ritchie, Jordan S.; Johnson, Quentin R.; Shen, Tongye

    2018-01-01

    We have developed a method to capture the essential conformational dynamics of folded biopolymers using statistical analysis of coarse-grained segment-segment contacts. Previously, the residue-residue contact analysis of simulation trajectories was successfully applied to the detection of conformational switching motions in biomolecular complexes. However, the application to large protein systems (larger than 1000 amino acid residues) is challenging using the description of residue contacts. Also, the residue-based method cannot be used to compare proteins with different sequences. To expand the scope of the method, we have tested several coarse-graining schemes that group a collection of consecutive residues into a segment. The definition of these segments may be derived from structural and sequence information, while the interaction strength of the coarse-grained segment-segment contacts is a function of the residue-residue contacts. We then perform covariance calculations on these coarse-grained contact matrices. We monitored how well the principal components of the contact matrices is preserved using various rendering functions. The new method was demonstrated to assist the reduction of the degrees of freedom for describing the conformation space, and it potentially allows for the analysis of a system that is approximately tenfold larger compared with the corresponding residue contact-based method. This method can also render a family of similar proteins into the same conformational space, and thus can be used to compare the structures of proteins with different sequences.

  11. Hierarchical organization in the temporal structure of infant-direct speech and song.

    Science.gov (United States)

    Falk, Simone; Kello, Christopher T

    2017-06-01

    Caregivers alter the temporal structure of their utterances when talking and singing to infants compared with adult communication. The present study tested whether temporal variability in infant-directed registers serves to emphasize the hierarchical temporal structure of speech. Fifteen German-speaking mothers sang a play song and told a story to their 6-months-old infants, or to an adult. Recordings were analyzed using a recently developed method that determines the degree of nested clustering of temporal events in speech. Events were defined as peaks in the amplitude envelope, and clusters of various sizes related to periods of acoustic speech energy at varying timescales. Infant-directed speech and song clearly showed greater event clustering compared with adult-directed registers, at multiple timescales of hundreds of milliseconds to tens of seconds. We discuss the relation of this newly discovered acoustic property to temporal variability in linguistic units and its potential implications for parent-infant communication and infants learning the hierarchical structures of speech and language. Copyright © 2017 Elsevier B.V. All rights reserved.

  12. Spatial and temporal patterns of beetles associated with coarse woody debris in managed bottomland hardwood forests

    Science.gov (United States)

    Michael D. Ulyshen; James L. Hanula; Scott Horn; John C. Kilgo; Christopher E. Moorman

    2004-01-01

    Malaise traps were used to sample beetles in artificial canopy gaps of different size (0.13 ha, 0.26 ha, and 0.50 ha) and age in a South Carolina bottomland hardwood forest. Traps were placed at the center, edge, and in the surrounding forest of each gap. Young gaps (~1 year) had large amounts of coarse woody debris compared to the surrounding forest, while older gaps...

  13. Musical intervention enhances infants' neural processing of temporal structure in music and speech.

    Science.gov (United States)

    Zhao, T Christina; Kuhl, Patricia K

    2016-05-10

    Individuals with music training in early childhood show enhanced processing of musical sounds, an effect that generalizes to speech processing. However, the conclusions drawn from previous studies are limited due to the possible confounds of predisposition and other factors affecting musicians and nonmusicians. We used a randomized design to test the effects of a laboratory-controlled music intervention on young infants' neural processing of music and speech. Nine-month-old infants were randomly assigned to music (intervention) or play (control) activities for 12 sessions. The intervention targeted temporal structure learning using triple meter in music (e.g., waltz), which is difficult for infants, and it incorporated key characteristics of typical infant music classes to maximize learning (e.g., multimodal, social, and repetitive experiences). Controls had similar multimodal, social, repetitive play, but without music. Upon completion, infants' neural processing of temporal structure was tested in both music (tones in triple meter) and speech (foreign syllable structure). Infants' neural processing was quantified by the mismatch response (MMR) measured with a traditional oddball paradigm using magnetoencephalography (MEG). The intervention group exhibited significantly larger MMRs in response to music temporal structure violations in both auditory and prefrontal cortical regions. Identical results were obtained for temporal structure changes in speech. The intervention thus enhanced temporal structure processing not only in music, but also in speech, at 9 mo of age. We argue that the intervention enhanced infants' ability to extract temporal structure information and to predict future events in time, a skill affecting both music and speech processing.

  14. Single Particulate SEM-EDX Analysis of Iron-Containing Coarse Particulate Matter in an Urban Environment: Sources and Distribution of Iron within Cleveland, Ohio

    Science.gov (United States)

    The physicochemical properties of coarse-mode, iron-containing particles, and their temporal and spatial distributions are poorly understood. Single particle analysis combining x-ray elemental mapping and computer-controlled scanning electron microscopy (CCSEM-EDX) of passively ...

  15. Coarse graining for synchronization in directed networks

    Science.gov (United States)

    Zeng, An; Lü, Linyuan

    2011-05-01

    Coarse-graining model is a promising way to analyze and visualize large-scale networks. The coarse-grained networks are required to preserve statistical properties as well as the dynamic behaviors of the initial networks. Some methods have been proposed and found effective in undirected networks, while the study on coarse-graining directed networks lacks of consideration. In this paper we proposed a path-based coarse-graining (PCG) method to coarse grain the directed networks. Performing the linear stability analysis of synchronization and numerical simulation of the Kuramoto model on four kinds of directed networks, including tree networks and variants of Barabási-Albert networks, Watts-Strogatz networks, and Erdös-Rényi networks, we find our method can effectively preserve the network synchronizability.

  16. Hybrid continuum-coarse-grained modeling of erythrocytes

    Science.gov (United States)

    Lyu, Jinming; Chen, Paul G.; Boedec, Gwenn; Leonetti, Marc; Jaeger, Marc

    2018-06-01

    The red blood cell (RBC) membrane is a composite structure, consisting of a phospholipid bilayer and an underlying membrane-associated cytoskeleton. Both continuum and particle-based coarse-grained RBC models make use of a set of vertices connected by edges to represent the RBC membrane, which can be seen as a triangular surface mesh for the former and a spring network for the latter. Here, we present a modeling approach combining an existing continuum vesicle model with a coarse-grained model for the cytoskeleton. Compared to other two-component approaches, our method relies on only one mesh, representing the cytoskeleton, whose velocity in the tangential direction of the membrane may be different from that of the lipid bilayer. The finitely extensible nonlinear elastic (FENE) spring force law in combination with a repulsive force defined as a power function (POW), called FENE-POW, is used to describe the elastic properties of the RBC membrane. The mechanical interaction between the lipid bilayer and the cytoskeleton is explicitly computed and incorporated into the vesicle model. Our model includes the fundamental mechanical properties of the RBC membrane, namely fluidity and bending rigidity of the lipid bilayer, and shear elasticity of the cytoskeleton while maintaining surface-area and volume conservation constraint. We present three simulation examples to demonstrate the effectiveness of this hybrid continuum-coarse-grained model for the study of RBCs in fluid flows.

  17. Variational approach to coarse-graining of generalized gradient flows

    NARCIS (Netherlands)

    Duong, M.H.; Lamacz, A.; Peletier, M.A.; Sharma, U.

    2017-01-01

    In this paper we present a variational technique that handles coarse-graining and passing to a limit in a unified manner. The technique is based on a duality structure, which is present in many gradient flows and other variational evolutions, and which often arises from a large-deviations principle.

  18. Tomography and Purification of the Temporal-Mode Structure of Quantum Light

    Science.gov (United States)

    Ansari, Vahid; Donohue, John M.; Allgaier, Markus; Sansoni, Linda; Brecht, Benjamin; Roslund, Jonathan; Treps, Nicolas; Harder, Georg; Silberhorn, Christine

    2018-05-01

    High-dimensional quantum information processing promises capabilities beyond the current state of the art, but addressing individual information-carrying modes presents a significant experimental challenge. Here we demonstrate effective high-dimensional operations in the time-frequency domain of nonclassical light. We generate heralded photons with tailored temporal-mode structures through the pulse shaping of a broadband parametric down-conversion pump. We then implement a quantum pulse gate, enabled by dispersion-engineered sum-frequency generation, to project onto programmable temporal modes, reconstructing the quantum state in seven dimensions. We also manipulate the time-frequency structure by selectively removing temporal modes, explicitly demonstrating the effectiveness of engineered nonlinear processes for the mode-selective manipulation of quantum states.

  19. The Structural Plasticity of White Matter Networks Following Anterior Temporal Lobe Resection

    Science.gov (United States)

    Yogarajah, Mahinda; Focke, Niels K.; Bonelli, Silvia B.; Thompson, Pamela; Vollmar, Christian; McEvoy, Andrew W.; Alexander, Daniel C.; Symms, Mark R.; Koepp, Matthias J.; Duncan, John S.

    2010-01-01

    Anterior temporal lobe resection is an effective treatment for refractory temporal lobe epilepsy. The structural consequences of such surgery in the white matter, and how these relate to language function after surgery remain unknown. We carried out a longitudinal study with diffusion tensor imaging in 26 left and 20 right temporal lobe epilepsy…

  20. Calculation of accurate small angle X-ray scattering curves from coarse-grained protein models

    Directory of Open Access Journals (Sweden)

    Stovgaard Kasper

    2010-08-01

    Full Text Available Abstract Background Genome sequencing projects have expanded the gap between the amount of known protein sequences and structures. The limitations of current high resolution structure determination methods make it unlikely that this gap will disappear in the near future. Small angle X-ray scattering (SAXS is an established low resolution method for routinely determining the structure of proteins in solution. The purpose of this study is to develop a method for the efficient calculation of accurate SAXS curves from coarse-grained protein models. Such a method can for example be used to construct a likelihood function, which is paramount for structure determination based on statistical inference. Results We present a method for the efficient calculation of accurate SAXS curves based on the Debye formula and a set of scattering form factors for dummy atom representations of amino acids. Such a method avoids the computationally costly iteration over all atoms. We estimated the form factors using generated data from a set of high quality protein structures. No ad hoc scaling or correction factors are applied in the calculation of the curves. Two coarse-grained representations of protein structure were investigated; two scattering bodies per amino acid led to significantly better results than a single scattering body. Conclusion We show that the obtained point estimates allow the calculation of accurate SAXS curves from coarse-grained protein models. The resulting curves are on par with the current state-of-the-art program CRYSOL, which requires full atomic detail. Our method was also comparable to CRYSOL in recognizing native structures among native-like decoys. As a proof-of-concept, we combined the coarse-grained Debye calculation with a previously described probabilistic model of protein structure, TorusDBN. This resulted in a significant improvement in the decoy recognition performance. In conclusion, the presented method shows great promise for

  1. Musical structure analysis using similarity matrix and dynamic programming

    Science.gov (United States)

    Shiu, Yu; Jeong, Hong; Kuo, C.-C. Jay

    2005-10-01

    Automatic music segmentation and structure analysis from audio waveforms based on a three-level hierarchy is examined in this research, where the three-level hierarchy includes notes, measures and parts. The pitch class profile (PCP) feature is first extracted at the note level. Then, a similarity matrix is constructed at the measure level, where a dynamic time warping (DTW) technique is used to enhance the similarity computation by taking the temporal distortion of similar audio segments into account. By processing the similarity matrix, we can obtain a coarse-grain music segmentation result. Finally, dynamic programming is applied to the coarse-grain segments so that a song can be decomposed into several major parts such as intro, verse, chorus, bridge and outro. The performance of the proposed music structure analysis system is demonstrated for pop and rock music.

  2. Compressive strength of structural concrete made with locally available coarse aggregates

    International Nuclear Information System (INIS)

    Kumar, A.; Khaskheli, G.B.

    2009-01-01

    Quality of CA (Coarse Aggregate) is one of the prime factors to control the quality of concrete. But construction industry of Sindh is not very much bothered about the quality of CA in concrete manufacturing. In Sindh, Hyderabad vicinity is comparatively rich in production of CA. This research is to evaluate the compressive strength of structural concrete made with CA obtained from five different crush plants (Petaro, Parker, Palari, Ghulam Hyder Baloch and Ongar), available in the vicinity of Hyderabad. ln total 360 concrete cubes (150x150x150mm) were manufactured, 72 for each source of CA by keeping 1:2:4 and 1:1.5:3 material ratios. The cubes were manufactured with 0.45 w/c (water cement ratio), 0.5 and 0.55 w/c and tested for compressive strength after 3, 7, 14 and 28 days of curing. Results show that performance of CA obtained from all the five crush plants remained in agreement with BS and ACI Code recommendations. Concrete made with CA obtained from Petaro and Parker gave higher early strength than that of others while concrete made with CA obtained from Petaro, Parker together with Palari gave higher 28th day compressive strength. (author)

  3. Segregation of Brain Structural Networks Supports Spatio-Temporal Predictive Processing

    Directory of Open Access Journals (Sweden)

    Valentina Ciullo

    2018-05-01

    Full Text Available The ability to generate probabilistic expectancies regarding when and where sensory stimuli will occur, is critical to derive timely and accurate inferences about updating contexts. However, the existence of specialized neural networks for inferring predictive relationships between events is still debated. Using graph theoretical analysis applied to structural connectivity data, we tested the extent of brain connectivity properties associated with spatio-temporal predictive performance across 29 healthy subjects. Participants detected visual targets appearing at one out of three locations after one out of three intervals; expectations about stimulus location (spatial condition or onset (temporal condition were induced by valid or invalid symbolic cues. Connectivity matrices and centrality/segregation measures, expressing the relative importance of, and the local interactions among specific cerebral areas respect to the behavior under investigation, were calculated from whole-brain tractography and cortico-subcortical parcellation.Results: Response preparedness to cued stimuli relied on different structural connectivity networks for the temporal and spatial domains. Significant covariance was observed between centrality measures of regions within a subcortical-fronto-parietal-occipital network -comprising the left putamen, the right caudate nucleus, the left frontal operculum, the right inferior parietal cortex, the right paracentral lobule and the right superior occipital cortex-, and the ability to respond after a short cue-target delay suggesting that the local connectedness of such nodes plays a central role when the source of temporal expectation is explicit. When the potential for functional segregation was tested, we found highly clustered structural connectivity across the right superior, the left middle inferior frontal gyrus and the left caudate nucleus as related to explicit temporal orienting. Conversely, when the interaction between

  4. Segregation of Brain Structural Networks Supports Spatio-Temporal Predictive Processing.

    Science.gov (United States)

    Ciullo, Valentina; Vecchio, Daniela; Gili, Tommaso; Spalletta, Gianfranco; Piras, Federica

    2018-01-01

    The ability to generate probabilistic expectancies regarding when and where sensory stimuli will occur, is critical to derive timely and accurate inferences about updating contexts. However, the existence of specialized neural networks for inferring predictive relationships between events is still debated. Using graph theoretical analysis applied to structural connectivity data, we tested the extent of brain connectivity properties associated with spatio-temporal predictive performance across 29 healthy subjects. Participants detected visual targets appearing at one out of three locations after one out of three intervals; expectations about stimulus location (spatial condition) or onset (temporal condition) were induced by valid or invalid symbolic cues. Connectivity matrices and centrality/segregation measures, expressing the relative importance of, and the local interactions among specific cerebral areas respect to the behavior under investigation, were calculated from whole-brain tractography and cortico-subcortical parcellation. Results: Response preparedness to cued stimuli relied on different structural connectivity networks for the temporal and spatial domains. Significant covariance was observed between centrality measures of regions within a subcortical-fronto-parietal-occipital network -comprising the left putamen, the right caudate nucleus, the left frontal operculum, the right inferior parietal cortex, the right paracentral lobule and the right superior occipital cortex-, and the ability to respond after a short cue-target delay suggesting that the local connectedness of such nodes plays a central role when the source of temporal expectation is explicit. When the potential for functional segregation was tested, we found highly clustered structural connectivity across the right superior, the left middle inferior frontal gyrus and the left caudate nucleus as related to explicit temporal orienting. Conversely, when the interaction between explicit and

  5. Phylogenetic community structure: temporal variation in fish assemblage

    OpenAIRE

    Santorelli, Sergio; Magnusson, William; Ferreira, Efrem; Caramaschi, Erica; Zuanon, Jansen; Amadio, Sidnéia

    2014-01-01

    Hypotheses about phylogenetic relationships among species allow inferences about the mechanisms that affect species coexistence. Nevertheless, most studies assume that phylogenetic patterns identified are stable over time. We used data on monthly samples of fish from a single lake over 10 years to show that the structure in phylogenetic assemblages varies over time and conclusions depend heavily on the time scale investigated. The data set was organized in guild structures and temporal scales...

  6. Parametrizing coarse grained models for molecular systems at equilibrium

    KAUST Repository

    Kalligiannaki, Evangelia; Chazirakis, A.; Tsourtis, A.; Katsoulakis, M. A.; Plechá č, P.; Harmandaris, V.

    2016-01-01

    Hierarchical coarse graining of atomistic molecular systems at equilibrium has been an intensive research topic over the last few decades. In this work we (a) review theoretical and numerical aspects of different parametrization methods (structural-based, force matching and relative entropy) to derive the effective interaction potential between coarse-grained particles. All methods approximate the many body potential of mean force; resulting, however, in different optimization problems. (b) We also use a reformulation of the force matching method by introducing a generalized force matching condition for the local mean force in the sense that allows the approximation of the potential of mean force under both linear and non-linear coarse graining mappings (E. Kalligiannaki, et al., J. Chem. Phys. 2015). We apply and compare these methods to: (a) a benchmark system of two isolated methane molecules; (b) methane liquid; (c) water; and (d) an alkane fluid. Differences between the effective interactions, derived from the various methods, are found that depend on the actual system under study. The results further reveal the relation of the various methods and the sensitivities that may arise in the implementation of numerical methods used in each case.

  7. Parametrizing coarse grained models for molecular systems at equilibrium

    KAUST Repository

    Kalligiannaki, Evangelia

    2016-10-18

    Hierarchical coarse graining of atomistic molecular systems at equilibrium has been an intensive research topic over the last few decades. In this work we (a) review theoretical and numerical aspects of different parametrization methods (structural-based, force matching and relative entropy) to derive the effective interaction potential between coarse-grained particles. All methods approximate the many body potential of mean force; resulting, however, in different optimization problems. (b) We also use a reformulation of the force matching method by introducing a generalized force matching condition for the local mean force in the sense that allows the approximation of the potential of mean force under both linear and non-linear coarse graining mappings (E. Kalligiannaki, et al., J. Chem. Phys. 2015). We apply and compare these methods to: (a) a benchmark system of two isolated methane molecules; (b) methane liquid; (c) water; and (d) an alkane fluid. Differences between the effective interactions, derived from the various methods, are found that depend on the actual system under study. The results further reveal the relation of the various methods and the sensitivities that may arise in the implementation of numerical methods used in each case.

  8. Non-Galerkin Coarse Grids for Algebraic Multigrid

    Energy Technology Data Exchange (ETDEWEB)

    Falgout, Robert D. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Schroder, Jacob B. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2014-06-26

    Algebraic multigrid (AMG) is a popular and effective solver for systems of linear equations that arise from discretized partial differential equations. And while AMG has been effectively implemented on large scale parallel machines, challenges remain, especially when moving to exascale. Particularly, stencil sizes (the number of nonzeros in a row) tend to increase further down in the coarse grid hierarchy, and this growth leads to more communication. Therefore, as problem size increases and the number of levels in the hierarchy grows, the overall efficiency of the parallel AMG method decreases, sometimes dramatically. This growth in stencil size is due to the standard Galerkin coarse grid operator, $P^T A P$, where $P$ is the prolongation (i.e., interpolation) operator. For example, the coarse grid stencil size for a simple three-dimensional (3D) seven-point finite differencing approximation to diffusion can increase into the thousands on present day machines, causing an associated increase in communication costs. We therefore consider algebraically truncating coarse grid stencils to obtain a non-Galerkin coarse grid. First, the sparsity pattern of the non-Galerkin coarse grid is determined by employing a heuristic minimal “safe” pattern together with strength-of-connection ideas. Second, the nonzero entries are determined by collapsing the stencils in the Galerkin operator using traditional AMG techniques. The result is a reduction in coarse grid stencil size, overall operator complexity, and parallel AMG solve phase times.

  9. Deciphering structural and temporal interplays during the architectural development of mango trees.

    Science.gov (United States)

    Dambreville, Anaëlle; Lauri, Pierre-Éric; Trottier, Catherine; Guédon, Yann; Normand, Frédéric

    2013-05-01

    Plant architecture is commonly defined by the adjacency of organs within the structure and their properties. Few studies consider the effect of endogenous temporal factors, namely phenological factors, on the establishment of plant architecture. This study hypothesized that, in addition to the effect of environmental factors, the observed plant architecture results from both endogenous structural and temporal components, and their interplays. Mango tree, which is characterized by strong phenological asynchronisms within and between trees and by repeated vegetative and reproductive flushes during a growing cycle, was chosen as a plant model. During two consecutive growing cycles, this study described vegetative and reproductive development of 20 trees submitted to the same environmental conditions. Four mango cultivars were considered to assess possible cultivar-specific patterns. Integrative vegetative and reproductive development models incorporating generalized linear models as components were built. These models described the occurrence, intensity, and timing of vegetative and reproductive development at the growth unit scale. This study showed significant interplays between structural and temporal components of plant architectural development at two temporal scales. Within a growing cycle, earliness of bud burst was highly and positively related to earliness of vegetative development and flowering. Between growing cycles, flowering growth units delayed vegetative development compared to growth units that did not flower. These interplays explained how vegetative and reproductive phenological asynchronisms within and between trees were generated and maintained. It is suggested that causation networks involving structural and temporal components may give rise to contrasted tree architectures.

  10. HIRENASD coarse unstructured

    Data.gov (United States)

    National Aeronautics and Space Administration — Unstructured HIRENASD mesh: - coarse size (5.7 million nodes, 14.4 million elements) - for node centered solvers - 01.06.2011 - caution: dimensions in mm

  11. Adaptive resolution simulation of polarizable supramolecular coarse-grained water models

    International Nuclear Information System (INIS)

    Zavadlav, Julija; Praprotnik, Matej; Melo, Manuel N.; Marrink, Siewert J.

    2015-01-01

    Multiscale simulations methods, such as adaptive resolution scheme, are becoming increasingly popular due to their significant computational advantages with respect to conventional atomistic simulations. For these kind of simulations, it is essential to develop accurate multiscale water models that can be used to solvate biophysical systems of interest. Recently, a 4-to-1 mapping was used to couple the bundled-simple point charge water with the MARTINI model. Here, we extend the supramolecular mapping to coarse-grained models with explicit charges. In particular, the two tested models are the polarizable water and big multiple water models associated with the MARTINI force field. As corresponding coarse-grained representations consist of several interaction sites, we couple orientational degrees of freedom of the atomistic and coarse-grained representations via a harmonic energy penalty term. This additional energy term aligns the dipole moments of both representations. We test this coupling by studying the system under applied static external electric field. We show that our approach leads to the correct reproduction of the relevant structural and dynamical properties

  12. A coarse-graining approach for molecular simulation that retains the dynamics of the all-atom reference system by implementing hydrodynamic interactions

    Energy Technology Data Exchange (ETDEWEB)

    Markutsya, Sergiy [Ames Laboratory, Iowa State University, Ames, Iowa 50011 (United States); Lamm, Monica H., E-mail: mhlamm@iastate.edu [Ames Laboratory, Iowa State University, Ames, Iowa 50011 (United States); Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011 (United States)

    2014-11-07

    We report on a new approach for deriving coarse-grained intermolecular forces that retains the frictional contribution that is often discarded by conventional coarse-graining methods. The approach is tested for water and an aqueous glucose solution, and the results from the new implementation for coarse-grained molecular dynamics simulation show remarkable agreement with the dynamics obtained from reference all-atom simulations. The agreement between the structural properties observed in the coarse-grained and all-atom simulations is also preserved. We discuss how this approach may be applied broadly to any existing coarse-graining method where the coarse-grained models are rigorously derived from all-atom reference systems.

  13. A coarse-graining approach for molecular simulation that retains the dynamics of the all-atom reference system by implementing hydrodynamic interactions

    International Nuclear Information System (INIS)

    Markutsya, Sergiy; Lamm, Monica H.

    2014-01-01

    We report on a new approach for deriving coarse-grained intermolecular forces that retains the frictional contribution that is often discarded by conventional coarse-graining methods. The approach is tested for water and an aqueous glucose solution, and the results from the new implementation for coarse-grained molecular dynamics simulation show remarkable agreement with the dynamics obtained from reference all-atom simulations. The agreement between the structural properties observed in the coarse-grained and all-atom simulations is also preserved. We discuss how this approach may be applied broadly to any existing coarse-graining method where the coarse-grained models are rigorously derived from all-atom reference systems

  14. Temporal change in biological community structure in the Fountain Creek basin, Colorado, 2001-2008

    Science.gov (United States)

    Zuellig, Robert E.; Bruce, James F.; Stogner, Sr., Robert W.

    2010-01-01

    In 2001, the U.S. Geological Survey, in cooperation with Colorado Springs City Engineering, began a study to better understand the relations between environmental characteristics and biological communities in the Fountain Creek basin in order to aide water-resource management and guide future monitoring activities. To accomplish this task, environmental (streamflow, habitat, and water chemistry) and biological (fish and macroinvertebrate) data were collected annually at 24 sites over a 6- or 8-year period (fish, 2003 to 2008; macroinvertebrates, 2001 to 2008). For this report, these data were first analyzed to determine the presence of temporal change in macroinvertebrate and fish community structure among years using nonparametric multivariate statistics. Where temporal change in the biological communities was found, these data were further analyzed using additional nonparametric multivariate techniques to determine which subset of selected streamflow, habitat, or water-chemistry variables best described site-specific changes in community structure relative to a gradient of urbanization. This study identified significant directional patterns of temporal change in macroinvertebrate and fish community structure at 15 of 24 sites in the Fountain Creek basin. At four of these sites, changes in environmental variables were significantly correlated with the concurrent temporal change identified in macroinvertebrate and fish community structure (Monument Creek above Woodmen Road at Colorado Springs, Colo.; Monument Creek at Bijou Street at Colorado Springs, Colo.; Bear Creek near Colorado Springs, Colo.; Fountain Creek at Security, Colo.). Combinations of environmental variables describing directional temporal change in the biota appeared to be site specific as no single variable dominated the results; however, substrate composition variables (percent substrate composition composed of sand, gravel, or cobble) collectively were present in 80 percent of the environmental

  15. Coarse-mesh rebalancing acceleration for eigenvalue problems

    International Nuclear Information System (INIS)

    Asaoka, T.; Nakahara, Y.; Miyasaka, S.

    1974-01-01

    The coarse-mesh rebalance method is adopted for Monte Carlo schemes for aiming at accelerating the convergence of a source iteration process. At every completion of the Monte Carlo game for one batch of neutron histories, the scaling factor for the neutron flux is calculated to achieve the neutron balance in each coarse-mesh zone into which the total system is divided. This rebalance factor is multiplied to the weight of each fission source neutron in the coarse-mesh zone for playing the next Monte Carlo game. The numerical examples have shown that the coarse-mesh rebalance Monte Carlo calculation gives a good estimate of the eigenvalue already after several batches with a negligible extra computer time compared to the standard Monte Carlo. 5 references. (U.S.)

  16. SIRAH: a structurally unbiased coarse-grained force field for proteins with aqueous solvation and long-range electrostatics.

    Science.gov (United States)

    Darré, Leonardo; Machado, Matías Rodrigo; Brandner, Astrid Febe; González, Humberto Carlos; Ferreira, Sebastián; Pantano, Sergio

    2015-02-10

    Modeling of macromolecular structures and interactions represents an important challenge for computational biology, involving different time and length scales. However, this task can be facilitated through the use of coarse-grained (CG) models, which reduce the number of degrees of freedom and allow efficient exploration of complex conformational spaces. This article presents a new CG protein model named SIRAH, developed to work with explicit solvent and to capture sequence, temperature, and ionic strength effects in a topologically unbiased manner. SIRAH is implemented in GROMACS, and interactions are calculated using a standard pairwise Hamiltonian for classical molecular dynamics simulations. We present a set of simulations that test the capability of SIRAH to produce a qualitatively correct solvation on different amino acids, hydrophilic/hydrophobic interactions, and long-range electrostatic recognition leading to spontaneous association of unstructured peptides and stable structures of single polypeptides and protein-protein complexes.

  17. Conservative and dissipative force field for simulation of coarse-grained alkane molecules: A bottom-up approach

    Energy Technology Data Exchange (ETDEWEB)

    Trément, Sébastien; Rousseau, Bernard, E-mail: bernard.rousseau@u-psud.fr [Laboratoire de Chimie-Physique, UMR 8000 CNRS, Université Paris-Sud, Orsay (France); Schnell, Benoît; Petitjean, Laurent; Couty, Marc [Manufacture Française des Pneumatiques MICHELIN, Centre de Ladoux, 23 place des Carmes, 63000 Clermont-Ferrand (France)

    2014-04-07

    We apply operational procedures available in the literature to the construction of coarse-grained conservative and friction forces for use in dissipative particle dynamics (DPD) simulations. The full procedure rely on a bottom-up approach: large molecular dynamics trajectories of n-pentane and n-decane modeled with an anisotropic united atom model serve as input for the force field generation. As a consequence, the coarse-grained model is expected to reproduce at least semi-quantitatively structural and dynamical properties of the underlying atomistic model. Two different coarse-graining levels are studied, corresponding to five and ten carbon atoms per DPD bead. The influence of the coarse-graining level on the generated force fields contributions, namely, the conservative and the friction part, is discussed. It is shown that the coarse-grained model of n-pentane correctly reproduces self-diffusion and viscosity coefficients of real n-pentane, while the fully coarse-grained model for n-decane at ambient temperature over-predicts diffusion by a factor of 2. However, when the n-pentane coarse-grained model is used as a building block for larger molecule (e.g., n-decane as a two blobs model), a much better agreement with experimental data is obtained, suggesting that the force field constructed is transferable to large macro-molecular systems.

  18. Detecting the Community Structure and Activity Patterns of Temporal Networks: A Non-Negative Tensor Factorization Approach

    Science.gov (United States)

    Gauvin, Laetitia; Panisson, André; Cattuto, Ciro

    2014-01-01

    The increasing availability of temporal network data is calling for more research on extracting and characterizing mesoscopic structures in temporal networks and on relating such structure to specific functions or properties of the system. An outstanding challenge is the extension of the results achieved for static networks to time-varying networks, where the topological structure of the system and the temporal activity patterns of its components are intertwined. Here we investigate the use of a latent factor decomposition technique, non-negative tensor factorization, to extract the community-activity structure of temporal networks. The method is intrinsically temporal and allows to simultaneously identify communities and to track their activity over time. We represent the time-varying adjacency matrix of a temporal network as a three-way tensor and approximate this tensor as a sum of terms that can be interpreted as communities of nodes with an associated activity time series. We summarize known computational techniques for tensor decomposition and discuss some quality metrics that can be used to tune the complexity of the factorized representation. We subsequently apply tensor factorization to a temporal network for which a ground truth is available for both the community structure and the temporal activity patterns. The data we use describe the social interactions of students in a school, the associations between students and school classes, and the spatio-temporal trajectories of students over time. We show that non-negative tensor factorization is capable of recovering the class structure with high accuracy. In particular, the extracted tensor components can be validated either as known school classes, or in terms of correlated activity patterns, i.e., of spatial and temporal coincidences that are determined by the known school activity schedule. PMID:24497935

  19. A 2.5-million-year perspective on coarse-filter strategies for conserving nature's stage.

    Science.gov (United States)

    Gill, Jacquelyn L; Blois, Jessica L; Benito, Blas; Dobrowski, Solomon; Hunter, Malcolm L; McGuire, Jenny L

    2015-06-01

    Climate change will require novel conservation strategies. One such tactic is a coarse-filter approach that focuses on conserving nature's stage (CNS) rather than the actors (individual species). However, there is a temporal mismatch between the long-term goals of conservation and the short-term nature of most ecological studies, which leaves many assumptions untested. Paleoecology provides a valuable perspective on coarse-filter strategies by marshaling the natural experiments of the past to contextualize extinction risk due to the emerging impacts of climate change and anthropogenic threats. We reviewed examples from the paleoecological record that highlight the strengths, opportunities, and caveats of a CNS approach. We focused on the near-time geological past of the Quaternary, during which species were subjected to widespread changes in climate and concomitant changes in the physical environment in general. Species experienced a range of individualistic responses to these changes, including community turnover and novel associations, extinction and speciation, range shifts, changes in local richness and evenness, and both equilibrium and disequilibrium responses. Due to the dynamic nature of species responses to Quaternary climate change, a coarse-filter strategy may be appropriate for many taxa because it can accommodate dynamic processes. However, conservationists should also consider that the persistence of landforms varies across space and time, which could have potential long-term consequences for geodiversity and thus biodiversity. © 2015 Society for Conservation Biology.

  20. Implementing Non Power-of-Two FFTs on Coarse-Grain Reconfigurable Architectures

    NARCIS (Netherlands)

    Rivaton, Arnaud; Quevremont, Jérôme; Zhang, Q.; Wolkotte, P.T.; Smit, Gerardus Johannes Maria; Nurmi, J.; Takala, J.; Hamalainen, T.D.

    2005-01-01

    To improve power figures of a dual ARM9 RISC core architecture targeting low-power digital broadcasting applications, the addition of a coarse-grain architecture is considered. This paper introduces two of these structures: PACT's XPP technology and the Montium, developed by the University of

  1. Imaging structural and functional brain networks in temporal lobe epilepsy

    Science.gov (United States)

    Bernhardt, Boris C.; Hong, SeokJun; Bernasconi, Andrea; Bernasconi, Neda

    2013-01-01

    Early imaging studies in temporal lobe epilepsy (TLE) focused on the search for mesial temporal sclerosis, as its surgical removal results in clinically meaningful improvement in about 70% of patients. Nevertheless, a considerable subgroup of patients continues to suffer from post-operative seizures. Although the reasons for surgical failure are not fully understood, electrophysiological and imaging data suggest that anomalies extending beyond the temporal lobe may have negative impact on outcome. This hypothesis has revived the concept of human epilepsy as a disorder of distributed brain networks. Recent methodological advances in non-invasive neuroimaging have led to quantify structural and functional networks in vivo. While structural networks can be inferred from diffusion MRI tractography and inter-regional covariance patterns of structural measures such as cortical thickness, functional connectivity is generally computed based on statistical dependencies of neurophysiological time-series, measured through functional MRI or electroencephalographic techniques. This review considers the application of advanced analytical methods in structural and functional connectivity analyses in TLE. We will specifically highlight findings from graph-theoretical analysis that allow assessing the topological organization of brain networks. These studies have provided compelling evidence that TLE is a system disorder with profound alterations in local and distributed networks. In addition, there is emerging evidence for the utility of network properties as clinical diagnostic markers. Nowadays, a network perspective is considered to be essential to the understanding of the development, progression, and management of epilepsy. PMID:24098281

  2. Imaging structural and functional brain networks in temporal lobe epilepsy.

    Science.gov (United States)

    Bernhardt, Boris C; Hong, Seokjun; Bernasconi, Andrea; Bernasconi, Neda

    2013-10-01

    Early imaging studies in temporal lobe epilepsy (TLE) focused on the search for mesial temporal sclerosis, as its surgical removal results in clinically meaningful improvement in about 70% of patients. Nevertheless, a considerable subgroup of patients continues to suffer from post-operative seizures. Although the reasons for surgical failure are not fully understood, electrophysiological and imaging data suggest that anomalies extending beyond the temporal lobe may have negative impact on outcome. This hypothesis has revived the concept of human epilepsy as a disorder of distributed brain networks. Recent methodological advances in non-invasive neuroimaging have led to quantify structural and functional networks in vivo. While structural networks can be inferred from diffusion MRI tractography and inter-regional covariance patterns of structural measures such as cortical thickness, functional connectivity is generally computed based on statistical dependencies of neurophysiological time-series, measured through functional MRI or electroencephalographic techniques. This review considers the application of advanced analytical methods in structural and functional connectivity analyses in TLE. We will specifically highlight findings from graph-theoretical analysis that allow assessing the topological organization of brain networks. These studies have provided compelling evidence that TLE is a system disorder with profound alterations in local and distributed networks. In addition, there is emerging evidence for the utility of network properties as clinical diagnostic markers. Nowadays, a network perspective is considered to be essential to the understanding of the development, progression, and management of epilepsy.

  3. Imaging structural and functional brain networks in temporal lobe epilepsy

    Directory of Open Access Journals (Sweden)

    Boris eBernhardt

    2013-10-01

    Full Text Available Early imaging studies in temporal lobe epilepsy (TLE focused on the search for mesial temporal sclerosis, as its surgical removal results in clinically meaningful improvement in about 70% of patients. Nevertheless, a considerable subgroup of patients continues to suffer from post-operative seizures. Although the reasons for surgical failure are not fully understood, electrophysiological and imaging data suggest that anomalies extending beyond the temporal lobe may have negative impact on outcome. This hypothesis has revived the concept of human epilepsy as a disorder of distributed brain networks. Recent methodological advances in non-invasive neuroimaging have led to quantify structural and functional networks in vivo. While structural networks can be inferred from diffusion MRI tractography and inter-regional covariance patterns of structural measures such as cortical thickness, functional connectivity is generally computed based on statistical dependencies of neurophysiological time-series, measured through functional MRI or electroencephalographic techniques. This review considers the application of advanced analytical methods in structural and functional connectivity analyses in TLE. We will specifically highlight findings from graph-theoretical analysis that allow assessing topological organization of brain networks. These studies have provided compelling evidence that TLE is a system disorder with profound alterations in local and distributed networks. In addition, there is emerging evidence for the utility of network properties as clinical diagnostic markers. Nowadays, a network perspective is considered to be essential to the understanding of the development, progression, and management of epilepsy.

  4. Path-space variational inference for non-equilibrium coarse-grained systems

    International Nuclear Information System (INIS)

    Harmandaris, Vagelis; Kalligiannaki, Evangelia; Katsoulakis, Markos; Plecháč, Petr

    2016-01-01

    In this paper we discuss information-theoretic tools for obtaining optimized coarse-grained molecular models for both equilibrium and non-equilibrium molecular simulations. The latter are ubiquitous in physicochemical and biological applications, where they are typically associated with coupling mechanisms, multi-physics and/or boundary conditions. In general the non-equilibrium steady states are not known explicitly as they do not necessarily have a Gibbs structure. The presented approach can compare microscopic behavior of molecular systems to parametric and non-parametric coarse-grained models using the relative entropy between distributions on the path space and setting up a corresponding path-space variational inference problem. The methods can become entirely data-driven when the microscopic dynamics are replaced with corresponding correlated data in the form of time series. Furthermore, we present connections and generalizations of force matching methods in coarse-graining with path-space information methods. We demonstrate the enhanced transferability of information-based parameterizations to different observables, at a specific thermodynamic point, due to information inequalities. We discuss methodological connections between information-based coarse-graining of molecular systems and variational inference methods primarily developed in the machine learning community. However, we note that the work presented here addresses variational inference for correlated time series due to the focus on dynamics. The applicability of the proposed methods is demonstrated on high-dimensional stochastic processes given by overdamped and driven Langevin dynamics of interacting particles.

  5. Path-space variational inference for non-equilibrium coarse-grained systems

    Energy Technology Data Exchange (ETDEWEB)

    Harmandaris, Vagelis, E-mail: harman@uoc.gr [Department of Mathematics and Applied Mathematics, University of Crete (Greece); Institute of Applied and Computational Mathematics (IACM), Foundation for Research and Technology Hellas (FORTH), IACM/FORTH, GR-71110 Heraklion (Greece); Kalligiannaki, Evangelia, E-mail: ekalligian@tem.uoc.gr [Department of Mathematics and Applied Mathematics, University of Crete (Greece); Katsoulakis, Markos, E-mail: markos@math.umass.edu [Department of Mathematics and Statistics, University of Massachusetts at Amherst (United States); Plecháč, Petr, E-mail: plechac@math.udel.edu [Department of Mathematical Sciences, University of Delaware, Newark, Delaware (United States)

    2016-06-01

    In this paper we discuss information-theoretic tools for obtaining optimized coarse-grained molecular models for both equilibrium and non-equilibrium molecular simulations. The latter are ubiquitous in physicochemical and biological applications, where they are typically associated with coupling mechanisms, multi-physics and/or boundary conditions. In general the non-equilibrium steady states are not known explicitly as they do not necessarily have a Gibbs structure. The presented approach can compare microscopic behavior of molecular systems to parametric and non-parametric coarse-grained models using the relative entropy between distributions on the path space and setting up a corresponding path-space variational inference problem. The methods can become entirely data-driven when the microscopic dynamics are replaced with corresponding correlated data in the form of time series. Furthermore, we present connections and generalizations of force matching methods in coarse-graining with path-space information methods. We demonstrate the enhanced transferability of information-based parameterizations to different observables, at a specific thermodynamic point, due to information inequalities. We discuss methodological connections between information-based coarse-graining of molecular systems and variational inference methods primarily developed in the machine learning community. However, we note that the work presented here addresses variational inference for correlated time series due to the focus on dynamics. The applicability of the proposed methods is demonstrated on high-dimensional stochastic processes given by overdamped and driven Langevin dynamics of interacting particles.

  6. Coarse-grained simulations of polyelectrolyte complexes: MARTINI models for poly(styrene sulfonate) and poly(diallyldimethylammonium)

    Energy Technology Data Exchange (ETDEWEB)

    Vögele, Martin [Institute for Computational Physics, University of Stuttgart, Stuttgart (Germany); Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt a. M. (Germany); Holm, Christian; Smiatek, Jens, E-mail: smiatek@icp.uni-stuttgart.de [Institute for Computational Physics, University of Stuttgart, Stuttgart (Germany)

    2015-12-28

    We present simulations of aqueous polyelectrolyte complexes with new MARTINI models for the charged polymers poly(styrene sulfonate) and poly(diallyldimethylammonium). Our coarse-grained polyelectrolyte models allow us to study large length and long time scales with regard to chemical details and thermodynamic properties. The results are compared to the outcomes of previous atomistic molecular dynamics simulations and verify that electrostatic properties are reproduced by our MARTINI coarse-grained approach with reasonable accuracy. Structural similarity between the atomistic and the coarse-grained results is indicated by a comparison between the pair radial distribution functions and the cumulative number of surrounding particles. Our coarse-grained models are able to quantitatively reproduce previous findings like the correct charge compensation mechanism and a reduced dielectric constant of water. These results can be interpreted as the underlying reason for the stability of polyelectrolyte multilayers and complexes and validate the robustness of the proposed models.

  7. Coarse-grained simulations of polyelectrolyte complexes: MARTINI models for poly(styrene sulfonate) and poly(diallyldimethylammonium)

    International Nuclear Information System (INIS)

    Vögele, Martin; Holm, Christian; Smiatek, Jens

    2015-01-01

    We present simulations of aqueous polyelectrolyte complexes with new MARTINI models for the charged polymers poly(styrene sulfonate) and poly(diallyldimethylammonium). Our coarse-grained polyelectrolyte models allow us to study large length and long time scales with regard to chemical details and thermodynamic properties. The results are compared to the outcomes of previous atomistic molecular dynamics simulations and verify that electrostatic properties are reproduced by our MARTINI coarse-grained approach with reasonable accuracy. Structural similarity between the atomistic and the coarse-grained results is indicated by a comparison between the pair radial distribution functions and the cumulative number of surrounding particles. Our coarse-grained models are able to quantitatively reproduce previous findings like the correct charge compensation mechanism and a reduced dielectric constant of water. These results can be interpreted as the underlying reason for the stability of polyelectrolyte multilayers and complexes and validate the robustness of the proposed models

  8. Learning to Play Efficient Coarse Correlated Equilibria

    KAUST Repository

    Borowski, Holly P.

    2018-03-10

    The majority of the distributed learning literature focuses on convergence to Nash equilibria. Coarse correlated equilibria, on the other hand, can often characterize more efficient collective behavior than even the best Nash equilibrium. However, there are no existing distributed learning algorithms that converge to specific coarse correlated equilibria. In this paper, we provide one such algorithm, which guarantees that the agents’ collective joint strategy will constitute an efficient coarse correlated equilibrium with high probability. The key to attaining efficient correlated behavior through distributed learning involves incorporating a common random signal into the learning environment.

  9. Reconciling structural and thermodynamic predictions using all-atom and coarse-grain force fields: the case of charged oligo-arginine translocation into DMPC bilayers.

    Science.gov (United States)

    Hu, Yuan; Sinha, Sudipta Kumar; Patel, Sandeep

    2014-10-16

    Using the translocation of short, charged cationic oligo-arginine peptides (mono-, di-, and triarginine) from bulk aqueous solution into model DMPC bilayers, we explore the question of the similarity of thermodynamic and structural predictions obtained from molecular dynamics simulations using all-atom and Martini coarse-grain force fields. Specifically, we estimate potentials of mean force associated with translocation using standard all-atom (CHARMM36 lipid) and polarizable and nonpolarizable Martini force fields, as well as a series of modified Martini-based parameter sets. We find that we are able to reproduce qualitative features of potentials of mean force of single amino acid side chain analogues into model bilayers. In particular, modifications of peptide-water and peptide-membrane interactions allow prediction of free energy minima at the bilayer-water interface as obtained with all-atom force fields. In the case of oligo-arginine peptides, the modified parameter sets predict interfacial free energy minima as well as free energy barriers in almost quantitative agreement with all-atom force field based simulations. Interfacial free energy minima predicted by a modified coarse-grained parameter set are -2.51, -4.28, and -5.42 for mono-, di-, and triarginine; corresponding values from all-atom simulations are -0.83, -3.33, and -3.29, respectively, all in units of kcal/mol. We found that a stronger interaction between oligo-arginine and the membrane components and a weaker interaction between oligo-arginine and water are crucial for producing such minima in PMFs using the polarizable CG model. The difference between bulk aqueous and bilayer center states predicted by the modified coarse-grain force field are 11.71, 14.14, and 16.53 kcal/mol, and those by the all-atom model are 6.94, 8.64, and 12.80 kcal/mol; those are of almost the same order of magnitude. Our simulations also demonstrate a remarkable similarity in the structural aspects of the ensemble of

  10. Characteristics of Spatial Structural Patterns and Temporal Variability of Annual Precipitation in Ningxia

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    [Objective] The aim was to study the characteristics of the spatial structural patterns and temporal variability of annual precipitation in Ningxia.[Method] Using rotated empirical orthogonal function,the precipitation concentration index,wavelet analysis and Mann-Kendall rank statistic method,the characteristics of precipitation on the spatial-temporal variability and trend were analyzed by the monthly precipitation series in Ningxia during 1951-2008.[Result] In Ningxia,the spatial structural patterns of a...

  11. Characterization of coarse particulate matter in school gyms

    International Nuclear Information System (INIS)

    Branis, Martin; Safranek, Jiri

    2011-01-01

    We investigated the mass concentration, mineral composition and morphology of particles resuspended by children during scheduled physical education in urban, suburban and rural elementary school gyms in Prague (Czech Republic). Cascade impactors were deployed to sample the particulate matter. Two fractions of coarse particulate matter (PM 10-2.5 and PM 2.5-1.0 ) were characterized by gravimetry, energy dispersive X-ray spectrometry and scanning electron microscopy. Two indicators of human activity, the number of exercising children and the number of physical education hours, were also recorded. Lower mass concentrations of coarse particulate matter were recorded outdoors (average PM 10-2.5 4.1-7.4 μg m -3 and PM 2.5-1.0 2.0-3.3 μg m -3 ) than indoors (average PM 10-2.5 13.6-26.7 μg m -3 and PM 2.5-1.0 3.7-7.4 μg m -3 ). The indoor concentrations of coarse aerosol were elevated during days with scheduled physical education with an average indoor-outdoor (I/O) ratio of 2.5-16.3 for the PM 10-2.5 and 1.4-4.8 for the PM 2.5-1.0 values. Under extreme conditions, the I/O ratios reached 180 (PM 10-2.5 ) and 19.1 (PM 2.5-1.0 ). The multiple regression analysis based on the number of students and outdoor coarse PM as independent variables showed that the main predictor of the indoor coarse PM concentrations is the number of students in the gym. The effect of outdoor coarse PM was weak and inconsistent. The regression models for the three schools explained 60-70% of the particular dataset variability. X-ray spectrometry revealed 6 main groups of minerals contributing to resuspended indoor dust. The most abundant particles were those of crustal origin composed of Si, Al, O and Ca. Scanning electron microscopy showed that, in addition to numerous inorganic particles, various types of fibers and particularly skin scales make up the main part of the resuspended dust in the gyms. In conclusion, school gyms were found to be indoor microenvironments with high concentrations of

  12. The Relative Importance of Spatial Versus Temporal Structure in the Perception of Biological Motion: An Event-Related Potential Study

    Science.gov (United States)

    Hirai, Masahiro; Hiraki, Kazuo

    2006-01-01

    We investigated how the spatiotemporal structure of animations of biological motion (BM) affects brain activity. We measured event-related potentials (ERPs) during the perception of BM under four conditions: normal spatial and temporal structure; scrambled spatial and normal temporal structure; normal spatial and scrambled temporal structure; and…

  13. Effect of fly ash on the strength of porous concrete using recycled coarse aggregate to replace low-quality natural coarse aggregate

    Science.gov (United States)

    Arifi, Eva; Cahya, Evi Nur; Christin Remayanti, N.

    2017-09-01

    The performance of porous concrete made of recycled coarse aggregate was investigated. Fly ash was used as cement partial replacement. In this study, the strength of recycled aggregate was coMPared to low quality natural coarse aggregate which has high water absorption. Compression strength and tensile splitting strength test were conducted to evaluate the performance of porous concrete using fly ash as cement replacement. Results have shown that the utilization of recycled coarse aggregate up to 75% to replace low quality natural coarse aggregate with high water absorption increases compressive strength and splitting tensile strength of porous concrete. Using fly ash up to 25% as cement replacement improves compressive strength and splitting tensile strength of porous concrete.

  14. A Method Based on Semi-Solid Forming for Eliminating Coarse Dendrites and Shrinkage Porosity of H13 Tool Steel

    Directory of Open Access Journals (Sweden)

    Yifeng Guo

    2018-04-01

    Full Text Available A method called forging solidifying metal (FSM, which is applied for eliminating coarse dendrites and shrinkage porosity defects of ferrous alloys was proposed based on semi-solid forming technology (SSF. To verify its feasibility, the effects of liquid fraction (FL on the microstructure of the deformed H13 steel were investigated experimentally. The coarse dendrites structure still existed and cracks appeared when the 0.1/s 50% FSM method was carried out at ~20% FL. What is significantly different from that is, the elimination of the coarse dendrites structure and shrinkage porosity defects became more significant, when this method was conducted at the end of solidification (FL < 10%. The microstructure of H13 steel was significantly refined and also became dense in such condition.

  15. The temporal structure of pollution levels in developed cities.

    Science.gov (United States)

    Barrigón Morillas, Juan Miguel; Ortiz-Caraballo, Carmen; Prieto Gajardo, Carlos

    2015-06-01

    Currently, the need for mobility can cause significant pollution levels in cities, with important effects on health and quality of life. Any approach to the study of urban pollution and its effects requires an analysis of spatial distribution and temporal variability. It is a crucial dilemma to obtain proven methodologies that allow an increase in the quality of the prediction and the saving of resources in the spatial and temporal sampling. This work proposes a new analytical methodology in the study of temporal structure. As a result, a model for estimating annual levels of urban traffic noise was proposed. The average errors are less than one decibel in all acoustics indicators. A new working methodology of urban noise has begun. Additionally, a general application can be found for the study of the impacts of pollution associated with traffic, with implications for urban design and possibly in economic and sociological aspects. Copyright © 2015 Elsevier B.V. All rights reserved.

  16. Susceptibility of coarse-textured soils to soil erosion by water in the tropics

    International Nuclear Information System (INIS)

    Salako, F.K.

    2004-01-01

    The application of soil physics for the evaluation of factors of soil erosion in the tropics received considerable attention in the last four decades. In Nigeria, physical characteristics of rainfall such as drop size and drop-size distribution, rainfall intensity at short intervals and kinetic energy of rainfall were evaluated using different methods. Thus, compound erosivity indices were evaluated which showed a similar trend in annual rainfall erosivity with annual rainfall amounts. Attempts have also been made to use geostatistical tools and fractal theory to describe temporal variability in rainfall erosivity. High erosivity aggravates the vulnerability of coarse-textured soils to erosion. These soils, high in sand content were poorly aggregated and structurally weak. Thus, they were easily detached and transported by runoff. Long-term data are needed to describe factors of soil erosion in the tropics but quite often, equipment are not available or poorly maintained where available such that useful data are not collected. A greater cooperation of pure physicists, soil physicists and engineers in the developing nations is needed to improve or design equipment and methods for the characterization of factors of soil erosion in the tropics. (author)

  17. Quantization of systems with temporally varying discretization. I. Evolving Hilbert spaces

    International Nuclear Information System (INIS)

    Höhn, Philipp A.

    2014-01-01

    A temporally varying discretization often features in discrete gravitational systems and appears in lattice field theory models subject to a coarse graining or refining dynamics. To better understand such discretization changing dynamics in the quantum theory, an according formalism for constrained variational discrete systems is constructed. While this paper focuses on global evolution moves and, for simplicity, restricts to flat configuration spaces R N , a Paper II [P. A. Höhn, “Quantization of systems with temporally varying discretization. II. Local evolution moves,” J. Math. Phys., e-print http://arxiv.org/abs/arXiv:1401.7731 [gr-qc].] discusses local evolution moves. In order to link the covariant and canonical picture, the dynamics of the quantum states is generated by propagators which satisfy the canonical constraints and are constructed using the action and group averaging projectors. This projector formalism offers a systematic method for tracing and regularizing divergences in the resulting state sums. Non-trivial coarse graining evolution moves lead to non-unitary, and thus irreversible, projections of physical Hilbert spaces and Dirac observables such that these concepts become evolution move dependent on temporally varying discretizations. The formalism is illustrated in a toy model mimicking a “creation from nothing.” Subtleties arising when applying such a formalism to quantum gravity models are discussed

  18. Multiscale coarse-graining of the protein energy landscape.

    Directory of Open Access Journals (Sweden)

    Ronald D Hills

    2010-06-01

    Full Text Available A variety of coarse-grained (CG models exists for simulation of proteins. An outstanding problem is the construction of a CG model with physically accurate conformational energetics rivaling all-atom force fields. In the present work, atomistic simulations of peptide folding and aggregation equilibria are force-matched using multiscale coarse-graining to develop and test a CG interaction potential of general utility for the simulation of proteins of arbitrary sequence. The reduced representation relies on multiple interaction sites to maintain the anisotropic packing and polarity of individual sidechains. CG energy landscapes computed from replica exchange simulations of the folding of Trpzip, Trp-cage and adenylate kinase resemble those of other reduced representations; non-native structures are observed with energies similar to those of the native state. The artifactual stabilization of misfolded states implies that non-native interactions play a deciding role in deviations from ideal funnel-like cooperative folding. The role of surface tension, backbone hydrogen bonding and the smooth pairwise CG landscape is discussed. Ab initio folding aside, the improved treatment of sidechain rotamers results in stability of the native state in constant temperature simulations of Trpzip, Trp-cage, and the open to closed conformational transition of adenylate kinase, illustrating the potential value of the CG force field for simulating protein complexes and transitions between well-defined structural states.

  19. Characterization of coarse particulate matter in school gyms

    Energy Technology Data Exchange (ETDEWEB)

    Branis, Martin, E-mail: branis@natur.cuni.cz [Charles University in Prague, Faculty of Science, Institute for Environmental Studies, Prague (Czech Republic); Safranek, Jiri [Charles University in Prague, Faculty of Physical Education, Department of Outdoor Sports, Prague (Czech Republic)

    2011-05-15

    We investigated the mass concentration, mineral composition and morphology of particles resuspended by children during scheduled physical education in urban, suburban and rural elementary school gyms in Prague (Czech Republic). Cascade impactors were deployed to sample the particulate matter. Two fractions of coarse particulate matter (PM{sub 10-2.5} and PM{sub 2.5-1.0}) were characterized by gravimetry, energy dispersive X-ray spectrometry and scanning electron microscopy. Two indicators of human activity, the number of exercising children and the number of physical education hours, were also recorded. Lower mass concentrations of coarse particulate matter were recorded outdoors (average PM{sub 10-2.5} 4.1-7.4 {mu}g m{sup -3} and PM{sub 2.5-1.0} 2.0-3.3 {mu}g m{sup -3}) than indoors (average PM{sub 10-2.5} 13.6-26.7 {mu}g m{sup -3} and PM{sub 2.5-1.0} 3.7-7.4 {mu}g m{sup -3}). The indoor concentrations of coarse aerosol were elevated during days with scheduled physical education with an average indoor-outdoor (I/O) ratio of 2.5-16.3 for the PM{sub 10-2.5} and 1.4-4.8 for the PM{sub 2.5-1.0} values. Under extreme conditions, the I/O ratios reached 180 (PM{sub 10-2.5}) and 19.1 (PM{sub 2.5-1.0}). The multiple regression analysis based on the number of students and outdoor coarse PM as independent variables showed that the main predictor of the indoor coarse PM concentrations is the number of students in the gym. The effect of outdoor coarse PM was weak and inconsistent. The regression models for the three schools explained 60-70% of the particular dataset variability. X-ray spectrometry revealed 6 main groups of minerals contributing to resuspended indoor dust. The most abundant particles were those of crustal origin composed of Si, Al, O and Ca. Scanning electron microscopy showed that, in addition to numerous inorganic particles, various types of fibers and particularly skin scales make up the main part of the resuspended dust in the gyms. In conclusion, school

  20. Nucleotide-induced conformational dynamics in ABC transporters from structure-based coarse grained modelling.

    Science.gov (United States)

    Flechsig, Holger

    2016-02-01

    ATP-binding cassette (ABC) transporters are integral membrane proteins which mediate the exchange of diverse substrates across membranes powered by ATP molecules. Our understanding of their activity is still hampered since the conformational dynamics underlying the operation of such proteins cannot yet be resolved in detailed molecular dynamics studies. Here a coarse grained model which allows to mimic binding of nucleotides and follow subsequent conformational motions of full-length transporter structures in computer simulations is proposed and implemented. To justify its explanatory quality, the model is first applied to the maltose transporter system for which multiple conformations are known and we find that the model predictions agree remarkably well with the experimental data. For the MalK subunit the switching from open to the closed dimer configuration upon ATP binding is reproduced and, moreover, for the full-length maltose transporter, progression from inward-facing to the outward-facing state is correctly obtained. For the heme transporter HmuUV, for which only the free structure could yet be determined, the model was then applied to predict nucleotide-induced conformational motions. Upon binding of ATP-mimicking ligands the structure changed from a conformation in which the nucleotide-binding domains formed an open shape, to a conformation in which they were found in tight contact, while, at the same time, a pronounced rotation of the transmembrane domains was observed. This finding is supported by normal mode analysis, and, comparison with structural data of the homologous vitamin B12 transporter BtuCD suggests that the observed rotation mechanism may contribute a common functional aspect for this class of ABC transporters. Although in HmuuV noticeable rearrangement of essential transmembrane helices was detected, there are no indications from our simulations that ATP binding alone may facilitate propagation of substrate molecules in this transporter

  1. Temporal event structure and timing in schizophrenia: preserved binding in a longer "now".

    Science.gov (United States)

    Martin, Brice; Giersch, Anne; Huron, Caroline; van Wassenhove, Virginie

    2013-01-01

    Patients with schizophrenia experience a loss of temporal continuity or subjective fragmentation along the temporal dimension. Here, we develop the hypothesis that impaired temporal awareness results from a perturbed structuring of events in time-i.e., canonical neural dynamics. To address this, 26 patients and their matched controls took part in two psychophysical studies using desynchronized audiovisual speech. Two tasks were used and compared: first, an identification task testing for multisensory binding impairments in which participants reported what they heard while looking at a speaker's face; in a second task, we tested the perceived simultaneity of the same audiovisual speech stimuli. In both tasks, we used McGurk fusion and combination that are classic ecologically valid multisensory illusions. First, and contrary to previous reports, our results show that patients do not significantly differ from controls in their rate of illusory reports. Second, the illusory reports of patients in the identification task were more sensitive to audiovisual speech desynchronies than those of controls. Third, and surprisingly, patients considered audiovisual speech to be synchronized for longer delays than controls. As such, the temporal tolerance profile observed in a temporal judgement task was less of a predictor for sensory binding in schizophrenia than for that obtained in controls. We interpret our results as an impairment of temporal event structuring in schizophrenia which does not specifically affect sensory binding operations but rather, the explicit access to timing information associated here with audiovisual speech processing. Our findings are discussed in the context of curent neurophysiological frameworks for the binding and the structuring of sensory events in time. Copyright © 2012 Elsevier Ltd. All rights reserved.

  2. How spatio-temporal habitat connectivity affects amphibian genetic structure.

    Science.gov (United States)

    Watts, Alexander G; Schlichting, Peter E; Billerman, Shawn M; Jesmer, Brett R; Micheletti, Steven; Fortin, Marie-Josée; Funk, W Chris; Hapeman, Paul; Muths, Erin; Murphy, Melanie A

    2015-01-01

    Heterogeneous landscapes and fluctuating environmental conditions can affect species dispersal, population genetics, and genetic structure, yet understanding how biotic and abiotic factors affect population dynamics in a fluctuating environment is critical for species management. We evaluated how spatio-temporal habitat connectivity influences dispersal and genetic structure in a population of boreal chorus frogs (Pseudacris maculata) using a landscape genetics approach. We developed gravity models to assess the contribution of various factors to the observed genetic distance as a measure of functional connectivity. We selected (a) wetland (within-site) and (b) landscape matrix (between-site) characteristics; and (c) wetland connectivity metrics using a unique methodology. Specifically, we developed three networks that quantify wetland connectivity based on: (i) P. maculata dispersal ability, (ii) temporal variation in wetland quality, and (iii) contribution of wetland stepping-stones to frog dispersal. We examined 18 wetlands in Colorado, and quantified 12 microsatellite loci from 322 individual frogs. We found that genetic connectivity was related to topographic complexity, within- and between-wetland differences in moisture, and wetland functional connectivity as contributed by stepping-stone wetlands. Our results highlight the role that dynamic environmental factors have on dispersal-limited species and illustrate how complex asynchronous interactions contribute to the structure of spatially-explicit metapopulations.

  3. How spatio-temporal habitat connectivity affects amphibian genetic structure

    Science.gov (United States)

    Watts, Alexander G.; Schlichting, P; Billerman, S; Jesmer, B; Micheletti, S; Fortin, M.-J.; Funk, W.C.; Hapeman, P; Muths, Erin L.; Murphy, M.A.

    2015-01-01

    Heterogeneous landscapes and fluctuating environmental conditions can affect species dispersal, population genetics, and genetic structure, yet understanding how biotic and abiotic factors affect population dynamics in a fluctuating environment is critical for species management. We evaluated how spatio-temporal habitat connectivity influences dispersal and genetic structure in a population of boreal chorus frogs (Pseudacris maculata) using a landscape genetics approach. We developed gravity models to assess the contribution of various factors to the observed genetic distance as a measure of functional connectivity. We selected (a) wetland (within-site) and (b) landscape matrix (between-site) characteristics; and (c) wetland connectivity metrics using a unique methodology. Specifically, we developed three networks that quantify wetland connectivity based on: (i) P. maculata dispersal ability, (ii) temporal variation in wetland quality, and (iii) contribution of wetland stepping-stones to frog dispersal. We examined 18 wetlands in Colorado, and quantified 12 microsatellite loci from 322 individual frogs. We found that genetic connectivity was related to topographic complexity, within- and between-wetland differences in moisture, and wetland functional connectivity as contributed by stepping-stone wetlands. Our results highlight the role that dynamic environmental factors have on dispersal-limited species and illustrate how complex asynchronous interactions contribute to the structure of spatially-explicit metapopulations.

  4. Extracting the Textual and Temporal Structure of Supercomputing Logs

    Energy Technology Data Exchange (ETDEWEB)

    Jain, S; Singh, I; Chandra, A; Zhang, Z; Bronevetsky, G

    2009-05-26

    Supercomputers are prone to frequent faults that adversely affect their performance, reliability and functionality. System logs collected on these systems are a valuable resource of information about their operational status and health. However, their massive size, complexity, and lack of standard format makes it difficult to automatically extract information that can be used to improve system management. In this work we propose a novel method to succinctly represent the contents of supercomputing logs, by using textual clustering to automatically find the syntactic structures of log messages. This information is used to automatically classify messages into semantic groups via an online clustering algorithm. Further, we describe a methodology for using the temporal proximity between groups of log messages to identify correlated events in the system. We apply our proposed methods to two large, publicly available supercomputing logs and show that our technique features nearly perfect accuracy for online log-classification and extracts meaningful structural and temporal message patterns that can be used to improve the accuracy of other log analysis techniques.

  5. Autobiographical memory in temporal lobe epilepsy: role of hippocampal and temporal lateral structures.

    Science.gov (United States)

    Herfurth, Kirsten; Kasper, Burkhard; Schwarz, Michael; Stefan, Hermann; Pauli, Elisabeth

    2010-11-01

    The present study was aimed at investigating the impact of hippocampal and temporal cortical lesions on remote autobiographical memories in temporal lobe epilepsy (TLE). Episodic specificity, episodic richness, and personal semantic memory from different life periods were assessed using a modified version of the Autobiographical Memory Interview (AMI) (M.D. Kopelman, A.E. Wilson, A. Baddeley, The autobiographical memory interview. Bury St. Edmunds: Thames Valley Test Co.; 1990) in 47 patients with unilateral mesial or lateral TLE and 38 healthy controls. Patients with TLE performed significantly more poorly than controls. Patients with left and right mTLE were equally moderately impaired, but patients with left lateral TLE had the most severe episodic memory deficits, particularly for childhood memories. With respect to personal semantic memory, patients with left TLE were significantly more impaired than those with right TLE, most pronounced for childhood memories. Both autobiographical memory aspects, episodic and personal semantic memory, were significantly intercorrelated, but both did not correlate with anterograde memory, indicating a structural dissociation between both functions. Copyright © 2010 Elsevier Inc. All rights reserved.

  6. Coarse-grained model for the interconversion between different crystalline cellulose allomorphs

    Energy Technology Data Exchange (ETDEWEB)

    Langan, Paul [ORNL

    2012-01-01

    We present the results of Langevin dynamics simulations on a coarse grained model for crystalline cellulose. In particular, we analyze two different cellulose crystalline forms: cellulose I (the natural form of cellulose) and cellulose IIII (obtained after cellulose I is treated with anhydrous liquid ammonia). Cellulose IIII has been the focus of wide interest in the field of cellulosic biofuels as it can be efficiently hydrolyzed to glucose (its enzymatic degradation rates are up to 5 fold higher than those of cellulose I ). In turn, glucose can eventually be fermented into fuels. The coarse-grained model presented in this study is based on a simplified geometry and on an effective potential mimicking the changes in both intracrystalline hydrogen bonds and stacking interactions during the transition from cellulose I to cellulose IIII. The model accurately reproduces both structural and thermomechanical properties of cellulose I and IIII. The work presented herein describes the structural transition from cellulose I to cellulose IIII as driven by the change in the equilibrium state of two degrees of freedom in the cellulose chains. The structural transition from cellulose I to cellulose IIII is essentially reduced to a search for optimal spatial arrangement of the cellulose chains.

  7. Remote Sensing of River Delta Inundation: Exploiting the Potential of Coarse Spatial Resolution, Temporally-Dense MODIS Time Series

    Directory of Open Access Journals (Sweden)

    Claudia Kuenzer

    2015-07-01

    Full Text Available River deltas belong to the most densely settled places on earth. Although they only account for 5% of the global land surface, over 550 million people live in deltas. These preferred livelihood locations, which feature flat terrain, fertile alluvial soils, access to fluvial and marine resources, a rich wetland biodiversity and other advantages are, however, threatened by numerous internal and external processes. Socio-economic development, urbanization, climate change induced sea level rise, as well as flood pulse changes due to upstream water diversion all lead to changes in these highly dynamic systems. A thorough understanding of a river delta’s general setting and intra-annual as well as long-term dynamic is therefore crucial for an informed management of natural resources. Here, remote sensing can play a key role in analyzing and monitoring these vast areas at a global scale. The goal of this study is to demonstrate the potential of intra-annual time series analyses at dense temporal, but coarse spatial resolution for inundation characterization in five river deltas located in four different countries. Based on 250 m MODIS reflectance data we analyze inundation dynamics in four densely populated Asian river deltas—namely the Yellow River Delta (China, the Mekong Delta (Vietnam, the Irrawaddy Delta (Myanmar, and the Ganges-Brahmaputra (Bangladesh, India—as well as one very contrasting delta: the nearly uninhabited polar Mackenzie Delta Region in northwestern Canada for the complete time span of one year (2013. A complex processing chain of water surface derivation on a daily basis allows the generation of intra-annual time series, which indicate inundation duration in each of the deltas. Our analyses depict distinct inundation patterns within each of the deltas, which can be attributed to processes such as overland flooding, irrigation agriculture, aquaculture, or snowmelt and thermokarst processes. Clear differences between mid

  8. Structural variation of alpha-synuclein with temperature by a coarse-grained approach with knowledge-based interactions

    Directory of Open Access Journals (Sweden)

    Peter Mirau

    2015-09-01

    Full Text Available Despite enormous efforts, our understanding the structure and dynamics of α-synuclein (ASN, a disordered protein (that plays a key role in neurodegenerative disease is far from complete. In order to better understand sequence-structure-property relationships in α-SYNUCLEIN we have developed a coarse-grained model using knowledge-based residue-residue interactions and used it to study the structure of free ASN as a function of temperature (T with a large-scale Monte Carlo simulation. Snapshots of the simulation and contour contact maps show changes in structure formation due to self-assembly as a function of temperature. Variations in the residue mobility profiles reveal clear distinction among three segments along the protein sequence. The N-terminal (1-60 and C-terminal (96-140 regions contain the least mobile residues, which are separated by the higher mobility non-amyloid component (NAC (61-95. Our analysis of the intra-protein contact profile shows a higher frequency of residue aggregation (clumping in the N-terminal region relative to that in the C-terminal region, with little or no aggregation in the NAC region. The radius of gyration (Rg of ASN decays monotonically with decreasing the temperature, consistent with the finding of Allison et al. (JACS, 2009. Our analysis of the structure function provides an insight into the mass (N distribution of ASN, and the dimensionality (D of the structure as a function of temperature. We find that the globular structure with D ≈ 3 at low T, a random coil, D ≈ 2 at high T and in between (2 ≤ D ≤ 3 at the intermediate temperatures. The magnitudes of D are in agreement with experimental estimates (J. Biological Chem 2002.

  9. Early seizure propagation from the occipital lobe to medial temporal structures and its surgical implication.

    Science.gov (United States)

    Usui, Naotaka; Mihara, Tadahiro; Baba, Koichi; Matsuda, Kazumi; Tottori, Takayasu; Umeoka, Shuichi; Nakamura, Fumihiro; Terada, Kiyohito; Usui, Keiko; Inoue, Yushi

    2008-12-01

    Intracranial EEG documentation of seizure propagation from the occipital lobe to medial temporal structures is relatively rare. We retrospectively analyzed intracranial EEG recorded with electrodes implanted in the medial temporal lobe in patients who underwent occipital lobe surgery. Four patients with occipital lesions, who underwent intracranial EEG monitoring with intracerebral electrodes implanted in the medial temporal lobe prior to occipital lobe surgery, were studied. Subdural electrodes were placed over the occipital lobe and adjacent areas. Intracerebral electrodes were implanted into bilateral hippocampi and the amygdala in three patients, and in the hippocampus and amygdala ipsilateral to the lesion in one. In light of the intracranial EEG findings, the occipital lobe was resected but the medial temporal lobe was spared in all patients. The follow-up period ranged from six to 16 years, and seizure outcome was Engel Class I in all patients. Sixty six seizures were analyzed. The majority of the seizures originated from the occipital lobe. In complex partial seizures, ictal discharges propagated to the medial temporal lobe. No seizures originating from the temporal lobe were documented. In some seizures, the ictal-onset zone could not be identified. In these seizures, very early propagation to the medial temporal lobe was observed. Interictal spikes were recorded in the medial temporal lobe in all cases. Intracranial EEG revealed very early involvement of the medial temporal lobe in some seizures. Seizure control was achieved without resection of the medial temporal structures.

  10. Effect of solvent on the structure of a protein (H3.1) with a coarse-grained model with knowledge-based interactions

    Science.gov (United States)

    Pandey, Ras; Farmer, Barry

    2013-03-01

    Quality of solvent plays a critical role in modulating the structure of a protein along with the temperature. Using a coarse-grained Monte Carlo simulation based on three knowledge-based contact potentials (MJ, BT, BFKV) we examine the structure and dynamics of a histone (H3.1). The empty lattice sites constitute the effective solvent medium in which the protein is embedded. Residue-solvent characteristic interaction is based on the hydropathy index while the residue-residue interaction is used from the knowledge-based contact matrices derived from ensembles of protein structures in the protein data bank. Large scale simulations are performed to analyze the structure of protein for a range of residue-solvent interaction strength, a measure of the solvent quality with each potential. Unlike the monotonic thermal response, the radius of gyration of the protein exhibits non-monotonic dependence of the solvent strength. Quantitative comparison of the structure and dynamics emerging from three knowledge-based potentials will be presented in this talk. This work is supported by Air Force Research Laboratory.

  11. Visualization of subtle temporal bone structures. Comparison of cone beam CT and MDCT

    International Nuclear Information System (INIS)

    Pein, M.K.; Plontke, S.K.; Brandt, S.; Koesling, S.

    2014-01-01

    The purpose of this study was to compare the visualization of subtle, non-pathological temporal bone structures on cone beam computed tomography (CBCT) and multi-detector computed tomography (MDCT) in vivo. Temporal bone studies of images from 38 patients archived in the picture archiving and communication system (PACS) were analyzed (slice thickness MDCT 0.6 mm and CBCT 0.125 mm) of which 23 were imaged by MDCT and 15 by CBCT using optimized standard protocols. Inclusion criteria were normal radiological findings, absence of previous surgery and anatomical variants. Images were evaluated blind by three trained observers. Using a five-point scale the visualization of ten subtle structures of the temporal bone was analyzed. Subtle middle ear structures showed a tendency to be more easily distinguishable by CBCT with significantly better visualization of the tendon of the stapedius muscle and the crura of the stapes on CBCT (p = 0.003 and p = 0.033, respectively). In contrast, inner ear components, such as the osseus spiral lamina and the modiolus tended to be better detectable on MDCT, showing significant differences for the osseous spiral lamina (p = 0.001). The interrater reliability was 0.73 (Cohen's kappa coefficient) and intraobserver reliability was 0.89. The use of CBCT and MDCT allows equivalent and excellent imaging results if optimized protocols are chosen. With both imaging techniques subtle temporal bone structures could be visualized with a similar degree of definition. In vivo differences do not seem to be as large as suggested in several previous studies. (orig.) [de

  12. Field description of coarse bioclastic fabrics

    Energy Technology Data Exchange (ETDEWEB)

    Kidwell, S.M.; Holland, S.M. (Univ. of Chicago, IL (United States))

    1991-08-01

    Shell- and bone-bearing rocks can be readily categorized into 9 macroscopic fabric types using semi-quantitative scales for close-packing and size-sorting of bioclasts greater than 2 mm in diameter. Although designed to describe fossiliferous siliciclastics and volcaniclastics, this system of field description can also be used to enlarge upon standard petrographic descriptions of fossiliferous carbonates. In cross-sectional bed views, coarse bioclasts may be densely packed. These coarse bioclasts (>2 mm) may be well sorted (central 80% of bioclasts lie within 1 or 2 adjacent phi size-classes), bimodal (well sorted but with a distinct second mode), or poorly sorted (central 80% of bioclasts distributed over 3 or more adjacent size-classes). Despite the complicating effects of bioclast shape, novices show 90% accuracy in estimating close-packing from photographs. They have only 60% accuracy in estimating size-sorting (the most common error is underestimating goodness of sorting), underscoring the importance of size-tallies to cross-check visual estimates when first using this scheme. This packing/sorting approach provides a good visual image of the fabric, and narrows the range of possible modes of origin more than alternative criteria such as volumetric percent-abundance (which shows no one-to-one equivalence with close-packing), orientation, and fragmentation. However, detailed interpretations of fabrics usually require more information on these and other features of the deposit, including bioclast condition, associated sedimentary structures, life-habits of bioclast-producers, and stratigraphic context.

  13. Early deterioration of coarse woody debris.

    Energy Technology Data Exchange (ETDEWEB)

    Tainter, Frank, H.; McMinn, James, W.

    1999-02-16

    Tainter, F.H., and J.W. McMinn. 1999. Early deterioration of coarse woody debris. In: Proc. Tenth Bien. South. Silv. Res. Conf. Shreveport, LA, February 16-18, 1999. Pp. 232-237 Abstract - Coarse woody debris (CWD) is an important structural component of southern forest ecosystems. CWD loading may be affected by different decomposition rates on sites of varying quality. Bolts of red oak and loblolly pine were placed on plots at each of three (hydric, mesic. and xerlc) sites at the Savannah River Site and sampled over a I6-week period. Major changes were in moisture content and nonstructural carbohydrate content (total carbohydrates, reducing sugars, and starch) of sapwood. Early changes in nonstructural carbohydrate levels following placement of the bolts were likely due to reallocation of these materials by sapwood parenchyma cells. These carbohydrates later formed pools increasingly metabolized by bacteria and invading fungi. Most prevalent fungi in sapwood were Ceratocysfis spp. in pine and Hypoxy/on spp. in oak. Although pine sapwood became blue stained and oak sapwood exhibited yellow soft decay with black zone lines, estimators of decay (specific gravity, sodium hydroxide solubility, and holocellulose content) were unchanged during the 16-week study period. A small effect of site was detected for starch content of sapwood of both species. Fungal biomass in sapwood of both species, as measured by ergosterol content, was detectable at week zero, increased somewhat by week three and increased significantly by week 16.

  14. Role of Neutral Lipids in Tear Fluid Lipid Layer: Coarse-Grained Simulation Study

    DEFF Research Database (Denmark)

    Telenius, J.; Koivuniemi, A.; Kulovesi, P.

    2012-01-01

    Tear fluid lipid layer (TFLL) residing at the air-water interface of tears has been recognized to play an important role in the development of dry eye syndrome. Yet, the composition, structure, and mechanical properties of TFLL are only partly known. Here, we report results of coarse...

  15. Radiative Heat Transfer in Combustion Applications: Parallel Efficiencies of Two Gas Models, Turbulent Radiation Interactions in Particulate Laden Flows, and Coarse Mesh Finite Difference Acceleration for Improved Temporal Accuracy

    Science.gov (United States)

    Cleveland, Mathew A.

    We investigate several aspects of the numerical solution of the radiative transfer equation in the context of coal combustion: the parallel efficiency of two commonly-used opacity models, the sensitivity of turbulent radiation interaction (TRI) effects to the presence of coal particulate, and an improvement of the order of temporal convergence using the coarse mesh finite difference (CMFD) method. There are four opacity models commonly employed to evaluate the radiative transfer equation in combustion applications; line-by-line (LBL), multigroup, band, and global. Most of these models have been rigorously evaluated for serial computations of a spectrum of problem types [1]. Studies of these models for parallel computations [2] are limited. We assessed the performance of the Spectral-Line-Based weighted sum of gray gasses (SLW) model, a global method related to K-distribution methods [1], and the LBL model. The LBL model directly interpolates opacity information from large data tables. The LBL model outperforms the SLW model in almost all cases, as suggested by Wang et al. [3]. The SLW model, however, shows superior parallel scaling performance and a decreased sensitivity to load imbalancing, suggesting that for some problems, global methods such as the SLW model, could outperform the LBL model. Turbulent radiation interaction (TRI) effects are associated with the differences in the time scales of the fluid dynamic equations and the radiative transfer equations. Solving on the fluid dynamic time step size produces large changes in the radiation field over the time step. We have modified the statistically homogeneous, non-premixed flame problem of Deshmukh et al. [4] to include coal-type particulate. The addition of low mass loadings of particulate minimally impacts the TRI effects. Observed differences in the TRI effects from variations in the packing fractions and Stokes numbers are difficult to analyze because of the significant effect of variations in problem

  16. Coarse Thinking and Pricing a Financial Option

    OpenAIRE

    Siddiqi, Hammad

    2009-01-01

    Mullainathan et al [Quarterly Journal of Economics, May 2008] present a formalization of the concept of coarse thinking in the context of a model of persuasion. The essential idea behind coarse thinking is that people put situations into categories and the values assigned to attributes in a given situation are affected by the values of corresponding attributes in other co-categorized situations. We derive a new option pricing formula based on the assumption that the market consists of coars...

  17. Temporal structure in neuronal activity during working memory in Macaque parietal cortex

    CERN Document Server

    Pesaran, B; Sahami, M; Mitra, P; Andersen, R A

    2000-01-01

    A number of cortical structures are reported to have elevated single unit firing rates sustained throughout the memory period of a working memory task. How the nervous system forms and maintains these memories is unknown but reverberating neuronal network activity is thought to be important. We studied the temporal structure of single unit (SU) activity and simultaneously recorded local field potential (LFP) activity from area LIP in the inferior parietal lobe of two awake macaques during a memory-saccade task. Using multitaper techniques for spectral analysis, which play an important role in obtaining the present results, we find elevations in spectral power in a 50--90 Hz (gamma) frequency band during the memory period in both SU and LFP activity. The activity is tuned to the direction of the saccade providing evidence for temporal structure that codes for movement plans during working memory. We also find SU and LFP activity are coherent during the memory period in the 50--90 Hz gamma band and no consisten...

  18. Behaviour of fibre reinforced concrete using steel slag coarse aggregate produced in Qatar

    Directory of Open Access Journals (Sweden)

    Alnahhal Wael

    2017-01-01

    Full Text Available The state of Qatar suffers from the shortage of natural resources needed for concrete production. Therefore, it is essential to investigate the feasibility of using by-product recycled materials as aggregates to maintain the concrete construction industry. Several types of recyclable materials are currently used in concrete. One of the potential resources of recycled concrete is steel slag. Knowing that Steel slag is the most significant solid waste generated by Qatar Steel Company in Qatar, replacing of natural coarse aggregate with steel slag aggregate will have a significant environmental and economic impact to the state of Qatar. This paper presents the compression and flexural test results of different concrete mixes made of steel slag coarse aggregate combined with a newly developed basalt chopped fibres. The parameters investigated included the volume fraction of the fibre used and the type of coarse aggregates (natural aggregates “Gabbro” and steel slag aggregates. Plain concrete specimens containing natural coarse aggregates and steel slag aggregates with no fibres added were also tested to serve as control. Test results showed that adding the basalt chopped fibres to the concrete mixes enhanced their flexural tensile strengths at different percentages. In addition, the compressive strength of concrete made with steel slag aggregate was higher than that made with natural gabbro aggregate. Test results clearly showed that steel slag aggregates can be used as sustainable and eco-friendly alternative materials in concrete structures.

  19. Classical density functional theory & simulations on a coarse-grained model of aromatic ionic liquids.

    Science.gov (United States)

    Turesson, Martin; Szparaga, Ryan; Ma, Ke; Woodward, Clifford E; Forsman, Jan

    2014-05-14

    A new classical density functional approach is developed to accurately treat a coarse-grained model of room temperature aromatic ionic liquids. Our major innovation is the introduction of charge-charge correlations, which are treated in a simple phenomenological way. We test this theory on a generic coarse-grained model for aromatic RTILs with oligomeric forms for both cations and anions, approximating 1-alkyl-3-methyl imidazoliums and BF₄⁻, respectively. We find that predictions by the new density functional theory for fluid structures at charged surfaces are very accurate, as compared with molecular dynamics simulations, across a range of surface charge densities and lengths of the alkyl chain. Predictions of interactions between charged surfaces are also presented.

  20. Preferential binding effects on protein structure and dynamics revealed by coarse-grained Monte Carlo simulation

    Science.gov (United States)

    Pandey, R. B.; Jacobs, D. J.; Farmer, B. L.

    2017-05-01

    The effect of preferential binding of solute molecules within an aqueous solution on the structure and dynamics of the histone H3.1 protein is examined by a coarse-grained Monte Carlo simulation. The knowledge-based residue-residue and hydropathy-index-based residue-solvent interactions are used as input to analyze a number of local and global physical quantities as a function of the residue-solvent interaction strength (f). Results from simulations that treat the aqueous solution as a homogeneous effective solvent medium are compared to when positional fluctuations of the solute molecules are explicitly considered. While the radius of gyration (Rg) of the protein exhibits a non-monotonic dependence on solvent interaction over a wide range of f within an effective medium, an abrupt collapse in Rg occurs in a narrow range of f when solute molecules rapidly bind to a preferential set of sites on the protein. The structure factor S(q) of the protein with wave vector (q) becomes oscillatory in the collapsed state, which reflects segmental correlations caused by spatial fluctuations in solute-protein binding. Spatial fluctuations in solute binding also modify the effective dimension (D) of the protein in fibrous (D ˜ 1.3), random-coil (D ˜ 1.75), and globular (D ˜ 3) conformational ensembles as the interaction strength increases, which differ from an effective medium with respect to the magnitude of D and the length scale.

  1. Property A and Coarse Embedding for Locally Compact Groups

    DEFF Research Database (Denmark)

    Li, Kang

    property A. In a joint work with Knudby, we characterize the connected simple Lie groups with the discrete topology that have different approximation properties (see Article B). Moreover, we give a contractive Schur multiplier characterization of locally compact groups coarsely embeddable into Hilbert......In the study of the Novikov conjecture, property A and coarse embedding of metric spaces were introduced by Yu and Gromov, respectively. The main topic of the thesis is property A and coarse embedding for locally compact second countable groups. We prove that many of the results that are known...... to hold in the discrete setting, hold also in the locally compact setting.In a joint work with Deprez, we show that property A is equivalent to amenability at infinity and the strong Novikov conjecture is true for every locally compact group that embeds coarsely into a Hilbert space (see Article A...

  2. Two-level method with coarse space size independent convergence

    Energy Technology Data Exchange (ETDEWEB)

    Vanek, P.; Brezina, M. [Univ. of Colorado, Denver, CO (United States); Tezaur, R.; Krizkova, J. [UWB, Plzen (Czech Republic)

    1996-12-31

    The basic disadvantage of the standard two-level method is the strong dependence of its convergence rate on the size of the coarse-level problem. In order to obtain the optimal convergence result, one is limited to using a coarse space which is only a few times smaller than the size of the fine-level one. Consequently, the asymptotic cost of the resulting method is the same as in the case of using a coarse-level solver for the original problem. Today`s two-level domain decomposition methods typically offer an improvement by yielding a rate of convergence which depends on the ratio of fine and coarse level only polylogarithmically. However, these methods require the use of local subdomain solvers for which straightforward application of iterative methods is problematic, while the usual application of direct solvers is expensive. We suggest a method diminishing significantly these difficulties.

  3. Estimating spatio-temporal dynamics of size-structured populations

    DEFF Research Database (Denmark)

    Kristensen, Kasper; Thygesen, Uffe Høgsbro; Andersen, Ken Haste

    2014-01-01

    with simple stock dynamics, to estimate simultaneously how size distributions and spatial distributions develop in time. We demonstrate the method for a cod population sampled by trawl surveys. Particular attention is paid to correlation between size classes within each trawl haul due to clustering...... of individuals with similar size. The model estimates growth, mortality and reproduction, after which any aspect of size-structure, spatio-temporal population dynamics, as well as the sampling process can be probed. This is illustrated by two applications: 1) tracking the spatial movements of a single cohort...

  4. Quantum Mechanics/Molecular Mechanics Method Combined with Hybrid All-Atom and Coarse-Grained Model: Theory and Application on Redox Potential Calculations.

    Science.gov (United States)

    Shen, Lin; Yang, Weitao

    2016-04-12

    We developed a new multiresolution method that spans three levels of resolution with quantum mechanical, atomistic molecular mechanical, and coarse-grained models. The resolution-adapted all-atom and coarse-grained water model, in which an all-atom structural description of the entire system is maintained during the simulations, is combined with the ab initio quantum mechanics and molecular mechanics method. We apply this model to calculate the redox potentials of the aqueous ruthenium and iron complexes by using the fractional number of electrons approach and thermodynamic integration simulations. The redox potentials are recovered in excellent accordance with the experimental data. The speed-up of the hybrid all-atom and coarse-grained water model renders it computationally more attractive. The accuracy depends on the hybrid all-atom and coarse-grained water model used in the combined quantum mechanical and molecular mechanical method. We have used another multiresolution model, in which an atomic-level layer of water molecules around redox center is solvated in supramolecular coarse-grained waters for the redox potential calculations. Compared with the experimental data, this alternative multilayer model leads to less accurate results when used with the coarse-grained polarizable MARTINI water or big multipole water model for the coarse-grained layer.

  5. Dispersal Ability Determines the Role of Environmental, Spatial and Temporal Drivers of Metacommunity Structure

    Science.gov (United States)

    Padial, André A.; Ceschin, Fernanda; Declerck, Steven A. J.; De Meester, Luc; Bonecker, Cláudia C.; Lansac-Tôha, Fabio A.; Rodrigues, Liliana; Rodrigues, Luzia C.; Train, Sueli; Velho, Luiz F. M.; Bini, Luis M.

    2014-01-01

    Recently, community ecologists are focusing on the relative importance of local environmental factors and proxies to dispersal limitation to explain spatial variation in community structure. Albeit less explored, temporal processes may also be important in explaining species composition variation in metacommunities occupying dynamic systems. We aimed to evaluate the relative role of environmental, spatial and temporal variables on the metacommunity structure of different organism groups in the Upper Paraná River floodplain (Brazil). We used data on macrophytes, fish, benthic macroinvertebrates, zooplankton, periphyton, and phytoplankton collected in up to 36 habitats during a total of eight sampling campaigns over two years. According to variation partitioning results, the importance of predictors varied among biological groups. Spatial predictors were particularly important for organisms with comparatively lower dispersal ability, such as aquatic macrophytes and fish. On the other hand, environmental predictors were particularly important for organisms with high dispersal ability, such as microalgae, indicating the importance of species sorting processes in shaping the community structure of these organisms. The importance of watercourse distances increased when spatial variables were the main predictors of metacommunity structure. The contribution of temporal predictors was low. Our results emphasize the strength of a trait-based analysis and of better defining spatial variables. More importantly, they supported the view that “all-or- nothing” interpretations on the mechanisms structuring metacommunities are rather the exception than the rule. PMID:25340577

  6. Temporal lobe structures and facial emotion recognition in schizophrenia patients and nonpsychotic relatives.

    Science.gov (United States)

    Goghari, Vina M; Macdonald, Angus W; Sponheim, Scott R

    2011-11-01

    Temporal lobe abnormalities and emotion recognition deficits are prominent features of schizophrenia and appear related to the diathesis of the disorder. This study investigated whether temporal lobe structural abnormalities were associated with facial emotion recognition deficits in schizophrenia and related to genetic liability for the disorder. Twenty-seven schizophrenia patients, 23 biological family members, and 36 controls participated. Several temporal lobe regions (fusiform, superior temporal, middle temporal, amygdala, and hippocampus) previously associated with face recognition in normative samples and found to be abnormal in schizophrenia were evaluated using volumetric analyses. Participants completed a facial emotion recognition task and an age recognition control task under time-limited and self-paced conditions. Temporal lobe volumes were tested for associations with task performance. Group status explained 23% of the variance in temporal lobe volume. Left fusiform gray matter volume was decreased by 11% in patients and 7% in relatives compared with controls. Schizophrenia patients additionally exhibited smaller hippocampal and middle temporal volumes. Patients were unable to improve facial emotion recognition performance with unlimited time to make a judgment but were able to improve age recognition performance. Patients additionally showed a relationship between reduced temporal lobe gray matter and poor facial emotion recognition. For the middle temporal lobe region, the relationship between greater volume and better task performance was specific to facial emotion recognition and not age recognition. Because schizophrenia patients exhibited a specific deficit in emotion recognition not attributable to a generalized impairment in face perception, impaired emotion recognition may serve as a target for interventions.

  7. Coarse-graining stochastic biochemical networks: adiabaticity and fast simulations

    Energy Technology Data Exchange (ETDEWEB)

    Nemenman, Ilya [Los Alamos National Laboratory; Sinitsyn, Nikolai [Los Alamos National Laboratory; Hengartner, Nick [Los Alamos National Laboratory

    2008-01-01

    We propose a universal approach for analysis and fast simulations of stiff stochastic biochemical kinetics networks, which rests on elimination of fast chemical species without a loss of information about mesoscoplc, non-Poissonian fluctuations of the slow ones. Our approach, which is similar to the Born-Oppenhelmer approximation in quantum mechanics, follows from the stochastic path Integral representation of the cumulant generating function of reaction events. In applications with a small number of chemIcal reactions, It produces analytical expressions for cumulants of chemical fluxes between the slow variables. This allows for a low-dimensional, Interpretable representation and can be used for coarse-grained numerical simulation schemes with a small computational complexity and yet high accuracy. As an example, we derive the coarse-grained description for a chain of biochemical reactions, and show that the coarse-grained and the microscopic simulations are in an agreement, but the coarse-gralned simulations are three orders of magnitude faster.

  8. Object-Based Paddy Rice Mapping Using HJ-1A/B Data and Temporal Features Extracted from Time Series MODIS NDVI Data.

    Science.gov (United States)

    Singha, Mrinal; Wu, Bingfang; Zhang, Miao

    2016-12-22

    Accurate and timely mapping of paddy rice is vital for food security and environmental sustainability. This study evaluates the utility of temporal features extracted from coarse resolution data for object-based paddy rice classification of fine resolution data. The coarse resolution vegetation index data is first fused with the fine resolution data to generate the time series fine resolution data. Temporal features are extracted from the fused data and added with the multi-spectral data to improve the classification accuracy. Temporal features provided the crop growth information, while multi-spectral data provided the pattern variation of paddy rice. The achieved overall classification accuracy and kappa coefficient were 84.37% and 0.68, respectively. The results indicate that the use of temporal features improved the overall classification accuracy of a single-date multi-spectral image by 18.75% from 65.62% to 84.37%. The minimum sensitivity (MS) of the paddy rice classification has also been improved. The comparison showed that the mapped paddy area was analogous to the agricultural statistics at the district level. This work also highlighted the importance of feature selection to achieve higher classification accuracies. These results demonstrate the potential of the combined use of temporal and spectral features for accurate paddy rice classification.

  9. Characterization of coarse particulate matter in school gyms.

    Science.gov (United States)

    Braniš, Martin; Šafránek, Jiří

    2011-05-01

    We investigated the mass concentration, mineral composition and morphology of particles resuspended by children during scheduled physical education in urban, suburban and rural elementary school gyms in Prague (Czech Republic). Cascade impactors were deployed to sample the particulate matter. Two fractions of coarse particulate matter (PM(10-2.5) and PM(2.5-1.0)) were characterized by gravimetry, energy dispersive X-ray spectrometry and scanning electron microscopy. Two indicators of human activity, the number of exercising children and the number of physical education hours, were also recorded. Lower mass concentrations of coarse particulate matter were recorded outdoors (average PM(10-2.5) 4.1-7.4 μg m(-3) and PM(2.5-1.0) 2.0-3.3 μg m(-3)) than indoors (average PM(10-2.5) 13.6-26.7 μg m(-3) and PM(2.5-1.0) 3.7-7.4 μg m(-3)). The indoor concentrations of coarse aerosol were elevated during days with scheduled physical education with an average indoor-outdoor (I/O) ratio of 2.5-16.3 for the PM(10-2.5) and 1.4-4.8 for the PM(2.5-1.0) values. Under extreme conditions, the I/O ratios reached 180 (PM(10-2.5)) and 19.1 (PM(2.5-1.0)). The multiple regression analysis based on the number of students and outdoor coarse PM as independent variables showed that the main predictor of the indoor coarse PM concentrations is the number of students in the gym. The effect of outdoor coarse PM was weak and inconsistent. The regression models for the three schools explained 60-70% of the particular dataset variability. X-ray spectrometry revealed 6 main groups of minerals contributing to resuspended indoor dust. The most abundant particles were those of crustal origin composed of Si, Al, O and Ca. Scanning electron microscopy showed that, in addition to numerous inorganic particles, various types of fibers and particularly skin scales make up the main part of the resuspended dust in the gyms. In conclusion, school gyms were found to be indoor microenvironments with high

  10. Non-periodic molecular dynamics simulations of coarse grained lipid bilayer in water

    DEFF Research Database (Denmark)

    Kotsalis, E. M.; Hanasaki, I.; Walther, Jens Honore

    2010-01-01

    We present a multiscale algorithm that couples coarse grained molecular dynamics (CGMD) with continuum solver. The coupling requires the imposition of non-periodic boundary conditions on the coarse grained Molecular Dynamics which, when not properly enforced, may result in spurious fluctuations o...... in simulating more complex systems by performing a non-periodic Molecular Dynamics simulation of a DPPC lipid in liquid coarse grained water.......We present a multiscale algorithm that couples coarse grained molecular dynamics (CGMD) with continuum solver. The coupling requires the imposition of non-periodic boundary conditions on the coarse grained Molecular Dynamics which, when not properly enforced, may result in spurious fluctuations...... of the material properties of the system represented by CGMD. In this paper we extend a control algorithm originally developed for atomistic simulations [3], to conduct simulations involving coarse grained water molecules without periodic boundary conditions. We demonstrate the applicability of our method...

  11. Grasping the mechanisms of narratives' incoherence in schizophrenia: an analysis of the temporal structure of patients' life story.

    Science.gov (United States)

    Allé, M C; Gandolphe, M-C; Doba, K; Köber, C; Potheegadoo, J; Coutelle, R; Habermas, T; Nandrino, J-L; Danion, J-M; Berna, F

    2016-08-01

    Life narratives of patients with schizophrenia are characterized by impaired coherence so that the listener has often difficulties to grasp the life trajectory of the patients. In order to better understand what causes this reduced temporal coherence, we investigated the temporal structure of patients' life narratives through different temporal narrative elements (elaboration of beginnings and endings, local temporal indicators and temporal deviations from a linear order), across two complementary studies. Life narratives were collected by means of two different methods; a free recall in study 1 and a more structured protocol, aiming at reducing the cognitive task demands in study 2. All narratives from the two studies were analyzed using the same validated method. Both studies showed that global temporal coherence is significantly reduced in patients with schizophrenia (ps.02). This is mainly due to their stronger tendency to temporally deviate from a linear temporal order without marking the deviation as such. We also observed significant correlations in the patient groups between global temporal coherence and executive dysfunction (p=.008) or their higher tendency to temporally deviate from a linear temporal order in their life narratives (p<.001). These results shed light on narrative correlates of temporal narrative incoherence in schizophrenia and highlight the central role of executive dysfunction in this incoherence. Copyright © 2016 Elsevier Inc. All rights reserved.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-11-15

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

  13. Temporal and spatial influences incur reconfiguration of Arctic heathland soil bacterial community structure.

    Science.gov (United States)

    Hill, Richard; Saetnan, Eli R; Scullion, John; Gwynn-Jones, Dylan; Ostle, Nick; Edwards, Arwyn

    2016-06-01

    Microbial responses to Arctic climate change could radically alter the stability of major stores of soil carbon. However, the sensitivity of plot-scale experiments simulating climate change effects on Arctic heathland soils to potential confounding effects of spatial and temporal changes in soil microbial communities is unknown. Here, the variation in heathland soil bacterial communities at two survey sites in Sweden between spring and summer 2013 and at scales between 0-1 m and, 1-100 m and between sites (> 100 m) were investigated in parallel using 16S rRNA gene T-RFLP and amplicon sequencing. T-RFLP did not reveal spatial structuring of communities at scales structuring effects may not confound comparison between plot-scale treatments, temporal change is a significant influence. Moreover, the prominence of two temporally exclusive keystone taxa suggests that the stability of Arctic heathland soil bacterial communities could be disproportionally influenced by seasonal perturbations affecting individual taxa. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

  14. FROM ATOMISTIC TO SYSTEMATIC COARSE-GRAINED MODELS FOR MOLECULAR SYSTEMS

    KAUST Repository

    Harmandaris, Vagelis; Kalligiannaki, Evangelia; Katsoulakis, Markos; Plechac, Petr

    2017-01-01

    The development of systematic (rigorous) coarse-grained mesoscopic models for complex molecular systems is an intense research area. Here we first give an overview of methods for obtaining optimal parametrized coarse-grained models, starting from

  15. Influence of musical training on sensitivity to temporal fine structure.

    Science.gov (United States)

    Mishra, Srikanta K; Panda, Manasa R; Raj, Swapna

    2015-04-01

    The objective of this study was to extend the findings that temporal fine structure encoding is altered in musicians by examining sensitivity to temporal fine structure (TFS) in an alternative (non-Western) musician model that is rarely adopted--Indian classical music. The sensitivity to TFS was measured by the ability to discriminate two complex tones that differed in TFS but not in envelope repetition rate. Sixteen South Indian classical (Carnatic) musicians and 28 non-musicians with normal hearing participated in this study. Musicians have significantly lower relative frequency shift at threshold in the TFS task compared to non-musicians. A significant negative correlation was observed between years of musical experience and relative frequency shift at threshold in the TFS task. Test-retest repeatability of thresholds in the TFS tasks was similar for both musicians and non-musicians. The enhanced performance of the Carnatic-trained musicians suggests that the musician advantage for frequency and harmonicity discrimination is not restricted to training in Western classical music, on which much of the previous research on musical training has narrowly focused. The perceptual judgments obtained from non-musicians were as reliable as those of musicians.

  16. Modelling airborne dispersion of coarse particulate material

    International Nuclear Information System (INIS)

    Apsley, D.D.

    1989-03-01

    Methods of modelling the airborne dispersion and deposition of coarse particulates are presented, with the emphasis on the heavy particles identified as possible constituents of releases from damaged AGR fuel. The first part of this report establishes the physical characteristics of the irradiated particulate in airborne emissions from AGR stations. The second part is less specific and describes procedures for extending current dispersion/deposition models to incorporate a coarse particulate component: the adjustment to plume spread parameters, dispersion from elevated sources and dispersion in conjunction with building effects and plume rise. (author)

  17. Recycled Coarse Aggregate Produced by Pulsed Discharge in Water

    Science.gov (United States)

    Namihira, Takao; Shigeishi, Mitsuhiro; Nakashima, Kazuyuki; Murakami, Akira; Kuroki, Kaori; Kiyan, Tsuyoshi; Tomoda, Yuichi; Sakugawa, Takashi; Katsuki, Sunao; Akiyama, Hidenori; Ohtsu, Masayasu

    In Japan, the recycling ratio of concrete scraps has been kept over 98 % after the Law for the Recycling of Construction Materials was enforced in 2000. In the present, most of concrete scraps were recycled as the Lower Subbase Course Material. On the other hand, it is predicted to be difficult to keep this higher recycling ratio in the near future because concrete scraps increase rapidly and would reach to over 3 times of present situation in 2010. In addition, the demand of concrete scraps as the Lower Subbase Course Material has been decreased. Therefore, new way to reuse concrete scraps must be developed. Concrete scraps normally consist of 70 % of coarse aggregate, 19 % of water and 11 % of cement. To obtain the higher recycling ratio, the higher recycling ratio of coarse aggregate is desired. In this paper, a new method for recycling coarse aggregate from concrete scraps has been developed and demonstrated. The system includes a Marx generator and a point to hemisphere mesh electrode immersed in water. In the demonstration, the test piece of concrete scrap was located between the electrodes and was treated by the pulsed discharge. After discharge treatment of test piece, the recycling coarse aggregates were evaluated under JIS and TS and had enough quality for utilization as the coarse aggregate.

  18. Near equilibrium dynamics and one-dimensional spatial—temporal structures of polar active liquid crystals

    International Nuclear Information System (INIS)

    Yang Xiao-Gang; Wang Qi; Forest, M. Gregory

    2014-01-01

    We systematically explore near equilibrium, flow-driven, and flow-activity coupled dynamics of polar active liquid crystals using a continuum model. Firstly, we re-derive the hydrodynamic model to ensure the thermodynamic laws are obeyed and elastic stresses and forces are consistently accounted. We then carry out a linear stability analysis about constant steady states to study near equilibrium dynamics around the steady states, revealing long-wave instability inherent in this model system and how active parameters in the model affect the instability. We then study model predictions for one-dimensional (1D) spatial—temporal structures of active liquid crystals in a channel subject to physical boundary conditions. We discuss the model prediction in two selected regimes, one is the viscous stress dominated regime, also known as the flow-driven regime, while the other is the full regime, in which all active mechanisms are included. In the viscous stress dominated regime, the polarity vector is driven by the prescribed flow field. Dynamics depend sensitively on the physical boundary condition and the type of the driven flow field. Bulk-dominated temporal periodic states and spatially homogeneous states are possible under weak anchoring conditions while spatially inhomogeneous states exist under strong anchoring conditions. In the full model, flow-orientation interaction generates a host of planar as well as out-of-plane spatial—temporal structures related to the spontaneous flows due to the molecular self-propelled motion. These results provide contact with the recent literature on active nematic suspensions. In addition, symmetry breaking patterns emerge as the additional active viscous stress due to the polarity vector is included in the force balance. The inertia effect is found to limit the long-time survival of spatial structures to those with small wave numbers, i.e., an asymptotic coarsening to long wave structures. A rich set of mechanisms for generating

  19. Chemical-mineralogical characterisation of coarse recycled concrete aggregate

    International Nuclear Information System (INIS)

    Limbachiya, M.C.; Marrocchino, E.; Koulouris, A.

    2007-01-01

    The construction industry is now putting greater emphasis than ever before on increasing recycling and promoting more sustainable waste management practices. In keeping with this approach, many sectors of the industry have actively sought to encourage the use of recycled concrete aggregate (RCA) as an alternative to primary aggregates in concrete production. The results of a laboratory experimental programme aimed at establishing chemical and mineralogical characteristics of coarse RCA and its likely influence on concrete performance are reported in this paper. Commercially produced coarse RCA and natural aggregates (16-4 mm size fraction) were tested. Results of X-ray fluorescence (XRF) analyses showed that original source of RCA had a negligible effect on the major elements and a comparable chemical composition between recycled and natural aggregates. X-ray diffraction (XRD) analyses results indicated the presence of calcite, portlandite and minor peaks of muscovite/illite in recycled aggregates, although they were directly proportioned to their original composition. The influence of 30%, 50%, and 100% coarse RCA on the chemical composition of equal design strength concrete has been established, and its suitability for use in a concrete application has been assessed. In this work, coarse RCA was used as a direct replacement for natural gravel in concrete production. Test results indicated that up to 30% coarse RCA had no effect on the main three oxides (SiO 2 , Al 2 O 3 and CaO) of concrete, but thereafter there was a marginal decrease in SiO 2 and increase in Al 2 O 3 and CaO contents with increase in RCA content in the mix, reflecting the original constituent's composition

  20. Chemical-mineralogical characterisation of coarse recycled concrete aggregate.

    Science.gov (United States)

    Limbachiya, M C; Marrocchino, E; Koulouris, A

    2007-01-01

    The construction industry is now putting greater emphasis than ever before on increasing recycling and promoting more sustainable waste management practices. In keeping with this approach, many sectors of the industry have actively sought to encourage the use of recycled concrete aggregate (RCA) as an alternative to primary aggregates in concrete production. The results of a laboratory experimental programme aimed at establishing chemical and mineralogical characteristics of coarse RCA and its likely influence on concrete performance are reported in this paper. Commercially produced coarse RCA and natural aggregates (16-4 mm size fraction) were tested. Results of X-ray fluorescence (XRF) analyses showed that original source of RCA had a negligible effect on the major elements and a comparable chemical composition between recycled and natural aggregates. X-ray diffraction (XRD) analyses results indicated the presence of calcite, portlandite and minor peaks of muscovite/illite in recycled aggregates, although they were directly proportioned to their original composition. The influence of 30%, 50%, and 100% coarse RCA on the chemical composition of equal design strength concrete has been established, and its suitability for use in a concrete application has been assessed. In this work, coarse RCA was used as a direct replacement for natural gravel in concrete production. Test results indicated that up to 30% coarse RCA had no effect on the main three oxides (SiO2, Al2O3 and CaO) of concrete, but thereafter there was a marginal decrease in SiO2 and increase in Al2O3 and CaO contents with increase in RCA content in the mix, reflecting the original constituent's composition.

  1. Testing for entanglement with periodic coarse graining

    Science.gov (United States)

    Tasca, D. S.; Rudnicki, Łukasz; Aspden, R. S.; Padgett, M. J.; Souto Ribeiro, P. H.; Walborn, S. P.

    2018-04-01

    Continuous-variable systems find valuable applications in quantum information processing. To deal with an infinite-dimensional Hilbert space, one in general has to handle large numbers of discretized measurements in tasks such as entanglement detection. Here we employ the continuous transverse spatial variables of photon pairs to experimentally demonstrate entanglement criteria based on a periodic structure of coarse-grained measurements. The periodization of the measurements allows an efficient evaluation of entanglement using spatial masks acting as mode analyzers over the entire transverse field distribution of the photons and without the need to reconstruct the probability densities of the conjugate continuous variables. Our experimental results demonstrate the utility of the derived criteria with a success rate in entanglement detection of ˜60 % relative to 7344 studied cases.

  2. Coarse graining of atactic polystyrene and its derivatives

    Science.gov (United States)

    Agrawal, Anupriya; Perahia, Dvora; Grest, Gary S.

    2014-03-01

    Capturing large length scales in polymers and soft matter while retaining atomistic properties is imperative to computational studies of dynamic systems. Here we present a new methodology developing coarse-grain model based on atomistic simulation of atactic polystyrene (PS). Similar to previous work by Fritz et al., each monomer is described by two coarse grained beads. In contrast to this earlier work where intramolecular potentials were based on Monte Carlo simulation of both isotactic and syndiotactic single PS molecule to capture stereochemistry, we obtained intramolecular interactions from a single molecular dynamics simulation of an all-atom atactic PS melts. The non-bonded interactions are obtained using the iterative Boltzmann inversion (IBI) scheme. This methodology has been extended to coarse graining of poly-(t-butyl-styrene) (PtBS). An additional coarse-grained bead is used to describe the t-butyl group. Similar to the process for PS, the intramolecular interactions are obtained from a single all atom atactic melt simulation. Starting from the non-bonded interactions for PS, we show that the IBI method for the non-bonded interactions of PtBS converges relatively fast. A generalized scheme for substituted PS is currently in development. We would like to acknowledge Prof. Kurt Kremer for helpful discussions during this work.

  3. Temperature dependent mechanical properties and thermal activation plasticity of nanocrystalline and coarse grained Ni-18.75 at.% Fe alloy

    International Nuclear Information System (INIS)

    Tabachnikova, E D; Podolskiy, A V; Smirnov, S N; Psaruk, I A; Liao, P K

    2014-01-01

    Mechanical properties of Ni-18.75 at.% Fe in coarse grained (average grain size 15 gm) and nanocrystalline (average grain size 22 nm) states were studied in uniaxial compression in the temperature range 4.2-350 K. Temperature dependences of the flow stress, strain rate sensitivity and activation volume of plastic deformation were measured. The thermal activation analysis of the experimental data has been fulfilled for the the plastic deformation value of 2 %. It was shown that plastic deformation in temperature range from 35 to 350 K in both studied structural states has the thermally activated type. Comparative analysis of low temperature thermal activation plastic deformation was carried out for the alloy in coarse grained and nanocrystalline states. Empirical estimates of parameters of the dislocation interaction with local barriers and internal stress value estimates were obtained for the both studied structural states. Analysis of the results indicates that different mechanisms control the thermal activation plasticity of the Ni-18.75 at.% Fe alloy in coarse grained and nanocrystalline states. Possible mechanisms, which control plactisity of the studied states, are disscussed

  4. Coarse-graining free theories with gauge symmetries: the linearized case

    International Nuclear Information System (INIS)

    Bahr, Benjamin; Dittrich, Bianca; He Song

    2011-01-01

    Discretizations of continuum theories often do not preserve the gauge symmetry content. This occurs in particular for diffeomorphism symmetry in general relativity, which leads to severe difficulties in both canonical and covariant quantization approaches. We discuss here the method of perfect actions, which attempts to restore gauge symmetries by mirroring exactly continuum physics on a lattice via a coarse graining process. Analytical results can only be obtained via a perturbative approach, for which we consider the first step, namely the coarse graining of the linearized theory. The linearized gauge symmetries are exact also in the discretized theory; hence, we develop a formalism to deal with gauge systems. Finally, we provide a discretization of linearized gravity as well as a coarse graining map and show that with this choice the three-dimensional (3D) linearized gravity action is invariant under coarse graining.

  5. Nonlinear Multigrid solver exploiting AMGe Coarse Spaces with Approximation Properties

    DEFF Research Database (Denmark)

    Christensen, Max la Cour; Villa, Umberto; Engsig-Karup, Allan Peter

    The paper introduces a nonlinear multigrid solver for mixed finite element discretizations based on the Full Approximation Scheme (FAS) and element-based Algebraic Multigrid (AMGe). The main motivation to use FAS for unstructured problems is the guaranteed approximation property of the AMGe coarse...... properties of the coarse spaces. With coarse spaces with approximation properties, our FAS approach on unstructured meshes has the ability to be as powerful/successful as FAS on geometrically refined meshes. For comparison, Newton’s method and Picard iterations with an inner state-of-the-art linear solver...... are compared to FAS on a nonlinear saddle point problem with applications to porous media flow. It is demonstrated that FAS is faster than Newton’s method and Picard iterations for the experiments considered here. Due to the guaranteed approximation properties of our AMGe, the coarse spaces are very accurate...

  6. Technological possibilities for increasing coarse coal yield in the Staszic mine

    Energy Technology Data Exchange (ETDEWEB)

    Sikora, W; Major, M

    1985-06-01

    Experiments carried out in the Staszic underground black coal mine in Upper Silesia showed that there is a correlation of coarse coal yield and yield strength of shield supports used at longwall faces. The faces were equipped with Pioma 25-45, Fazos 15-31 and Fazos 19-32 shield supports, KWB 3RDU shearer loaders and Rybnik chain conveyors. Pressure of oil in water emulsion used in the Pioma 25/45 shield supports was reduced from the recommended 30 MPa to 15 MPa or to 10 MPa. Reducing emulsion pressure (and support yield strength) caused an increase in coarse coal yield. Coarse coal yield was also increased by use of Fazos 19/32 shield supports with reduced yield strength. During the tests coarse coal yield increased 1.68% and 2.65%. Test results are shown in 3 diagrams. Investigations carried out in the Staszic mine in 1983 showed that by optimizing yield strength of shield supports coarse coal yield could be increased 2 to 8%. 6 references.

  7. Temporal organization of cellular self-replication

    Science.gov (United States)

    Alexandrov, Victor; Pugatch, Rami

    Recent experiments demonstrate that single cells grow exponentially in time. A coarse grained model of cellular self-replication is presented based on a novel concept - the cell is viewed as a self-replicating queue. This allows to have a more fundamental look into various temporal organizations and, importantly, the inherent non-Markovianity of noise distributions. As an example, the distribution of doubling times can be inferred and compared to single cell experiments in bacteria. We observe data collapse upon scaling by the average doubling time for different environments and present an inherent task allocation trade-off. Support from the Simons Center for Systems Biology, IAS, Princeon.

  8. Effects of Particle Size on the Shear Behavior of Coarse Grained Soils Reinforced with Geogrid.

    Science.gov (United States)

    Kim, Daehyeon; Ha, Sungwoo

    2014-02-07

    In order to design civil structures that are supported by soils, the shear strength parameters of soils are required. Due to the large particle size of coarse-grained soils, large direct shear tests should be performed. In this study, large direct shear tests on three types of coarse grained soils (4.5 mm, 7.9 mm, and 15.9 mm) were performed to evaluate the effects of particle size on the shear behavior of coarse grained soils with/without geogrid reinforcements. Based on the direct shear test results, it was found that, in the case of no-reinforcement, the larger the maximum particle size became, the larger the friction angle was. Compared with the no-reinforcement case, the cases reinforced with either soft geogrid or stiff geogrid have smaller friction angles. The cohesion of the soil reinforced with stiff geogrid was larger than that of the soil reinforced with soft geogrid. The difference in the shear strength occurs because the case with a stiff geogrid has more soil to geogrid contact area, leading to the reduction in interlocking between soil particles.

  9. Temporal networks

    CERN Document Server

    Saramäki, Jari

    2013-01-01

    The concept of temporal networks is an extension of complex networks as a modeling framework to include information on when interactions between nodes happen. Many studies of the last decade examine how the static network structure affect dynamic systems on the network. In this traditional approach  the temporal aspects are pre-encoded in the dynamic system model. Temporal-network methods, on the other hand, lift the temporal information from the level of system dynamics to the mathematical representation of the contact network itself. This framework becomes particularly useful for cases where there is a lot of structure and heterogeneity both in the timings of interaction events and the network topology. The advantage compared to common static network approaches is the ability to design more accurate models in order to explain and predict large-scale dynamic phenomena (such as, e.g., epidemic outbreaks and other spreading phenomena). On the other hand, temporal network methods are mathematically and concept...

  10. Volume calculations of coarse woody debris; evaluation of coarse woody debris volume calculations and consequences for coarse woody debris volume estimates in forest reserves

    NARCIS (Netherlands)

    Wijdeven, S.M.J.; Vaessen, O.H.B.; Hees, van A.F.M.; Olsthoorn, A.F.M.

    2005-01-01

    Dead wood is recognized as one of the key indicators for sustainable forest management and biodiversity. Accurate assessments of dead wood volume are thus necessary. In this study New volume models were designed based on actual volume measurements of coarse woody debris. The New generic model

  11. Spacetime coarse grainings in nonrelativistic quantum mechanics

    International Nuclear Information System (INIS)

    Hartle, J.B.

    1991-01-01

    Sum-over-histories generalizations of nonrelativistic quantum mechanics are explored in which probabilities are predicted, not just for alternatives defined on spacelike surfaces, but for alternatives defined by the behavior of spacetime histories with respect to spacetime regions. Closed, nonrelativistic systems are discussed whose histories are paths in a given configuration space. The action and the initial quantum state are assumed fixed and given. A formulation of quantum mechanics is used which assigns probabilities to members of sets of alternative coarse-grained histories of the system, that is, to the individual classes of a partition of its paths into exhaustive and exclusive classes. Probabilities are assigned to those sets which decohere, that is, whose probabilities are consistent with the sum rules of probability theory. Coarse graining by the behavior of paths with respect to regions of spacetime is described. For example, given a single region, the set of all paths may be partitioned into those which never pass through the region and those which pass through the region at least once. A sum-over-histories decoherence functional is defined for sets of alternative histories coarse-grained by spacetime regions. Techniques for the definition and effective computation of the relevant sums over histories by operator-product formulas are described and illustrated by examples. Methods based on Euclidean stochastic processes are also discussed and illustrated. Models of decoherence and measurement for spacetime coarse grainings are described. Issues of causality are investigated. Such spacetime generalizations of nonrelativistic quantum mechanics may be useful models for a generalized quantum mechanics of spacetime geometry

  12. Constructing Optimal Coarse-Grained Sites of Huge Biomolecules by Fluctuation Maximization.

    Science.gov (United States)

    Li, Min; Zhang, John Zenghui; Xia, Fei

    2016-04-12

    Coarse-grained (CG) models are valuable tools for the study of functions of large biomolecules on large length and time scales. The definition of CG representations for huge biomolecules is always a formidable challenge. In this work, we propose a new method called fluctuation maximization coarse-graining (FM-CG) to construct the CG sites of biomolecules. The defined residual in FM-CG converges to a maximal value as the number of CG sites increases, allowing an optimal CG model to be rigorously defined on the basis of the maximum. More importantly, we developed a robust algorithm called stepwise local iterative optimization (SLIO) to accelerate the process of coarse-graining large biomolecules. By means of the efficient SLIO algorithm, the computational cost of coarse-graining large biomolecules is reduced to within the time scale of seconds, which is far lower than that of conventional simulated annealing. The coarse-graining of two huge systems, chaperonin GroEL and lengsin, indicates that our new methods can coarse-grain huge biomolecular systems with up to 10,000 residues within the time scale of minutes. The further parametrization of CG sites derived from FM-CG allows us to construct the corresponding CG models for studies of the functions of huge biomolecular systems.

  13. Optimization of droplets for UV-NIL using coarse-grain simulation of resist flow

    Science.gov (United States)

    Sirotkin, Vadim; Svintsov, Alexander; Zaitsev, Sergey

    2009-03-01

    A mathematical model and numerical method are described, which make it possible to simulate ultraviolet ("step and flash") nanoimprint lithography (UV-NIL) process adequately even using standard Personal Computers. The model is derived from 3D Navier-Stokes equations with the understanding that the resist motion is largely directed along the substrate surface and characterized by ultra-low values of the Reynolds number. By the numerical approximation of the model, a special finite difference method is applied (a coarse-grain method). A coarse-grain modeling tool for detailed analysis of resist spreading in UV-NIL at the structure-scale level is tested. The obtained results demonstrate the high ability of the tool to calculate optimal dispensing for given stamp design and process parameters. This dispensing provides uniform filled areas and a homogeneous residual layer thickness in UV-NIL.

  14. Temporal variation in bat-fruit interactions: Foraging strategies influence network structure over time

    Science.gov (United States)

    Zapata-Mesa, Natalya; Montoya-Bustamante, Sebastián; Murillo-García, Oscar E.

    2017-11-01

    Mutualistic interactions, such as seed dispersal, are important for the maintenance of structure and stability of tropical communities. However, there is a lack of information about spatial and temporal variation in plant-animal interaction networks. Thus, our goal was to assess the effect of bat's foraging strategies on temporal variation in the structure and robustness of bat-fruit networks in both a dry and a rain tropical forest. We evaluated monthly variation in bat-fruit networks by using seven structure metrics: network size, average path length, nestedness, modularity, complementary specialization, normalized degree and betweenness centrality. Seed dispersal networks showed variations in size, species composition and modularity; did not present nested structures and their complementary specialization was high compared to other studies. Both networks presented short path lengths, and a constantly high robustness, despite their monthly variations. Sedentary bat species were recorded during all the study periods and occupied more central positions than nomadic species. We conclude that foraging strategies are important structuring factors that affect the dynamic of networks by determining the functional roles of frugivorous bats over time; thus sedentary bats are more important than nomadic species for the maintenance of the network structure, and their conservation is a must.

  15. Some modifications of temporal relation in the sentence with the temporal clause

    Directory of Open Access Journals (Sweden)

    Antonić Ivana N.

    2013-01-01

    Full Text Available The subject matter of this paper is the modification of temporal relation in the complex sentence with the temporal clause. At the functional different Serbian language corpus the author notices the next types of modified temporality: excepted locational simultaneity complete or partial, and excepted locationalorientational posteriority formalized by the structure V SAMO/JEDINO/OSIM/SEM/IZUZEV(ONDA KAD VSub, and excepted locational simultaneity/excepted terminativity formalized by the structure V SAMO DOK (Neg VSub; sutuational locational simultaneity complete or partial formalized by the structure V U SITUACIJI / U SLUČAJU KAD VSub, with the posibility to be exceptivly modified in the structure V IZUZEV U SITUACIJI / U SLUČAJU KAD VSub; situational-concessive locational simultaneity complete or partial formalized by the structure V (ČAK I (ONDA KAD VSub; situational-conditional locational-orientational posteriority formalized by the structure V TEK (ONDA KAD VSub, and situational-conditional orientational posteriority formalized by the structure V TEK POŠTO VSub or V TEK NAKON ŠTO VSub and situational-conditional orientational quantified posteriority formalized by the structure V Quant TEK POŠTO VSub, and finaly situational-conditional terminativity formalized by the structure (Neg V SVE DOK Neg VSub. It can ocure sporadically supstitutiv temporality formalized by the structure V DetTemp (UMESTO KAD VSub, and consecutive-adversative temporality formalized by the structure KAD VSub A (ONDA V. [Projekat Ministarstva nauke Republike Srbije, br. 178004: Sintaksička, semantička i pragmatička istraživanja standardnog srpskog jezika

  16. Generating spatial precipitation ensembles: impact of temporal correlation structure

    Science.gov (United States)

    Rakovec, O.; Hazenberg, P.; Torfs, P. J. J. F.; Weerts, A. H.; Uijlenhoet, R.

    2012-09-01

    Sound spatially distributed rainfall fields including a proper spatial and temporal error structure are of key interest for hydrologists to force hydrological models and to identify uncertainties in the simulated and forecasted catchment response. The current paper presents a temporally coherent error identification method based on time-dependent multivariate spatial conditional simulations, which are conditioned on preceding simulations. A sensitivity analysis and real-world experiment are carried out within the hilly region of the Belgian Ardennes. Precipitation fields are simulated for pixels of 10 km × 10 km resolution. Uncertainty analyses in the simulated fields focus on (1) the number of previous simulation hours on which the new simulation is conditioned, (2) the advection speed of the rainfall event, (3) the size of the catchment considered, and (4) the rain gauge density within the catchment. The results for a sensitivity analysis show for typical advection speeds >20 km h-1, no uncertainty is added in terms of across ensemble spread when conditioned on more than one or two previous hourly simulations. However, for the real-world experiment, additional uncertainty can still be added when conditioning on a larger number of previous simulations. This is because for actual precipitation fields, the dynamics exhibit a larger spatial and temporal variability. Moreover, by thinning the observation network with 50%, the added uncertainty increases only slightly and the cross-validation shows that the simulations at the unobserved locations are unbiased. Finally, the first-order autocorrelation coefficients show clear temporal coherence in the time series of the areal precipitation using the time-dependent multivariate conditional simulations, which was not the case using the time-independent univariate conditional simulations. The presented work can be easily implemented within a hydrological calibration and data assimilation framework and can be used as an

  17. Decreased functional connectivity and structural deficit in alertness network with right-sided temporal lobe epilepsy.

    Science.gov (United States)

    Gao, Yujun; Zheng, Jinou; Li, Yaping; Guo, Danni; Wang, Mingli; Cui, Xiangxiang; Ye, Wei

    2018-04-01

    Patients with temporal lobe epilepsy (TLE) often suffer from alertness alterations. However, specific regions connected with alertness remain controversial, and whether these regions have structural impairment is also elusive. This study aimed to investigate the characteristics and neural mechanisms underlying the functions and structures of alertness network in patients with right-sided temporal lobe epilepsy (rTLE) by performing the attentional network test (ANT), resting-state functional magnetic resonance imaging (R-SfMRI), and diffusion tensor imaging (DTI).A total of 47 patients with rTLE and 34 healthy controls underwent ANT, R-SfMRI, and DTI scan. The seed-based functional connectivity (FC) method and deterministic tractography were used to analyze the data.Patients with rTLE had longer reaction times in the no-cue and double-cue conditions. However, no differences were noted in the alertness effect between the 2 groups. The patient group had lower FC compared with the control group in the right inferior parietal lobe (IPL), amygdala, and insula. Structural deficits were found in the right parahippocampal gyrus, superior temporal pole, insula, and amygdala in the patient group compared with the control group. Also significantly negative correlations were observed between abnormal fractional anisotropy (between the right insula and the superior temporal pole) and illness duration in the patients with rTLE.The findings of this study suggested abnormal intrinsic and phasic alertness, decreased FC, and structural deficits within the alerting network in the rTLE. This study provided new insights into the mechanisms of alertness alterations in rTLE.

  18. Entropies from Coarse-graining: Convex Polytopes vs. Ellipsoids

    Directory of Open Access Journals (Sweden)

    Nikos Kalogeropoulos

    2015-09-01

    Full Text Available We examine the Boltzmann/Gibbs/Shannon SBGS and the non-additive Havrda-Charvát/Daróczy/Cressie-Read/Tsallis Sq and the Kaniadakis κ-entropy Sκ from the viewpoint of coarse-graining, symplectic capacities and convexity. We argue that the functional form of such entropies can be ascribed to a discordance in phase-space coarse-graining between two generally different approaches: the Euclidean/Riemannian metric one that reflects independence and picks cubes as the fundamental cells in coarse-graining and the symplectic/canonical one that picks spheres/ellipsoids for this role. Our discussion is motivated by and confined to the behaviour of Hamiltonian systems of many degrees of freedom. We see that Dvoretzky’s theorem provides asymptotic estimates for the minimal dimension beyond which these two approaches are close to each other. We state and speculate about the role that dualities may play in this viewpoint.

  19. On the relationship between multi-channel envelope and temporal fine structure

    DEFF Research Database (Denmark)

    Søndergaard, Peter Lempel; Decorsiere, Remi Julien Blaise; Dau, Torsten

    2011-01-01

    The envelope of a signal is broadly defined as the slow changes in time of the signal, where as the temporal fine structure (TFS) are the fast changes in time, i.e. the carrier wave(s) of the signal. The focus of this paper is on envelope and TFS in multi-channel systems. We discuss the differenc...

  20. Structured spatio-temporal shot-noise Cox point process models, with a view to modelling forest fires

    DEFF Research Database (Denmark)

    Møller, Jesper; Diaz-Avalos, Carlos

    Spatio-temporal Cox point process models with a multiplicative structure for the driving random intensity, incorporating covariate information into temporal and spatial components, and with a residual term modelled by a shot-noise process, are considered. Such models are flexible and tractable fo...... dataset consisting of 2796 days and 5834 spatial locations of fires. The model is compared with a spatio-temporal log-Gaussian Cox point process model, and likelihood-based methods are discussed to some extent....

  1. Structured Spatio-temporal shot-noise Cox point process models, with a view to modelling forest fires

    DEFF Research Database (Denmark)

    Møller, Jesper; Diaz-Avalos, Carlos

    2010-01-01

    Spatio-temporal Cox point process models with a multiplicative structure for the driving random intensity, incorporating covariate information into temporal and spatial components, and with a residual term modelled by a shot-noise process, are considered. Such models are flexible and tractable fo...... data set consisting of 2796 days and 5834 spatial locations of fires. The model is compared with a spatio-temporal log-Gaussian Cox point process model, and likelihood-based methods are discussed to some extent....

  2. Renormalization and Coarse-graining of Loop Quantum Gravity

    OpenAIRE

    Charles, Christoph

    2017-01-01

    The continuum limit of loop quantum gravity is still an open problem. Indeed, no proper dynamics in known to start with and we still lack the mathematical tools to study its would-be continuum limit. In the present PhD dissertation, we will investigate some coarse-graining methods that should become helpful in this enterprise. We concentrate on two aspects of the theory's coarse-graining: finding natural large scale observables on one hand and studying how the dynamics of varying graphs could...

  3. Influence of uncoated and coated plastic waste coarse aggregates to concrete compressive strength

    OpenAIRE

    Purnomo Heru; Pamudji Gandjar; Satim Madsuri

    2017-01-01

    The use of plastic waste as coarse aggregates in concrete is part of efforts to reduce environmental pollution. In one hand the use of plastic as aggregates can provide lighter weight of the concrete than concrete using natural aggregates, but on the other hand bond between plastic coarse aggregates and hard matrix give low concrete compressive strength. Improvement of the bond between plastic coarse aggregate and hard matrix through a sand coating to plastic coarse aggregate whole surface is...

  4. A coarse-grained model for DNA origami.

    Science.gov (United States)

    Reshetnikov, Roman V; Stolyarova, Anastasia V; Zalevsky, Arthur O; Panteleev, Dmitry Y; Pavlova, Galina V; Klinov, Dmitry V; Golovin, Andrey V; Protopopova, Anna D

    2018-02-16

    Modeling tools provide a valuable support for DNA origami design. However, current solutions have limited application for conformational analysis of the designs. In this work we present a tool for a thorough study of DNA origami structure and dynamics. The tool is based on a novel coarse-grained model dedicated to geometry optimization and conformational analysis of DNA origami. We explored the ability of the model to predict dynamic behavior, global shapes, and fine details of two single-layer systems designed in hexagonal and square lattices using atomic force microscopy, Förster resonance energy transfer spectroscopy, and all-atom molecular dynamic simulations for validation of the results. We also examined the performance of the model for multilayer systems by simulation of DNA origami with published cryo-electron microscopy and atomic force microscopy structures. A good agreement between the simulated and experimental data makes the model suitable for conformational analysis of DNA origami objects. The tool is available at http://vsb.fbb.msu.ru/cosm as a web-service and as a standalone version.

  5. Resolving Properties of Polymers and Nanoparticle Assembly through Coarse-Grained Computational Studies.

    Energy Technology Data Exchange (ETDEWEB)

    Grest, Gary S. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2017-09-01

    Coupled length and time scales determine the dynamic behavior of polymers and polymer nanocomposites and underlie their unique properties. To resolve the properties over large time and length scales it is imperative to develop coarse grained models which retain the atomistic specificity. Here we probe the degree of coarse graining required to simultaneously retain significant atomistic details a nd access large length and time scales. The degree of coarse graining in turn sets the minimum length scale instrumental in defining polymer properties and dynamics. Using polyethylene as a model system, we probe how the coarse - graining scale affects the measured dynamics with different number methylene group s per coarse - grained beads. Using these models we simulate polyethylene melts for times over 500 ms to study the viscoelastic properties of well - entangled polymer melts and large nanoparticle assembly as the nanoparticles are driven close enough to form nanostructures.

  6. Characteristics of thin and coarse particulates of urban and natural brazilian aerosols

    International Nuclear Information System (INIS)

    Orsini, C.Q.; Tabacnics, M.H.; Artaxo, P.; Andrade, M.F.; Kerr, A.S.

    1994-01-01

    Thin and coarse particulate were sampled during the period 1982-1985 in a natural coastal forest (Jureia), and five urban-industrial regions (Vitoria, Salvador, Porto Alegre, Sao Paulo and Belo Horizonte). The time variation of the concentration in the air, and the relative elementary composition of the thin and coarse particulate, sampled by thin and Coarse Particulate Sampler (AFG), were determined by gravimetric method and PIXE analysis respectively. The results demonstrated that the ground dust and salt from the sea are unequivocally one of the largest sources of coarse particulate, and also the ground is a significant thin particulate source. 25 refs, 22 figs, 28 tabs. (L.C.J.A.)

  7. Importance of Coarse Woody Debris to Avian Communities in Loblolly Pine Forests

    Energy Technology Data Exchange (ETDEWEB)

    Lohr, S.M.; Gauthreaux, S.A.; Kilgo, J.C.

    2001-06-14

    Investigates the importance of standing and down coarse woody debris to bird communities in loblolly pine forests, researchers compared breeding and nonbreeding responses of birds among two coarse woody debris removal and control treatments. Quantification of vegetation layers to determine their effects on the experimental outcome coarse woody debris removal had no effect on the nonbreeding bird community. Most breeding and nonbreeding species used habitats with sparse midstory and well-developed understory, where as sparse canopy cover and dense midstory were important to some nonbreeding species. Snag and down coarse woody debris practices that maintain a dense understory, sparse midstory and canopy will create favorable breeding habitat.

  8. Coarse-graining using the relative entropy and simplex-based optimization methods in VOTCA

    Science.gov (United States)

    Rühle, Victor; Jochum, Mara; Koschke, Konstantin; Aluru, N. R.; Kremer, Kurt; Mashayak, S. Y.; Junghans, Christoph

    2014-03-01

    Coarse-grained (CG) simulations are an important tool to investigate systems on larger time and length scales. Several methods for systematic coarse-graining were developed, varying in complexity and the property of interest. Thus, the question arises which method best suits a specific class of system and desired application. The Versatile Object-oriented Toolkit for Coarse-graining Applications (VOTCA) provides a uniform platform for coarse-graining methods and allows for their direct comparison. We present recent advances of VOTCA, namely the implementation of the relative entropy method and downhill simplex optimization for coarse-graining. The methods are illustrated by coarse-graining SPC/E bulk water and a water-methanol mixture. Both CG models reproduce the pair distributions accurately. SYM is supported by AFOSR under grant 11157642 and by NSF under grant 1264282. CJ was supported in part by the NSF PHY11-25915 at KITP. K. Koschke acknowledges funding by the Nestle Research Center.

  9. Design of low-power coarse-grained reconfigurable architectures

    CERN Document Server

    Kim, Yoonjin

    2010-01-01

    Coarse-grained reconfigurable architecture (CGRA) has emerged as a solution for flexible, application-specific optimization of embedded systems. Helping you understand the issues involved in designing and constructing embedded systems, Design of Low-Power Coarse-Grained Reconfigurable Architectures offers new frameworks for optimizing the architecture of components in embedded systems in order to decrease area and save power. Real application benchmarks and gate-level simulations substantiate these frameworks.The first half of the book explains how to reduce power in the configuration cache. T

  10. Thalamotemporal impairment in temporal lobe epilepsy: a combined MRI analysis of structure, integrity, and connectivity.

    Science.gov (United States)

    Keller, Simon S; O'Muircheartaigh, Jonathan; Traynor, Catherine; Towgood, Karren; Barker, Gareth J; Richardson, Mark P

    2014-02-01

    Thalamic abnormality in temporal lobe epilepsy (TLE) is well known from imaging studies, but evidence is lacking regarding connectivity profiles of the thalamus and their involvement in the disease process. We used a novel multisequence magnetic resonance imaging (MRI) protocol to elucidate the relationship between mesial temporal and thalamic pathology in TLE. For 23 patients with TLE and 23 healthy controls, we performed T1 -weighted (for analysis of tissue structure), diffusion tensor imaging (tissue connectivity), and T1 and T2 relaxation (tissue integrity) MRI across the whole brain. We used connectivity-based segmentation to determine connectivity patterns of thalamus to ipsilateral cortical regions (occipital, parietal, prefrontal, postcentral, precentral, and temporal). We subsequently determined volumes, mean tractography streamlines, and mean T1 and T2 relaxometry values for each thalamic segment preferentially connecting to a given cortical region, and of the hippocampus and entorhinal cortex. As expected, patients had significant volume reduction and increased T2 relaxation time in ipsilateral hippocampus and entorhinal cortex. There was bilateral volume loss, mean streamline reduction, and T2 increase of the thalamic segment preferentially connected to temporal lobe, corresponding to anterior, dorsomedial, and pulvinar thalamic regions, with no evidence of significant change in any other thalamic segments. Left and right thalamotemporal segment volume and T2 were significantly correlated with volume and T2 of ipsilateral (epileptogenic), but not contralateral (nonepileptogenic), mesial temporal structures. These convergent and robust data indicate that thalamic abnormality in TLE is restricted to the area of the thalamus that is preferentially connected to the epileptogenic temporal lobe. The degree of thalamic pathology is related to the extent of mesial temporal lobe damage in TLE. © 2014 The Authors. Epilepsia published by Wiley Periodicals, Inc

  11. Application of coarse-mesh methods to fluid dynamics equations

    International Nuclear Information System (INIS)

    Romstedt, P.; Werner, W.

    1977-01-01

    An Asymmetric Weighted Residual (ASWR) method for fluid dynamics equations is described. It leads to local operators with a 7-point Finite Difference (FD) structure, which is independent of the degree of the approximating polynomials. An 1-dimensional problem was solved by both this ASWR-method and a commonly used FD-method. The numerical results demonstrate that the ASWR-method combines high accuracy on a coarse computational mesh with short computing time per space point. The posibility of using fewer space points consequently brings about a considerable reduction in total running time for the ASWR-method as compared with conventional FD-methods. (orig.) [de

  12. Biofilm diatom community structure: Influence of temporal and substratum variability

    Digital Repository Service at National Institute of Oceanography (India)

    Patil, J.S.; Anil, A.C.

    ). The structure and composition of the fouling com- munity exhibit wide temporal and regional varia- tions, which are also influenced by the substratum. Dona Paula Bay, the site of this investigation, is highly dynamic in terms of its physico...-off and nutrient loading in coastal environments. In general, the waters are highly disturbed during the monsoon (June–September) and calm during the pre-monsoon (February–May) and post-monsoon (October–January) periods. Such changes are instrumental...

  13. Effects of Particle Size on the Shear Behavior of Coarse Grained Soils Reinforced with Geogrid

    Directory of Open Access Journals (Sweden)

    Daehyeon Kim

    2014-02-01

    Full Text Available In order to design civil structures that are supported by soils, the shear strength parameters of soils are required. Due to the large particle size of coarse-grained soils, large direct shear tests should be performed. In this study, large direct shear tests on three types of coarse grained soils (4.5 mm, 7.9 mm, and 15.9 mm were performed to evaluate the effects of particle size on the shear behavior of coarse grained soils with/without geogrid reinforcements. Based on the direct shear test results, it was found that, in the case of no-reinforcement, the larger the maximum particle size became, the larger the friction angle was. Compared with the no-reinforcement case, the cases reinforced with either soft geogrid or stiff geogrid have smaller friction angles. The cohesion of the soil reinforced with stiff geogrid was larger than that of the soil reinforced with soft geogrid. The difference in the shear strength occurs because the case with a stiff geogrid has more soil to geogrid contact area, leading to the reduction in interlocking between soil particles.

  14. THE IMPACT OF SPATIAL AND TEMPORAL RESOLUTIONS IN TROPICAL SUMMER RAINFALL DISTRIBUTION: PRELIMINARY RESULTS

    Directory of Open Access Journals (Sweden)

    Q. Liu

    2017-10-01

    Full Text Available The abundance or lack of rainfall affects peoples’ life and activities. As a major component of the global hydrological cycle (Chokngamwong & Chiu, 2007, accurate representations at various spatial and temporal scales are crucial for a lot of decision making processes. Climate models show a warmer and wetter climate due to increases of Greenhouse Gases (GHG. However, the models’ resolutions are often too coarse to be directly applicable to local scales that are useful for mitigation purposes. Hence disaggregation (downscaling procedures are needed to transfer the coarse scale products to higher spatial and temporal resolutions. The aim of this paper is to examine the changes in the statistical parameters of rainfall at various spatial and temporal resolutions. The TRMM Multi-satellite Precipitation Analysis (TMPA at 0.25 degree, 3 hourly grid rainfall data for a summer is aggregated to 0.5,1.0, 2.0 and 2.5 degree and at 6, 12, 24 hourly, pentad (five days and monthly resolutions. The probability distributions (PDF and cumulative distribution functions(CDF of rain amount at these resolutions are computed and modeled as a mixed distribution. Parameters of the PDFs are compared using the Kolmogrov-Smironov (KS test, both for the mixed and the marginal distribution. These distributions are shown to be distinct. The marginal distributions are fitted with Lognormal and Gamma distributions and it is found that the Gamma distributions fit much better than the Lognormal.

  15. The Impact of Spatial and Temporal Resolutions in Tropical Summer Rainfall Distribution: Preliminary Results

    Science.gov (United States)

    Liu, Q.; Chiu, L. S.; Hao, X.

    2017-10-01

    The abundance or lack of rainfall affects peoples' life and activities. As a major component of the global hydrological cycle (Chokngamwong & Chiu, 2007), accurate representations at various spatial and temporal scales are crucial for a lot of decision making processes. Climate models show a warmer and wetter climate due to increases of Greenhouse Gases (GHG). However, the models' resolutions are often too coarse to be directly applicable to local scales that are useful for mitigation purposes. Hence disaggregation (downscaling) procedures are needed to transfer the coarse scale products to higher spatial and temporal resolutions. The aim of this paper is to examine the changes in the statistical parameters of rainfall at various spatial and temporal resolutions. The TRMM Multi-satellite Precipitation Analysis (TMPA) at 0.25 degree, 3 hourly grid rainfall data for a summer is aggregated to 0.5,1.0, 2.0 and 2.5 degree and at 6, 12, 24 hourly, pentad (five days) and monthly resolutions. The probability distributions (PDF) and cumulative distribution functions(CDF) of rain amount at these resolutions are computed and modeled as a mixed distribution. Parameters of the PDFs are compared using the Kolmogrov-Smironov (KS) test, both for the mixed and the marginal distribution. These distributions are shown to be distinct. The marginal distributions are fitted with Lognormal and Gamma distributions and it is found that the Gamma distributions fit much better than the Lognormal.

  16. Coarse-Grained Modeling of Polyelectrolyte Solutions

    Science.gov (United States)

    Denton, Alan R.; May, Sylvio

    2014-03-01

    Ionic mixtures, such as electrolyte and polyelectrolyte solutions, have attracted much attention recently for their rich and challenging combination of electrostatic and non-electrostatic interparticle forces and their practical importance, from battery technologies to biological systems. Hydration of ions in aqueous solutions is known to entail ion-specific effects, including variable solubility of organic molecules, as manifested in the classic Hofmeister series for salting-in and salting-out of proteins. The physical mechanism by which the solvent (water) mediates effective interactions between ions, however, is still poorly understood. Starting from a microscopic model of a polyelectrolyte solution, we apply a perturbation theory to derive a coarse-grained model of ions interacting through both long-range electrostatic and short-range solvent-induced pair potentials. Taking these effective interactions as input to molecular dynamics simulations, we calculate structural and thermodynamic properties of aqueous ionic solutions. This work was supported by the National Science Foundation under Grant No. DMR-1106331.

  17. An Evaluation of Coarse-Grained Locking for Multicore Microkernels

    OpenAIRE

    Elphinstone, Kevin; Zarrabi, Amirreza; Danis, Adrian; Shen, Yanyan; Heiser, Gernot

    2016-01-01

    The trade-off between coarse- and fine-grained locking is a well understood issue in operating systems. Coarse-grained locking provides lower overhead under low contention, fine-grained locking provides higher scalability under contention, though at the expense of implementation complexity and re- duced best-case performance. We revisit this trade-off in the context of microkernels and tightly-coupled cores with shared caches and low inter-core migration latencies. We evaluate performance on ...

  18. Contrasting effects of vocabulary knowledge on temporal and parietal brain structure across lifespan.

    Science.gov (United States)

    Richardson, Fiona M; Thomas, Michael S C; Filippi, Roberto; Harth, Helen; Price, Cathy J

    2010-05-01

    Using behavioral, structural, and functional imaging techniques, we demonstrate contrasting effects of vocabulary knowledge on temporal and parietal brain structure in 47 healthy volunteers who ranged in age from 7 to 73 years. In the left posterior supramarginal gyrus, vocabulary knowledge was positively correlated with gray matter density in teenagers but not adults. This region was not activated during auditory or visual sentence processing, and activation was unrelated to vocabulary skills. Its gray matter density may reflect the use of an explicit learning strategy that links new words to lexical or conceptual equivalents, as used in formal education and second language acquisition. By contrast, in left posterior temporal regions, gray matter as well as auditory and visual sentence activation correlated with vocabulary knowledge throughout lifespan. We propose that these effects reflect the acquisition of vocabulary through context, when new words are learnt within the context of semantically and syntactically related words.

  19. Generating spatial precipitation ensembles: impact of temporal correlation structure

    Directory of Open Access Journals (Sweden)

    O. Rakovec

    2012-09-01

    Full Text Available Sound spatially distributed rainfall fields including a proper spatial and temporal error structure are of key interest for hydrologists to force hydrological models and to identify uncertainties in the simulated and forecasted catchment response. The current paper presents a temporally coherent error identification method based on time-dependent multivariate spatial conditional simulations, which are conditioned on preceding simulations. A sensitivity analysis and real-world experiment are carried out within the hilly region of the Belgian Ardennes. Precipitation fields are simulated for pixels of 10 km × 10 km resolution. Uncertainty analyses in the simulated fields focus on (1 the number of previous simulation hours on which the new simulation is conditioned, (2 the advection speed of the rainfall event, (3 the size of the catchment considered, and (4 the rain gauge density within the catchment. The results for a sensitivity analysis show for typical advection speeds >20 km h−1, no uncertainty is added in terms of across ensemble spread when conditioned on more than one or two previous hourly simulations. However, for the real-world experiment, additional uncertainty can still be added when conditioning on a larger number of previous simulations. This is because for actual precipitation fields, the dynamics exhibit a larger spatial and temporal variability. Moreover, by thinning the observation network with 50%, the added uncertainty increases only slightly and the cross-validation shows that the simulations at the unobserved locations are unbiased. Finally, the first-order autocorrelation coefficients show clear temporal coherence in the time series of the areal precipitation using the time-dependent multivariate conditional simulations, which was not the case using the time-independent univariate conditional simulations. The presented work can be easily implemented within a hydrological calibration and data assimilation

  20. Experimental investigation of coarse particle conveying in pipes

    Directory of Open Access Journals (Sweden)

    Vlasak Pavel

    2015-01-01

    Full Text Available The advanced knowledge of particle-water mixture flow behaviour is important for safe, reliable, and economical design and operation of the freight pipelines. The effect of the mixture velocity and concentration on the coarse particle – water mixtures flow behaviour was experimentally investigated on an experimental pipe loop of inner diameter D = 100 mm with horizontal, vertical, and inclined pipe sections. Narrow particle size distribution basalt pebbles were used as model of coarse-grained solid particles. The radiometric method was used to measure particle concentration distribution in pipe cross-section. Mixture flow behaviour and particles motion along the pipe invert were studied in a pipe viewing section. The study revealed that the coarse particlewater mixtures in the horizontal and inclined pipe sections were significantly stratified. The particles moved principally in a layer close to the pipe invert. However, for higher and moderate flow velocities the particles moved also in the central part of the pipe cross-section, and particle saltation was found to be dominant mode of particle conveying.

  1. Syntactic Structure Building in the Anterior Temporal Lobe during Natural Story Listening

    Science.gov (United States)

    Brennan, Jonathan; Nir, Yuval; Hasson, Uri; Malach, Rafael; Heeger, David J.; Pylkkanen, Liina

    2012-01-01

    The neural basis of syntax is a matter of substantial debate. In particular, the inferior frontal gyrus (IFG), or Broca's area, has been prominently linked to syntactic processing, but the anterior temporal lobe has been reported to be activated instead of IFG when manipulating the presence of syntactic structure. These findings are difficult to…

  2. Coarse-graining and hybrid methods for efficient simulation of stochastic multi-scale models of tumour growth

    Science.gov (United States)

    de la Cruz, Roberto; Guerrero, Pilar; Calvo, Juan; Alarcón, Tomás

    2017-12-01

    The development of hybrid methodologies is of current interest in both multi-scale modelling and stochastic reaction-diffusion systems regarding their applications to biology. We formulate a hybrid method for stochastic multi-scale models of cells populations that extends the remit of existing hybrid methods for reaction-diffusion systems. Such method is developed for a stochastic multi-scale model of tumour growth, i.e. population-dynamical models which account for the effects of intrinsic noise affecting both the number of cells and the intracellular dynamics. In order to formulate this method, we develop a coarse-grained approximation for both the full stochastic model and its mean-field limit. Such approximation involves averaging out the age-structure (which accounts for the multi-scale nature of the model) by assuming that the age distribution of the population settles onto equilibrium very fast. We then couple the coarse-grained mean-field model to the full stochastic multi-scale model. By doing so, within the mean-field region, we are neglecting noise in both cell numbers (population) and their birth rates (structure). This implies that, in addition to the issues that arise in stochastic-reaction diffusion systems, we need to account for the age-structure of the population when attempting to couple both descriptions. We exploit our coarse-graining model so that, within the mean-field region, the age-distribution is in equilibrium and we know its explicit form. This allows us to couple both domains consistently, as upon transference of cells from the mean-field to the stochastic region, we sample the equilibrium age distribution. Furthermore, our method allows us to investigate the effects of intracellular noise, i.e. fluctuations of the birth rate, on collective properties such as travelling wave velocity. We show that the combination of population and birth-rate noise gives rise to large fluctuations of the birth rate in the region at the leading edge of

  3. Thermodynamic forces in coarse-grained simulations

    Science.gov (United States)

    Noid, William

    Atomically detailed molecular dynamics simulations have profoundly advanced our understanding of the structure and interactions in soft condensed phases. Nevertheless, despite dramatic advances in the methodology and resources for simulating atomically detailed models, low-resolution coarse-grained (CG) models play a central and rapidly growing role in science. CG models not only empower researchers to investigate phenomena beyond the scope of atomically detailed simulations, but also to precisely tailor models for specific phenomena. However, in contrast to atomically detailed simulations, which evolve on a potential energy surface, CG simulations should evolve on a free energy surface. Therefore, the forces in CG models should reflect the thermodynamic information that has been eliminated from the CG configuration space. As a consequence of these thermodynamic forces, CG models often demonstrate limited transferability and, moreover, rarely provide an accurate description of both structural and thermodynamic properties. In this talk, I will present a framework that clarifies the origin and impact of these thermodynamic forces. Additionally, I will present computational methods for quantifying these forces and incorporating their effects into CG MD simulations. As time allows, I will demonstrate applications of this framework for liquids, polymers, and interfaces. We gratefully acknowledge the support of the National Science Foundation via CHE 1565631.

  4. Coarse-grained Simulations of Sugar Transport and Conformational Changes of Lactose Permease

    Science.gov (United States)

    Liu, Jin; Jewel, S. M. Yead; Dutta, Prashanta

    2016-11-01

    Escherichia coli lactose permease (LacY) actively transports lactose and other galactosides across cell membranes through lactose/H+ symport process. Lactose/H+ symport is a highly complex process that involves sugar translocation, H+ transfer, as well as large-scale protein conformational changes. The complete picture of lactose/H+ symport is largely unclear due to the complexity and multiscale nature of the process. In this work, we develop the force field for sugar molecules compatible with PACE, a hybrid and coarse-grained force field that couples the united-atom protein models with the coarse-grained MARTINI water/lipid. After validation, we implement the new force field to investigate the transport of a β-D-galactopyranosyl-1-thio- β-D-galactopyranoside (TDG) molecule across a wild-type LacY during lactose/H+ symport process. Results show that the local interactions between TDG and LacY at the binding pocket are consistent with the X-ray experiment. Protonation of Glu325 stabilizes the TDG and inward-facing conformation of LacY. Protonation of Glu269 induces a dramatic protein structural reorganization and causes the expulsion of TDG from LacY to both sides of the membrane. The structural changes occur primarily in the N-terminal domain of LacY. This work is supported by NSF Grants: CBET-1250107 and CBET -1604211.

  5. Spatio-temporal dynamics and laterality effects of face inversion, feature presence and configuration, and face outline

    Directory of Open Access Journals (Sweden)

    Ksenija eMarinkovic

    2014-11-01

    Full Text Available Although a crucial role of the fusiform gyrus in face processing has been demonstrated with a variety of methods, converging evidence suggests that face processing involves an interactive and overlapping processing cascade in distributed brain areas. Here we examine the spatio-temporal stages and their functional tuning to face inversion, presence and configuration of inner features, and face contour in healthy subjects during passive viewing. Anatomically-constrained magnetoencephalography (aMEG combines high-density whole-head MEG recordings and distributed source modeling with high-resolution structural MRI. Each person's reconstructed cortical surface served to constrain noise-normalized minimum norm inverse source estimates. The earliest activity was estimated to the occipital cortex at ~100 ms after stimulus onset and was sensitive to an initial coarse level visual analysis. Activity in the right-lateralized ventral temporal area (inclusive of the fusiform gyrus peaked at ~160ms and was largest to inverted faces. Images containing facial features in the veridical and rearranged configuration irrespective of the facial outline elicited intermediate level activity. The M160 stage may provide structural representations necessary for downstream distributed areas to process identity and emotional expression. However, inverted faces additionally engaged the left ventral temporal area at ~180 ms and were uniquely subserved by bilateral processing. This observation is consistent with the dual route model and spared processing of inverted faces in prosopagnosia. The subsequent deflection, peaking at ~240ms in the anterior temporal areas bilaterally, was largest to normal, upright faces. It may reflect initial engagement of the distributed network subserving individuation and familiarity. These results support dynamic models suggesting that processing of unfamiliar faces in the absence of a cognitive task is subserved by a distributed and

  6. Coarse-graining and hybrid methods for efficient simulation of stochastic multi-scale models of tumour growth

    International Nuclear Information System (INIS)

    Cruz, Roberto de la; Guerrero, Pilar; Calvo, Juan; Alarcón, Tomás

    2017-01-01

    The development of hybrid methodologies is of current interest in both multi-scale modelling and stochastic reaction–diffusion systems regarding their applications to biology. We formulate a hybrid method for stochastic multi-scale models of cells populations that extends the remit of existing hybrid methods for reaction–diffusion systems. Such method is developed for a stochastic multi-scale model of tumour growth, i.e. population-dynamical models which account for the effects of intrinsic noise affecting both the number of cells and the intracellular dynamics. In order to formulate this method, we develop a coarse-grained approximation for both the full stochastic model and its mean-field limit. Such approximation involves averaging out the age-structure (which accounts for the multi-scale nature of the model) by assuming that the age distribution of the population settles onto equilibrium very fast. We then couple the coarse-grained mean-field model to the full stochastic multi-scale model. By doing so, within the mean-field region, we are neglecting noise in both cell numbers (population) and their birth rates (structure). This implies that, in addition to the issues that arise in stochastic-reaction diffusion systems, we need to account for the age-structure of the population when attempting to couple both descriptions. We exploit our coarse-graining model so that, within the mean-field region, the age-distribution is in equilibrium and we know its explicit form. This allows us to couple both domains consistently, as upon transference of cells from the mean-field to the stochastic region, we sample the equilibrium age distribution. Furthermore, our method allows us to investigate the effects of intracellular noise, i.e. fluctuations of the birth rate, on collective properties such as travelling wave velocity. We show that the combination of population and birth-rate noise gives rise to large fluctuations of the birth rate in the region at the leading edge

  7. Telicity as a Cue to Temporal and Discourse Structure in Chinese-English Machine Translation

    National Research Council Canada - National Science Library

    Olsen, Mari; Traum, David; Van Ess-Dykema, Carol; Weinberg, Amy; Dolan, Ron

    2000-01-01

    ...) that must be explicit in English (e.g., by means of a discourse marker). Perfective and imperfective grammatical aspect markers can provide cues to temporal structure, but such information is not present in every sentence...

  8. Bottom-up coarse-grained models with predictive accuracy and transferability for both structural and thermodynamic properties of heptane-toluene mixtures.

    Science.gov (United States)

    Dunn, Nicholas J H; Noid, W G

    2016-05-28

    This work investigates the promise of a "bottom-up" extended ensemble framework for developing coarse-grained (CG) models that provide predictive accuracy and transferability for describing both structural and thermodynamic properties. We employ a force-matching variational principle to determine system-independent, i.e., transferable, interaction potentials that optimally model the interactions in five distinct heptane-toluene mixtures. Similarly, we employ a self-consistent pressure-matching approach to determine a system-specific pressure correction for each mixture. The resulting CG potentials accurately reproduce the site-site rdfs, the volume fluctuations, and the pressure equations of state that are determined by all-atom (AA) models for the five mixtures. Furthermore, we demonstrate that these CG potentials provide similar accuracy for additional heptane-toluene mixtures that were not included their parameterization. Surprisingly, the extended ensemble approach improves not only the transferability but also the accuracy of the calculated potentials. Additionally, we observe that the required pressure corrections strongly correlate with the intermolecular cohesion of the system-specific CG potentials. Moreover, this cohesion correlates with the relative "structure" within the corresponding mapped AA ensemble. Finally, the appendix demonstrates that the self-consistent pressure-matching approach corresponds to minimizing an appropriate relative entropy.

  9. Interplay between grain structure and protein adsorption on functional response of osteoblasts: ultrafine-grained versus coarse-grained substrates.

    Science.gov (United States)

    Misra, R D K; Nune, C; Pesacreta, T C; Somani, M C; Karjalainen, L P

    2013-01-01

    The rapid adsorption of proteins is the starting and primary biological response that occurs when a biomedical device is implanted in the physiological system. The biological response, however, depends on the surface characteristics of the device. Considering the significant interest in nano-/ultrafine surfaces and nanostructured coatings, we describe here, the interplay between grain structure and protein adsorption (bovine serum albumin: BSA) on osteoblasts functions by comparing nanograined/ultrafine-grained (NG/UFG) and coarse-grained (CG: grain size in the micrometer range) substrates by investigating cell-substrate interactions. The protein adsorption on NG/UFG surface was beneficial in favorably modulating biological functions including cell attachment, proliferation, and viability, whereas the effect was less pronounced on protein adsorbed CG surface. Additionally, immunofluorescence studies demonstrated stronger vinculin signals associated with actin stress fibers in the outer regions of the cells and cellular extensions on protein adsorbed NG/UFG surface. The functional response followed the sequence: NG/UFG(BSA) > NG/UFG > CG(BSA) > CG. The differences in the cellular response on bare and protein adsorbed NG/UFG and CG surfaces are attributed to cumulative contribution of grain structure and degree of hydrophilicity. The study underscores the potential advantages of protein adsorption on artificial biomedical devices to enhance the bioactivity and regulate biological functions. Copyright © 2012 Wiley Periodicals, Inc.

  10. Spatial and Temporal Extent of Ion Spectral Structures at the Inner Edge of the Plasma Sheet

    Science.gov (United States)

    Ferradas, C.; Reeves, G. D.; Zhang, J.; Spence, H. E.; Kistler, L. M.; Larsen, B.; Skoug, R. M.; Funsten, H. O.

    2017-12-01

    Several ion spectral structures are observed near the inner edge of the plasma sheet and constitute the signatures of ion drift and loss in the highly dynamic environment of the inner magnetosphere. Their study helps us understand ion access and losses in this region. Several studies have found that these structures vary with geomagnetic activity, local time, and ion species, but their spatial and temporal extent remain undetermined. We use data from the Helium, Oxygen, Proton, and Electron (HOPE) mass spectrometers onboard the Van Allen Probes to analyze the spectral structures in the energy range of 1- 50 keV. HOPE measurements on both Van Allen Probes spacecraft enable us to resolve the extent of these ion structures in space and time. As the structures respond to changes in the convection electric field on a variety of time scales, the lapping of the two spacecraft on time scales of minutes to hours helps determine their spatial and temporal evolution.

  11. Temporally coherent 4D video segmentation for teleconferencing

    Science.gov (United States)

    Ehmann, Jana; Guleryuz, Onur G.

    2013-09-01

    We develop an algorithm for 4-D (RGB+Depth) video segmentation targeting immersive teleconferencing ap- plications on emerging mobile devices. Our algorithm extracts users from their environments and places them onto virtual backgrounds similar to green-screening. The virtual backgrounds increase immersion and interac- tivity, relieving the users of the system from distractions caused by disparate environments. Commodity depth sensors, while providing useful information for segmentation, result in noisy depth maps with a large number of missing depth values. By combining depth and RGB information, our work signi¯cantly improves the other- wise very coarse segmentation. Further imposing temporal coherence yields compositions where the foregrounds seamlessly blend with the virtual backgrounds with minimal °icker and other artifacts. We achieve said improve- ments by correcting the missing information in depth maps before fast RGB-based segmentation, which operates in conjunction with temporal coherence. Simulation results indicate the e±cacy of the proposed system in video conferencing scenarios.

  12. Coarse-graining polymers with the MARTINI force-field: polystyrene as a benchmark case

    DEFF Research Database (Denmark)

    Rossi, G.; Monticelli, L.; Puisto, S. R.

    2011-01-01

    We hereby introduce a new hybrid thermodynamic-structural approach to the coarse-graining of polymers. The new model is developed within the framework of the MARTINI force-field (Marrink et al., J. Phys. Chem. B, 2007, 111, 7812), which uses mainly thermodynamic properties as targets...... of microseconds. Finally, we tested our model in dilute conditions. The collapse of the polymer chains in a bad solvent and the swelling in a good solvent could be reproduced....

  13. The role of temporal structure in the investigation of sensory memory, auditory scene analysis, and speech perception: a healthy-aging perspective.

    Science.gov (United States)

    Rimmele, Johanna Maria; Sussman, Elyse; Poeppel, David

    2015-02-01

    Listening situations with multiple talkers or background noise are common in everyday communication and are particularly demanding for older adults. Here we review current research on auditory perception in aging individuals in order to gain insights into the challenges of listening under noisy conditions. Informationally rich temporal structure in auditory signals--over a range of time scales from milliseconds to seconds--renders temporal processing central to perception in the auditory domain. We discuss the role of temporal structure in auditory processing, in particular from a perspective relevant for hearing in background noise, and focusing on sensory memory, auditory scene analysis, and speech perception. Interestingly, these auditory processes, usually studied in an independent manner, show considerable overlap of processing time scales, even though each has its own 'privileged' temporal regimes. By integrating perspectives on temporal structure processing in these three areas of investigation, we aim to highlight similarities typically not recognized. Copyright © 2014 Elsevier B.V. All rights reserved.

  14. Probing the folded state and mechanical unfolding pathways of T4 lysozyme using all-atom and coarse-grained molecular simulation

    Energy Technology Data Exchange (ETDEWEB)

    Zheng, Wenjun, E-mail: wjzheng@buffalo.edu; Glenn, Paul [Department of Physics, University at Buffalo, Buffalo, New York 14260 (United States)

    2015-01-21

    The Bacteriophage T4 Lysozyme (T4L) is a prototype modular protein comprised of an N-terminal and a C-domain domain, which was extensively studied to understand the folding/unfolding mechanism of modular proteins. To offer detailed structural and dynamic insights to the folded-state stability and the mechanical unfolding behaviors of T4L, we have performed extensive equilibrium and steered molecular dynamics simulations of both the wild-type (WT) and a circular permutation (CP) variant of T4L using all-atom and coarse-grained force fields. Our all-atom and coarse-grained simulations of the folded state have consistently found greater stability of the C-domain than the N-domain in isolation, which is in agreement with past thermostatic studies of T4L. While the all-atom simulation cannot fully explain the mechanical unfolding behaviors of the WT and the CP variant observed in an optical tweezers study, the coarse-grained simulations based on the Go model or a modified elastic network model (mENM) are in qualitative agreement with the experimental finding of greater unfolding cooperativity in the WT than the CP variant. Interestingly, the two coarse-grained models predict different structural mechanisms for the observed change in cooperativity between the WT and the CP variant—while the Go model predicts minor modification of the unfolding pathways by circular permutation (i.e., preserving the general order that the N-domain unfolds before the C-domain), the mENM predicts a dramatic change in unfolding pathways (e.g., different order of N/C-domain unfolding in the WT and the CP variant). Based on our simulations, we have analyzed the limitations of and the key differences between these models and offered testable predictions for future experiments to resolve the structural mechanism for cooperative folding/unfolding of T4L.

  15. Temporal Control over Transient Chemical Systems using Structurally Diverse Chemical Fuels.

    Science.gov (United States)

    Chen, Jack L-Y; Maiti, Subhabrata; Fortunati, Ilaria; Ferrante, Camilla; Prins, Leonard J

    2017-08-25

    The next generation of adaptive, intelligent chemical systems will rely on a continuous supply of energy to maintain the functional state. Such systems will require chemical methodology that provides precise control over the energy dissipation process, and thus, the lifetime of the transiently activated function. This manuscript reports on the use of structurally diverse chemical fuels to control the lifetime of two different systems under dissipative conditions: transient signal generation and the transient formation of self-assembled aggregates. The energy stored in the fuels is dissipated at different rates by an enzyme, which installs a dependence of the lifetime of the active system on the chemical structure of the fuel. In the case of transient signal generation, it is shown that different chemical fuels can be used to generate a vast range of signal profiles, allowing temporal control over two orders of magnitude. Regarding self-assembly under dissipative conditions, the ability to control the lifetime using different fuels turns out to be particularly important as stable aggregates are formed only at well-defined surfactant/fuel ratios, meaning that temporal control cannot be achieved by simply changing the fuel concentration. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Thermodynamically consistent coarse graining of biocatalysts beyond Michaelis–Menten

    Science.gov (United States)

    Wachtel, Artur; Rao, Riccardo; Esposito, Massimiliano

    2018-04-01

    Starting from the detailed catalytic mechanism of a biocatalyst we provide a coarse-graining procedure which, by construction, is thermodynamically consistent. This procedure provides stoichiometries, reaction fluxes (rate laws), and reaction forces (Gibbs energies of reaction) for the coarse-grained level. It can treat active transporters and molecular machines, and thus extends the applicability of ideas that originated in enzyme kinetics. Our results lay the foundations for systematic studies of the thermodynamics of large-scale biochemical reaction networks. Moreover, we identify the conditions under which a relation between one-way fluxes and forces holds at the coarse-grained level as it holds at the detailed level. In doing so, we clarify the speculations and broad claims made in the literature about such a general flux–force relation. As a further consequence we show that, in contrast to common belief, the second law of thermodynamics does not require the currents and the forces of biochemical reaction networks to be always aligned.

  17. Temporal networks

    Science.gov (United States)

    Holme, Petter; Saramäki, Jari

    2012-10-01

    A great variety of systems in nature, society and technology-from the web of sexual contacts to the Internet, from the nervous system to power grids-can be modeled as graphs of vertices coupled by edges. The network structure, describing how the graph is wired, helps us understand, predict and optimize the behavior of dynamical systems. In many cases, however, the edges are not continuously active. As an example, in networks of communication via e-mail, text messages, or phone calls, edges represent sequences of instantaneous or practically instantaneous contacts. In some cases, edges are active for non-negligible periods of time: e.g., the proximity patterns of inpatients at hospitals can be represented by a graph where an edge between two individuals is on throughout the time they are at the same ward. Like network topology, the temporal structure of edge activations can affect dynamics of systems interacting through the network, from disease contagion on the network of patients to information diffusion over an e-mail network. In this review, we present the emergent field of temporal networks, and discuss methods for analyzing topological and temporal structure and models for elucidating their relation to the behavior of dynamical systems. In the light of traditional network theory, one can see this framework as moving the information of when things happen from the dynamical system on the network, to the network itself. Since fundamental properties, such as the transitivity of edges, do not necessarily hold in temporal networks, many of these methods need to be quite different from those for static networks. The study of temporal networks is very interdisciplinary in nature. Reflecting this, even the object of study has many names-temporal graphs, evolving graphs, time-varying graphs, time-aggregated graphs, time-stamped graphs, dynamic networks, dynamic graphs, dynamical graphs, and so on. This review covers different fields where temporal graphs are considered

  18. The Martini Coarse-Grained Force Field

    NARCIS (Netherlands)

    Periole, X.; Marrink, S.J.; Monticelli, Luca; Salonen, Emppu

    2013-01-01

    The Martini force field is a coarse-grained force field suited for molecular dynamics simulations of biomolecular systems. The force field has been parameterized in a systematic way, based on the reproduction of partitioning free energies between polar and apolar phases of a large number of chemical

  19. Coarse-grain parallelism using remote method invocation

    Energy Technology Data Exchange (ETDEWEB)

    Hebert, A. [Ecole Polytechnique de Montreal, Qc. (Canada)

    2003-07-01

    The paper describes a user-oriented framework specifically designed to facilitate the development and supervision of coarse-grain parallel applications in reactor physics. The proposed user-oriented framework was designed and implemented in Java, in such a way to obtain a simple and robust application. The proposed approach is based on Java Native Interface(JNI) for integrating the Fortran legacy code and on Remote Method Invocation (RMI) for distributing the calculation load over the farm of processors. Dynamic code downloading over the network is possible. We are presenting the application of this approach to supervision of lattice calculations using the open source Dragon code. The Java layer surrounding Dragon can also be used to construct execution procedures, computational schemes and graphical user interfaces. This approach can be used with any existing legacy Fortran code, as soon as its input/output data structures are Dragon-compatible. (author)

  20. Coarse-grain parallelism using remote method invocation

    International Nuclear Information System (INIS)

    Hebert, A.

    2003-01-01

    The paper describes a user-oriented framework specifically designed to facilitate the development and supervision of coarse-grain parallel applications in reactor physics. The proposed user-oriented framework was designed and implemented in Java, in such a way to obtain a simple and robust application. The proposed approach is based on Java Native Interface(JNI) for integrating the Fortran legacy code and on Remote Method Invocation (RMI) for distributing the calculation load over the farm of processors. Dynamic code downloading over the network is possible. We are presenting the application of this approach to supervision of lattice calculations using the open source Dragon code. The Java layer surrounding Dragon can also be used to construct execution procedures, computational schemes and graphical user interfaces. This approach can be used with any existing legacy Fortran code, as soon as its input/output data structures are Dragon-compatible. (author)

  1. Coarse sediment oil persistence laboratory studies and model

    International Nuclear Information System (INIS)

    Humphrey, B.; Harper, J.R.

    1993-01-01

    To gain understanding of the factors which affect the fate of stranded oil on coarse sediment beaches, a series of oil penetration and tidal flushing experiments was conducted in columns containing sediments of two grain sizes: granules and pebbles. The experiments included changing oil properties by weathering and by emulsification. Factors examined included permeability, effective porosity, and residual capacity of the sediment for oil. The laboratory data provided input to an oil persistence model for coarse sediment beaches, and the model was modified on the basis of the new data. The permeability measurements suggest that the permeability of pebble/granule mixtures is close to that of the smaller component. For low viscosity oils, the permeability in coarse sediments is rapid enough to match the fall and rise of tidal water. Effective porosity of the pebbles was ca 90% of the measured porosity, but for both the granules and a 50-50 pebble/granule mixture, the effective porosity was ca 75% of measured porosity. Results of tidal flushing simulation imply that flushing may be rapid but not efficient. The emulsion completely entered the sediment in the case of pebbles only. 2 refs., 6 figs., 3 tabs

  2. Faunistic assemblages of a sublittoral coarse sand habitat of the northwestern Mediterranean

    Directory of Open Access Journals (Sweden)

    Eva Pubill

    2011-02-01

    Full Text Available The sublittoral megabenthic assemblages of a northwestern Mediterranean coarse sandy beach exploited for the bivalve Callista chione were studied. The spatial and bathymetric variability of its distinctive faunal assemblages was characterised by quantitative sampling performed with a clam dredge. The taxa studied were Mollusca Bivalvia and Gastropoda, Crustacea Decapoda, Echinodermata and Pisces, which accounted for over 99% of the total biomass. Three well-differentiated species assemblages were identified: (1 assemblage MSS (Medium Sand Shallow in medium sand (D50=0.37 mm and shallow waters (mean depth =6.5 m, (2 assemblage CSS (Coarse Sand Shallow in coarse sand (D50=0.62 mm in shallow waters (mean depth =6.7 m, and (3 assemblage CSD (Coarse Sand Deep in coarse sand (D50=0.64 mm in deeper waters (mean depth =16.2 m. Assemblage MSS was characterised by the codominance of the bivalves Mactra stultorum and Acanthocardia tuberculata. C. chione was dominant in both density and biomass in assemblages CSS and CSD. The occurrence of the crab Thia scutellata also characterised assemblage CSS, whereas the occurrence of the sea urchin Echinocardium mediterraneum characterised assemblage CSD. A depth breaking point of around 10 m determined the discontinuity between assemblages CSS and CSD, which was related to the closure depth of the beaches in the study area. Species richness was highest in the coarse sand communities; however, Shannon-Wiener diversity and Pielou equitability indexes were higher in the shallow fine sand community.

  3. Coarse graining flow of spin foam intertwiners

    Science.gov (United States)

    Dittrich, Bianca; Schnetter, Erik; Seth, Cameron J.; Steinhaus, Sebastian

    2016-12-01

    Simplicity constraints play a crucial role in the construction of spin foam models, yet their effective behavior on larger scales is scarcely explored. In this article we introduce intertwiner and spin net models for the quantum group SU (2 )k×SU (2 )k, which implement the simplicity constraints analogous to four-dimensional Euclidean spin foam models, namely the Barrett-Crane (BC) and the Engle-Pereira-Rovelli-Livine/Freidel-Krasnov (EPRL/FK) model. These models are numerically coarse grained via tensor network renormalization, allowing us to trace the flow of simplicity constraints to larger scales. In order to perform these simulations we have substantially adapted tensor network algorithms, which we discuss in detail as they can be of use in other contexts. The BC and the EPRL/FK model behave very differently under coarse graining: While the unique BC intertwiner model is a fixed point and therefore constitutes a two-dimensional topological phase, BC spin net models flow away from the initial simplicity constraints and converge to several different topological phases. Most of these phases correspond to decoupling spin foam vertices; however we find also a new phase in which this is not the case, and in which a nontrivial version of the simplicity constraints holds. The coarse graining flow of the BC spin net models indicates furthermore that the transitions between these phases are not of second order. The EPRL/FK model by contrast reveals a far more intricate and complex dynamics. We observe an immediate flow away from the original simplicity constraints; however, with the truncation employed here, the models generically do not converge to a fixed point. The results show that the imposition of simplicity constraints can indeed lead to interesting and also very complex dynamics. Thus we need to further develop coarse graining tools to efficiently study the large scale behavior of spin foam models, in particular for the EPRL/FK model.

  4. Synopsis of the temporal variation of particulate matter composition and size.

    Science.gov (United States)

    Demerjian, Kenneth L; Mohnen, Volker A

    2008-02-01

    A synopsis of the detailed temporal variation of the size and number distribution of particulate matter (PM) and its chemical composition on the basis of measurements performed by several regional research consortia funded by the U.S. Environmental Protection Agency (EPA) PM Supersite Program is presented. This program deployed and evaluated a variety of research and emerging commercial measurement technologies to investigate the physical and chemical properties of atmospheric aerosols at a level of detail never before achieved. Most notably these studies demonstrated that systematic size-segregated measurements of mass, number, and associated chemical composition of the fine (PM2.5) and ultrafine (PM0.1) fraction of ambient aerosol with a time resolution down to minutes and less is achievable. A wealth of new information on the temporal variation of aerosol has been added to the existing knowledge pool that can be mined to resolve outstanding research and policy-related questions. This paper explores the nature of temporal variations (on time scales from several minutes to hours) in the chemical and physical properties of PM and its implications in the identification of PM formation processes, and source attribution (primary versus secondary), the contribution of local versus transported PM and the development of effective PM control strategies. The PM Supersite results summarized indicate that location, time of day, and season significantly influence not only the mass and chemical composition but also the size-resolved chemical/elemental composition of PM. Ambient measurements also show that ultrafine particles have different compositions and make up only a small portion of the PM mass concentration compared with inhalable coarse and fine particles, but their number concentration is significantly larger than their coarse or fine counterparts. PM size classes show differences in the relative amounts of nitrates, sulfates, crustal materials, and most especially

  5. Dispersal Ability Determines the Role of Environmental, Spatial and Temporal Drivers of Metacommunity Structure

    NARCIS (Netherlands)

    Padial, André A.; Ceschin, Fernanda; Declerck, Steven A. J.; De Meester, Luc; Bonecker, Cláudia C.; Lansac-Tôha, Fabio A.; Rodrigues, Liliana; Rodrigues, Luzia C.; Train, Sueli; Velho, Luiz F. M.; Bini, Luis M.

    2014-01-01

    Recently, community ecologists are focusing on the relative importance of local environmental factors and proxies to dispersal limitation to explain spatial variation in community structure. Albeit less explored, temporal processes may also be important in explaining species composition variation in

  6. Coarse graining from variationally enhanced sampling applied to the Ginzburg-Landau model

    Science.gov (United States)

    Invernizzi, Michele; Valsson, Omar; Parrinello, Michele

    2017-03-01

    A powerful way to deal with a complex system is to build a coarse-grained model capable of catching its main physical features, while being computationally affordable. Inevitably, such coarse-grained models introduce a set of phenomenological parameters, which are often not easily deducible from the underlying atomistic system. We present a unique approach to the calculation of these parameters, based on the recently introduced variationally enhanced sampling method. It allows us to obtain the parameters from atomistic simulations, providing thus a direct connection between the microscopic and the mesoscopic scale. The coarse-grained model we consider is that of Ginzburg-Landau, valid around a second-order critical point. In particular, we use it to describe a Lennard-Jones fluid in the region close to the liquid-vapor critical point. The procedure is general and can be adapted to other coarse-grained models.

  7. The random phase transducer in ultrasonic NDT of coarse grain stainless steel

    International Nuclear Information System (INIS)

    Bordier, J.M.; Fink, M.; Le Brun, A.; Cohen-Tenoudji, F.

    1993-11-01

    Ultrasonic NDT of cast stainless steel is known to be difficult due to a huge loss of focussing of the ultrasonic beam, and to a high level speckle noise generated by the coarse grain structure. In this paper, we describe the principle of the ultrasonic random phase transducer. Experimental results are compared with those obtained with a standard spatial compound technique. We show that the random phase transducer is a good tool to characterize the multiple scattering process generated by these materials. (authors). 7 figs., 11 refs

  8. Learning to Play Efficient Coarse Correlated Equilibria

    KAUST Repository

    Borowski, Holly P.; Marden, Jason R.; Shamma, Jeff S.

    2018-01-01

    The majority of the distributed learning literature focuses on convergence to Nash equilibria. Coarse correlated equilibria, on the other hand, can often characterize more efficient collective behavior than even the best Nash equilibrium. However

  9. The combustion of sound and rotten coarse woody debris: a review

    Science.gov (United States)

    Joshua C. Hyde; Alistair M.S. Smith; Roger D. Ottmar; Ernesto C. Alvarado; Penelope Morgan

    2011-01-01

    Coarse woody debris serves many functions in forest ecosystem processes and has important implications for fire management as it affects air quality, soil heating and carbon budgets when it combusts. There is relatively little research evaluating the physical properties relating to the combustion of this coarse woody debris with even less specifically addressing...

  10. Adhesion between a rutile surface and a polyimide: a coarse grained molecular dynamics study

    Science.gov (United States)

    Kumar, Arun; Sudarkodi, V.; Parandekar, Priya V.; Sinha, Nishant K.; Prakash, Om; Nair, Nisanth N.; Basu, Sumit

    2018-04-01

    Titanium, due to its high strength to weight ratio and polyimides, due to their excellent thermal stability are being increasingly used in aerospace applications. We investigate the bonding between a (110) rutile substrate and a popular commercial polyimide, PMR-15, starting from the known atomic structure of the rutile substrate and the architecture of the polymer. First, the long PMR-15 molecule is divided into four fragments and an all-atom non-bonded forcefield governing the interaction between PMR-15 and a rutile substrate is developed. To this end, parameters of Buckingham potential for interaction between each atom in the fragments and the rutile surface are fitted, so as to ensure that the sum of non-bonded and electrostatic interaction energy between the substrate and a large number of configurations of each fragment, calculated by the quantum mechanical route and obtained from the fitted potential, is closely matched. Further, two coarse grained models of PMR-15 are developed—one for interaction between two coarse grained PMR-15 molecules and another for that between a coarse grained PMR-15 and the rutile substrate. Molecular dynamics simulations with the coarse grained models yields a traction separation law—a very useful tool for conducting continuum level finite element simulations of rutile-PMR-15 joints—governing the normal separation of a PMR-15 block from a flat rutile substrate. Moreover, detailed information about the affinity of various fragments to the substrate are also obtained. In fact, though the separation energy between rutile and PMR-15 turns out to be rather low, our analysis—with merely the molecular architecture of the polyimide as the starting point—provides a scheme for in-silico prediction of adhesion energies for new polyimide formulations.

  11. Temporal structure of neuronal population oscillations with empirical model decomposition

    International Nuclear Information System (INIS)

    Li Xiaoli

    2006-01-01

    Frequency analysis of neuronal oscillation is very important for understanding the neural information processing and mechanism of disorder in the brain. This Letter addresses a new method to analyze the neuronal population oscillations with empirical mode decomposition (EMD). Following EMD of neuronal oscillation, a series of intrinsic mode functions (IMFs) are obtained, then Hilbert transform of IMFs can be used to extract the instantaneous time frequency structure of neuronal oscillation. The method is applied to analyze the neuronal oscillation in the hippocampus of epileptic rats in vivo, the results show the neuronal oscillations have different descriptions during the pre-ictal, seizure onset and ictal periods of the epileptic EEG at the different frequency band. This new method is very helpful to provide a view for the temporal structure of neural oscillation

  12. Surgical Considerations of Intractable Mesial Temporal Lobe Epilepsy

    Science.gov (United States)

    Boling, Warren W.

    2018-01-01

    Surgery of temporal lobe epilepsy is the best opportunity for seizure freedom in medically intractable patients. The surgical approach has evolved to recognize the paramount importance of the mesial temporal structures in the majority of patients with temporal lobe epilepsy who have a seizure origin in the mesial temporal structures. For those individuals with medically intractable mesial temporal lobe epilepsy, a selective amygdalohippocampectomy surgery can be done that provides an excellent opportunity for seizure freedom and limits the resection to temporal lobe structures primarily involved in seizure genesis. PMID:29461485

  13. Surgical Considerations of Intractable Mesial Temporal Lobe Epilepsy

    Directory of Open Access Journals (Sweden)

    Warren W. Boling

    2018-02-01

    Full Text Available Surgery of temporal lobe epilepsy is the best opportunity for seizure freedom in medically intractable patients. The surgical approach has evolved to recognize the paramount importance of the mesial temporal structures in the majority of patients with temporal lobe epilepsy who have a seizure origin in the mesial temporal structures. For those individuals with medically intractable mesial temporal lobe epilepsy, a selective amygdalohippocampectomy surgery can be done that provides an excellent opportunity for seizure freedom and limits the resection to temporal lobe structures primarily involved in seizure genesis.

  14. Coarse woody debris carbon storage across a mean annual temperature gradient in tropical montane wet forest

    Science.gov (United States)

    Darcey K. Iwashita; Creighton M. Litton; Christian P. Giardina

    2013-01-01

    Coarse woody debris (CWD; defined here as fallen and standing dead trees and tree ferns) is a critical structural and functional component of forest ecosystems that typically comprises a large proportion of total aboveground carbon (C) storage. However, CWD estimates for the tropics are uncommon, and little is known about how C storage in CWD will respond to climate...

  15. Temporal lobe volume predicts Wada memory test performance in patients with mesial temporal sclerosis.

    Science.gov (United States)

    Ding, Kan; Gong, Yunhua; Modur, Pradeep N; Diaz-Arrastia, Ramon; Agostini, Mark; Gupta, Puneet; McColl, Roderick; Hays, Ryan; Van Ness, Paul

    2016-02-01

    The Wada test is widely used in the presurgical evaluation of potential temporal lobectomy patients to predict postoperative memory function. Expected asymmetry (EA), defined as Wada memory lateralized to the nonsurgical hemisphere, or a higher score after injection of the surgical hemisphere would be considered favorable in terms of postoperative memory outcome. However, in some cases, nonlateralized memory (NM) results, with no appreciable asymmetry, may occur because of impaired scores after both injections, often leading to denial of surgery. The reason for such nonlateralized Wada memory in patients with intractable temporal lobe epilepsy (TLE) remains unclear. Given that quantitative morphometric magnetic resonance imaging studies in TLE patients have shown bilateral regional atrophy in temporal and extratemporal structures, we hypothesized that the volume loss in contralateral temporal structures could contribute to nonlateralized Wada memory performance. To investigate this, we examined the relationship between the volume changes of temporal structures and Wada memory scores in patients with intractable TLE with mesial temporal sclerosis (MTS) using an age- and gender-matched control group. Memory was considered nonlateralized if the absolute difference in the total correct recall scores between ipsilateral and contralateral injections was memory was lateralized in 15 and nonlateralized in 6 patients, with all the nonlateralized scores being observed in left TLE. The recall scores after ipsilateral injection were significantly lower in patients with an NM profile than an EA profile (23 ± 14% vs. 59 ± 18% correct recall, p ≤ 0.001). However, the recall scores after contralateral injection were low but similar between the two groups (25 ± 17% vs. 25 ± 15% correct recall, p=0.97). Compared to controls, all the patients showed greater volume loss in the temporal regions. However, patients with a NM profile showed significantly more volume loss than those

  16. The role of temporal fine structure information for the low pitch of high-frequency complex tones

    DEFF Research Database (Denmark)

    Santurette, Sébastien; Dau, Torsten

    2011-01-01

    The fused low pitch evoked by complex tones containing only unresolved high-frequency components demonstrates the ability of the human auditory system to extract pitch using a temporal mechanism in the absence of spectral cues. However, the temporal features used by such a mechanism have been...... amplitude fluctuations, or temporal fine structure (TFS), of the conveyed signal can be processed. Using a pitch-matching paradigm, the present study found that the low pitch of inharmonic transposed tones with unresolved components was consistent with the timing between the most prominent TFS maxima...... coding as such, and that TFS representation might persist at higher frequencies than previously thought....

  17. NEW RSW & Wall Coarse Tet Only Grid

    Data.gov (United States)

    National Aeronautics and Space Administration — This is the RSW Coarse Tet Only grid with the root viscous tunnel wall. This grid is for a node-based unstructured solver. Quad Surface Faces= 0 Tria Surface Faces=...

  18. Impaired perception of temporal fine structure and musical timbre in cochlear implant users.

    Science.gov (United States)

    Heng, Joseph; Cantarero, Gabriela; Elhilali, Mounya; Limb, Charles J

    2011-10-01

    Cochlear implant (CI) users demonstrate severe limitations in perceiving musical timbre, a psychoacoustic feature of sound responsible for 'tone color' and one's ability to identify a musical instrument. The reasons for this limitation remain poorly understood. In this study, we sought to examine the relative contributions of temporal envelope and fine structure for timbre judgments, in light of the fact that speech processing strategies employed by CI systems typically employ envelope extraction algorithms. We synthesized "instrumental chimeras" that systematically combined variable amounts of envelope and fine structure in 25% increments from two different source instruments with either sustained or percussive envelopes. CI users and normal hearing (NH) subjects were presented with 150 chimeras and asked to determine which instrument the chimera more closely resembled in a single-interval two-alternative forced choice task. By combining instruments with similar and dissimilar envelopes, we controlled the valence of envelope for timbre identification and compensated for envelope reconstruction from fine structure information. Our results show that NH subjects utilize envelope and fine structure interchangeably, whereas CI subjects demonstrate overwhelming reliance on temporal envelope. When chimeras were created from dissimilar envelope instrument pairs, NH subjects utilized a combination of envelope (p = 0.008) and fine structure information (p = 0.009) to make timbre judgments. In contrast, CI users utilized envelope information almost exclusively to make timbre judgments (p < 0.001) and ignored fine structure information (p = 0.908). Interestingly, when the value of envelope as a cue was reduced, both NH subjects and CI users utilized fine structure information to make timbre judgments (p < 0.001), although the effect was quite weak in CI users. Our findings confirm that impairments in fine structure processing underlie poor perception of musical timbre in CI

  19. Mutually unbiased coarse-grained measurements of two or more phase-space variables

    Science.gov (United States)

    Paul, E. C.; Walborn, S. P.; Tasca, D. S.; Rudnicki, Łukasz

    2018-05-01

    Mutual unbiasedness of the eigenstates of phase-space operators—such as position and momentum, or their standard coarse-grained versions—exists only in the limiting case of infinite squeezing. In Phys. Rev. Lett. 120, 040403 (2018), 10.1103/PhysRevLett.120.040403, it was shown that mutual unbiasedness can be recovered for periodic coarse graining of these two operators. Here we investigate mutual unbiasedness of coarse-grained measurements for more than two phase-space variables. We show that mutual unbiasedness can be recovered between periodic coarse graining of any two nonparallel phase-space operators. We illustrate these results through optics experiments, using the fractional Fourier transform to prepare and measure mutually unbiased phase-space variables. The differences between two and three mutually unbiased measurements is discussed. Our results contribute to bridging the gap between continuous and discrete quantum mechanics, and they could be useful in quantum-information protocols.

  20. Coarse graining from variationally enhanced sampling applied to the Ginzburg–Landau model

    Science.gov (United States)

    Invernizzi, Michele; Valsson, Omar; Parrinello, Michele

    2017-01-01

    A powerful way to deal with a complex system is to build a coarse-grained model capable of catching its main physical features, while being computationally affordable. Inevitably, such coarse-grained models introduce a set of phenomenological parameters, which are often not easily deducible from the underlying atomistic system. We present a unique approach to the calculation of these parameters, based on the recently introduced variationally enhanced sampling method. It allows us to obtain the parameters from atomistic simulations, providing thus a direct connection between the microscopic and the mesoscopic scale. The coarse-grained model we consider is that of Ginzburg–Landau, valid around a second-order critical point. In particular, we use it to describe a Lennard–Jones fluid in the region close to the liquid–vapor critical point. The procedure is general and can be adapted to other coarse-grained models. PMID:28292890

  1. NEW RSW & Wall Coarse Mixed Element Grid

    Data.gov (United States)

    National Aeronautics and Space Administration — This is the Coarse Mixed Element Grid for the RSW with a viscous wall at the root. This grid is for a node-based unstructured solver. Quad Surface Faces= 9728 Tria...

  2. Estimating the shear strength of concrete with coarse aggregate replacement

    OpenAIRE

    Folagbade Olusoga Peter ORIOLA; George MOSES; Jacob Oyeniyi AFOLAYAN; John Engbonye SANI

    2017-01-01

    For economic, environmental and practical reasons, it is desirable to replace the constituents of concrete with wastes and cheaper alternative materials. However, it is best when such replacements are done at optimum replacement levels. In view of this, a laboratory investigative test was carried out to evaluate the shear strength of concrete with coarse aggregate replacement by Coconut Shell and by Waste Rubber Tyre. The coarse aggregate replacement was done at recommended optimum proportion...

  3. Coarse-grained electrostatic interactions of coronene: Towards the crystalline phase

    Energy Technology Data Exchange (ETDEWEB)

    Heinemann, Thomas, E-mail: thomas.heinemann@tu-berlin.de; Klapp, Sabine H. L., E-mail: klapp@physik.tu-berlin.de [Institut für Theoretische Physik, Technische Universität Berlin, Hardenbergstr. 36, 10623 Berlin (Germany); Palczynski, Karol, E-mail: karol.palczynski@helmholtz-berlin.de; Dzubiella, Joachim, E-mail: joachim.dzubiella@helmholtz-berlin.de [Institut für Physik, Humboldt Universität zu Berlin, Newtonstraße 15, 12489 Berlin (Germany); Institut für Weiche Materie und Funktionale Materialen, Helmholtz-Zentrum Berlin für Materialien und Energie, Hahn-Meitner Platz 1, 14109 Berlin (Germany)

    2015-11-07

    In this article, we present and compare two different, coarse-grained approaches to model electrostatic interactions of disc-shaped aromatic molecules, specifically coronene. Our study builds on our previous work [T. Heinemann et al., J. Chem. Phys. 141, 214110 (2014)], where we proposed, based on a systematic coarse-graining procedure starting from the atomistic level, an anisotropic effective (Gay-Berne-like) potential capable of describing van der Waals contributions to the interaction energy. To take into account electrostatics, we introduce, first, a linear quadrupole moment along the symmetry axis of the coronene disc. The second approach takes into account the fact that the partial charges within the molecules are distributed in a ring-like fashion. We then reparametrize the effective Gay-Berne-like potential such that it matches, at short distances, the ring-ring potential. To investigate the validity of these two approaches, we perform many-particle molecular dynamics simulations, focusing on the crystalline phase (karpatite) where electrostatic interaction effects are expected to be particularly relevant for the formation of tilted stacked columns. Specifically, we investigate various structural parameters as well as the melting transition. We find that the second approach yields consistent results with those from experiments despite the fact that the underlying potential decays with the wrong distance dependence at large molecule separations. Our strategy can be transferred to a broader class of molecules, such as benzene or hexabenzocoronene.

  4. Coarse-grained electrostatic interactions of coronene: Towards the crystalline phase

    International Nuclear Information System (INIS)

    Heinemann, Thomas; Klapp, Sabine H. L.; Palczynski, Karol; Dzubiella, Joachim

    2015-01-01

    In this article, we present and compare two different, coarse-grained approaches to model electrostatic interactions of disc-shaped aromatic molecules, specifically coronene. Our study builds on our previous work [T. Heinemann et al., J. Chem. Phys. 141, 214110 (2014)], where we proposed, based on a systematic coarse-graining procedure starting from the atomistic level, an anisotropic effective (Gay-Berne-like) potential capable of describing van der Waals contributions to the interaction energy. To take into account electrostatics, we introduce, first, a linear quadrupole moment along the symmetry axis of the coronene disc. The second approach takes into account the fact that the partial charges within the molecules are distributed in a ring-like fashion. We then reparametrize the effective Gay-Berne-like potential such that it matches, at short distances, the ring-ring potential. To investigate the validity of these two approaches, we perform many-particle molecular dynamics simulations, focusing on the crystalline phase (karpatite) where electrostatic interaction effects are expected to be particularly relevant for the formation of tilted stacked columns. Specifically, we investigate various structural parameters as well as the melting transition. We find that the second approach yields consistent results with those from experiments despite the fact that the underlying potential decays with the wrong distance dependence at large molecule separations. Our strategy can be transferred to a broader class of molecules, such as benzene or hexabenzocoronene

  5. An eco-friendly self-compacting concrete with recycled coarse aggregates

    Directory of Open Access Journals (Sweden)

    Pereira-de Oliveira, L. A.

    2013-09-01

    Full Text Available The potential uses of coarse recycled aggregates in the composition of SCC increases the ecological value and partly solve the issues of waste disposal sites generated by construction and demolition of structures. Thus, this paper present an experimental study of SCC properties where the normal coarse aggregates were replaced by different percentages of recycled aggregates, i.e., 0% (SCC, 10% (SCCR10, 20% (SCCR20, 30% (SCCR30 and 40% (SCCR40. The results from fresh concrete (rheological properties and self-compactability as the hardened concrete properties (compressive strength, density and dynamic modulus of elasticity, show only minor discrepancies. From the standpoint of mechanical behaviour, the results confirm the viability to incorporate coarse recycled aggregates in the SCC demonstrating the conservative character of the currently recommended limits.Los usos potenciales de áridos gruesos reciclados en la composición del hormigón autocompactante (SCC aumenta el valor ecológico y en parte resuelve los problemas de los sitios de disposición de residuos generados por la construcción y la demolición de las estructuras. Por lo tanto, este trabajo presenta un estudio experimental de las propiedades de SCC en el cual los áridos gruesos naturales fueron reemplazados por distintos porcentajes de áridos reciclados, es decir, 0% (SCC, el 10% (SCCR10, el 20% (SCCR20, el 30% (SCCR30 y el 40% (SCCR40. Los resultados del hormigón fresco (propiedades reológicas y la auto-compactación, como las propiedades de hormigón endurecido (resistencia a la compresión, densidad y módulo de elasticidad dinámico, muestran sólo pequeñas discrepancias. Desde el punto de vista del comportamiento mecánico, los resultados confirman la viabilidad de incorporar áridos gruesos reciclados en los SCC demostrando el carácter conservador de los límites actualmente recomendados.

  6. Coarse-to-fine region selection and matching

    KAUST Repository

    Yang, Yanchao

    2015-10-15

    We present a new approach to wide baseline matching. We propose to use a hierarchical decomposition of the image domain and coarse-to-fine selection of regions to match. In contrast to interest point matching methods, which sample salient regions to reduce the cost of comparing all regions in two images, our method eliminates regions systematically to achieve efficiency. One advantage of our approach is that it is not restricted to covariant salient regions, which is too restrictive under large viewpoint and leads to few corresponding regions. Affine invariant matching of regions in the hierarchy is achieved efficiently by a coarse-to-fine search of the affine space. Experiments on two benchmark datasets shows that our method finds more correct correspondence of the image (with fewer false alarms) than other wide baseline methods on large viewpoint change. © 2015 IEEE.

  7. Bayesian calibration of coarse-grained forces: Efficiently addressing transferability

    International Nuclear Information System (INIS)

    Patrone, Paul N.; Rosch, Thomas W.; Phelan, Frederick R.

    2016-01-01

    Generating and calibrating forces that are transferable across a range of state-points remains a challenging task in coarse-grained (CG) molecular dynamics. In this work, we present a coarse-graining workflow, inspired by ideas from uncertainty quantification and numerical analysis, to address this problem. The key idea behind our approach is to introduce a Bayesian correction algorithm that uses functional derivatives of CG simulations to rapidly and inexpensively recalibrate initial estimates f 0 of forces anchored by standard methods such as force-matching. Taking density-temperature relationships as a running example, we demonstrate that this algorithm, in concert with various interpolation schemes, can be used to efficiently compute physically reasonable force curves on a fine grid of state-points. Importantly, we show that our workflow is robust to several choices available to the modeler, including the interpolation schemes and tools used to construct f 0 . In a related vein, we also demonstrate that our approach can speed up coarse-graining by reducing the number of atomistic simulations needed as inputs to standard methods for generating CG forces.

  8. Bayesian calibration of coarse-grained forces: Efficiently addressing transferability

    Science.gov (United States)

    Patrone, Paul N.; Rosch, Thomas W.; Phelan, Frederick R.

    2016-04-01

    Generating and calibrating forces that are transferable across a range of state-points remains a challenging task in coarse-grained (CG) molecular dynamics. In this work, we present a coarse-graining workflow, inspired by ideas from uncertainty quantification and numerical analysis, to address this problem. The key idea behind our approach is to introduce a Bayesian correction algorithm that uses functional derivatives of CG simulations to rapidly and inexpensively recalibrate initial estimates f0 of forces anchored by standard methods such as force-matching. Taking density-temperature relationships as a running example, we demonstrate that this algorithm, in concert with various interpolation schemes, can be used to efficiently compute physically reasonable force curves on a fine grid of state-points. Importantly, we show that our workflow is robust to several choices available to the modeler, including the interpolation schemes and tools used to construct f0. In a related vein, we also demonstrate that our approach can speed up coarse-graining by reducing the number of atomistic simulations needed as inputs to standard methods for generating CG forces.

  9. Prediction of protein structure with the coarse-grained UNRES force field assisted by small X-ray scattering data and knowledge-based information.

    Science.gov (United States)

    Karczyńska, Agnieszka S; Mozolewska, Magdalena A; Krupa, Paweł; Giełdoń, Artur; Liwo, Adam; Czaplewski, Cezary

    2018-03-01

    A new approach to assisted protein-structure prediction has been proposed, which is based on running multiplexed replica exchange molecular dynamics simulations with the coarse-grained UNRES force field with restraints derived from knowledge-based models and distance distribution from small angle X-ray scattering (SAXS) measurements. The latter restraints are incorporated into the target function as a maximum-likelihood term that guides the shape of the simulated structures towards that defined by SAXS. The approach was first verified with the 1KOY protein, for which the distance distribution was calculated from the experimental structure, and subsequently used to predict the structures of 11 data-assisted targets in the CASP12 experiment. Major improvement of the GDT_TS was obtained for 2 targets, minor improvement for other 2 while, for 6 target GDT_TS deteriorated compared with that calculated for predictions without the SAXS data, partly because of assuming a wrong multimeric state (for Ts866) or because the crystal conformation was more compact than the solution conformation (for Ts942). Particularly good results were obtained for Ts909, in which use of SAXS data resulted in the selection of a correctly packed trimer and, subsequently, increased the GDT_TS of monomer prediction. It was found that running simulations with correct oligomeric state is essential for the success in SAXS-data-assisted prediction. © 2017 Wiley Periodicals, Inc.

  10. The multilayer temporal network of public transport in Great Britain

    Science.gov (United States)

    Gallotti, Riccardo; Barthelemy, Marc

    2015-01-01

    Despite the widespread availability of information concerning public transport coming from different sources, it is extremely hard to have a complete picture, in particular at a national scale. Here, we integrate timetable data obtained from the United Kingdom open-data program together with timetables of domestic flights, and obtain a comprehensive snapshot of the temporal characteristics of the whole UK public transport system for a week in October 2010. In order to focus on multi-modal aspects of the system, we use a coarse graining procedure and define explicitly the coupling between different transport modes such as connections at airports, ferry docks, rail, metro, coach and bus stations. The resulting weighted, directed, temporal and multilayer network is provided in simple, commonly used formats, ensuring easy access and the possibility of a straightforward use of old or specifically developed methods on this new and extensive dataset.

  11. Coarse and fine sediment transportation patterns and causes downstream of the Three Gorges Dam

    Science.gov (United States)

    Li, Songzhe; Yang, Yunping; Zhang, Mingjin; Sun, Zhaohua; Zhu, Lingling; You, Xingying; Li, Kanyu

    2017-11-01

    Reservoir construction within a basin affects the process of water and sediment transport downstream of the dam. The Three Gorges Reservoir (TGR) affects the sediment transport downstream of the dam. The impoundment of the TGR reduced total downstream sediment. The sediment group d≤0.125 mm (fine particle) increased along the path, but the average was still below what existed before the reservoir impoundment. The sediments group d>0.125 mm (coarse particle) was recharged in the Yichang to Jianli reach, but showed a deposition trend downstream of Jianli. The coarse sediment in the Yichang to Jianli section in 2003 to 2007 was above the value before the TGR impoundment. However, the increase of both coarse and fine sediments in 2008 to 2014 was less than that in 2003 to 2007. The sediment retained in the dam is the major reason for the sediment reduction downstream. However, the retention in different river reaches is affected by riverbed coarsening, discharge, flow process, and conditions of lake functioning and recharging from the tributaries. The main conclusions derived from our study are as follows: 1) The riverbed in the Yichang to Shashi section was relatively coarse, thereby limiting the supply of fine and coarse sediments. The fine sediment supply was mainly controlled by TGR discharge, whereas the coarse sediment supply was controlled by the duration of high flow and its magnitude. 2) The supply of both coarse and fine sediments in the Shashi to Jianli section was controlled by the amount of total discharge. The sediment supply from the riverbed was higher in flood years than that in the dry years. The coarse sediment tended to deposit, and the deposition in the dry years was larger than that in the flood years. 3) The feeding of the fine sediment in the Luoshan to Hankou section was mainly from the riverbed. The supply in 2008 to 2014 was more than that in 2003 to 2007. Around 2010, the coarse sediments transited from depositing to scouring that was

  12. Temporal genetic population structure and interannual variation in migration behavior of Pacific Lamprey Entosphenus tridentatus

    Science.gov (United States)

    Clemens, Benjamin J.; Wyss, Lance A.; McCoun, Rebecca; Courter, Ian; Schwabe, Lawrence; Peery, Christopher; Schreck, Carl B.; Spice, Erin K.; Docker, Margaret F.

    2017-01-01

    Studies using neutral loci suggest that Pacific lamprey, Entosphenus tridentatus, lack strong spatial genetic population structure. However, it is unknown whether temporal genetic population structure exists. We tested whether adult Pacific lamprey: (1) show temporal genetic population structure; and (2) migrate different distances between years. We non-lethally sampled lamprey for DNA in 2009 and 2010 and used eight microsatellite loci to test for genetic population structure. We used telemetry to record the migration behaviors of these fish. Lamprey were assignable to three moderately differentiated genetic clusters (FST = 0.16–0.24 for all pairwise comparisons): one cluster was composed of individuals from 2009, and the other two contained individuals from 2010. The FST value between years was 0.13 and between genetic clusters within 2010 was 0.20. A total of 372 (72.5%) fish were detected multiple times during their migrations. Most fish (69.9%) remained in the mainstem Willamette River; the remaining 30.1% migrated into tributaries. Eighty-two lamprey exhibited multiple back-and-forth movements among tributaries and the mainstem, which may indicate searching behaviors. All migration distances were significantly greater in 2010, when the amplitude of river discharge was greater. Our data suggest genetic structuring between and within years that may reflect different cohorts.

  13. Stability and dynamics of spatio-temporal structures. Progress report, September 15, 1993--September 14, 1994

    Energy Technology Data Exchange (ETDEWEB)

    Riecke, H.

    1994-05-01

    Goal is to contribute to understanding of localized spatial and spatio-temporal structures far from thermodynamic equilibrium. Here we report on our progress in the study of three classes of systems. (1) We have studied cellular flame structures arising in a circular burner. Using numerical computations we have found a number of traveling-wave structures in which different cells undergo different motion. Most strikingly, we have found a localized wave traveling through the array of steady cells. Results are interpreted using various asymptotic approaches. They are in qualitative agreement with recent experiments. (2) We have continued our investigation of localized waves in binary-mixture convection. Starting from the extended Ginzburg-Landau equations introduced earlier, we have derived equations of motion for interacting fronts connecting the conductive and the convective state. These equations reveal a repulsive interaction between the fronts which implies a new localization mechanism for waves. It is solely due to the long-wavelength mode specific to the extended Ginzburg-Landau equations. The stability properties of the resulting localized waves are in qualitative agreement with very recent experiments. (3) We have extended our investigation of domain structures to include their temporal evolution.

  14. Combining fine texture and coarse color features for color texture classification

    Science.gov (United States)

    Wang, Junmin; Fan, Yangyu; Li, Ning

    2017-11-01

    Color texture classification plays an important role in computer vision applications because texture and color are two fundamental visual features. To classify the color texture via extracting discriminative color texture features in real time, we present an approach of combining the fine texture and coarse color features for color texture classification. First, the input image is transformed from RGB to HSV color space to separate texture and color information. Second, the scale-selective completed local binary count (CLBC) algorithm is introduced to extract the fine texture feature from the V component in HSV color space. Third, both H and S components are quantized at an optimal coarse level. Furthermore, the joint histogram of H and S components is calculated, which is considered as the coarse color feature. Finally, the fine texture and coarse color features are combined as the final descriptor and the nearest subspace classifier is used for classification. Experimental results on CUReT, KTH-TIPS, and New-BarkTex databases demonstrate that the proposed method achieves state-of-the-art classification performance. Moreover, the proposed method is fast enough for real-time applications.

  15. A coarse-to-fine scheme for groupwise registration of multisensor images

    Directory of Open Access Journals (Sweden)

    Yinghao Li

    2016-11-01

    Full Text Available Ensemble registration is concerned with a group of images that need to be registered simultaneously. It is challenging but important for many image analysis tasks such as vehicle detection and medical image fusion. To solve this problem effectively, a novel coarse-to-fine scheme for groupwise image registration is proposed. First, in the coarse registration step, unregistered images are divided into reference image set and float image set. The images of the two sets are registered based on segmented region matching. The coarse registration results are used as an initial solution for the next step. Then, in the fine registration step, a Gaussian mixture model with a local template is used to model the joint intensity of coarse-registered images. Meanwhile, a minimum message length criterion-based method is employed to determine the unknown number of mixing components. Based on this mixture model, a maximum likelihood framework is used to register a group of images. To evaluate the performance of the proposed approach, some representative groupwise registration approaches are compared on different image data sets. The experimental results show that the proposed approach has improved performance compared to conventional approaches.

  16. Terrain aided navigation for autonomous underwater vehicles with coarse maps

    International Nuclear Information System (INIS)

    Zhou, Ling; Cheng, Xianghong; Zhu, Yixian

    2016-01-01

    Terrain aided navigation (TAN) is a form of geophysical localization technique for autonomous underwater vehicles (AUVs) operating in GPS-denied environments. TAN performance on sensor-rich AUVs has been evaluated in sea trials. However, many challenges remain before TAN can be successfully implemented on sensor-limited AUVs, especially with coarse maps. To improve TAN performance over coarse maps, a Gaussian process (GP) is proposed for the modeling of bathymetric terrain and integrated into the particle filter (GP-PF). GP is applied to provide not only the bathymetric value prediction through learning a set of bathymetric data from coarse maps but also the variance of the prediction. As a measurement update, calculated on bathymetric deviation is performed through the PF to obtain absolute and bounded positioning accuracy. Through the analysis of TAN performance on experimental data for two different terrains with map resolutions of 10–50 m, both the ability of the proposed model to represent the actual bathymetric terrain with accuracy and the effect of the GP-PF for TAN on sensor-limited systems in suited terrain are demonstrated. The experiment results further verify that there is an inverse relationship between the coarseness of the map and the overall TAN accuracy in rough terrains, but there is hardly any relationship between them in relatively flat terrains. (paper)

  17. Molecular dynamics simulation of coarse-grained poly(L-lysine) dendrimers.

    Science.gov (United States)

    Rahimi, Ali; Amjad-Iranagh, Sepideh; Modarress, Hamid

    2016-03-01

    Poly(L-lysine) (PLL) dendrimer are amino acid based macromolecules and can be used as drug delivery agents. Their branched structure allows them to be functionalized by various groups to encapsulate drug agents into their structure. In this work, at first, an attempt was made on all-atom simulation of PLL dendrimer of different generations. Based on all-atom results, a course-grained model of this dendrimer was designed and its parameters were determined, to be used for simulation of three generations of PLL dendrimer, at two pHs. Similar to the all-atom, the coarse-grained results indicated that by increasing the generation, the dendrimer becomes more spherical. At pH 7, the dendrimer had larger size, whereas at pH 12, due to back folding of branching chains, they had the tendency to penetrate into the inner layers. The calculated radial probability and radial distribution functions confirm that at pH 7, the PLL dendrimer has more cavities and as a result it can encapsulate more water molecules into its inner structure. By calculating the moment of inertia and the aspect ratio, the formation of spherical structure for PLL dendrimer was confirmed.

  18. The spatio-temporal structure of electrostatic turbulence in the WEGA stellarator

    International Nuclear Information System (INIS)

    Marsen, Stefan

    2008-03-01

    The main object of this work is to provide a detailed characterisation of electrostatic turbulence in WEGA and to identify the underlying instability mechanism driving turbulence. The spatio-temporal structure of turbulence is studied using multiple Langmuir probes providing a sufficiently high spatial and temporal resolution. Turbulence in WEGA is dominated by drift wave dynamics. The phase shift between density and potential fluctuations is close to zero, fluctuations are mainly driven by the density gradient, and the phase velocity of turbulent structures points in the direction of the electron diamagnetic drift. The structure of turbulence is studied mainly in the plasma edge region inside the last closed flux surface. WEGA can be operated in two regimes differing in the magnetic field strength by almost one order of magnitude (57 mT and 500 mT, respectively). At 57 mT large structures with a poloidal extent comparable to the machine dimensions are observed, whereas at 500 mT turbulent structures are much smaller. The poloidal structure size scales nearly linearly with the inverse magnetic field strength. This scaling may be argued to be related to the drift wave dispersion scale, ρ s =√(m i k B T e )/(qB). However, the structure size remains unchanged when the ion mass is changed by using different discharge gases. Inside the last closed flux surface the poloidal E x B drift in WEGA is negligible. The three-dimensional structure is studied in detail using probes which are toroidally separated but aligned along connecting magnetic field lines. A small but finite parallel wavenumber is found. The ratio between the average parallel and perpendicular wavenumber is in the order of anti κ parallel / anti κ θ ∼ 10 -2 . The parallel phase velocity of turbulent structures is in-between the ion sound velocity and the Alfven velocity. In the parallel dynamics a fundamental difference between the two operational regimes at different magnetic field strength is

  19. Coarse-to-Fine Segmentation with Shape-Tailored Continuum Scale Spaces

    KAUST Repository

    Khan, Naeemullah

    2017-11-09

    We formulate an energy for segmentation that is designed to have preference for segmenting the coarse over fine structure of the image, without smoothing across boundaries of regions. The energy is formulated by integrating a continuum of scales from a scale space computed from the heat equation within regions. We show that the energy can be optimized without computing a continuum of scales, but instead from a single scale. This makes the method computationally efficient in comparison to energies using a discrete set of scales. We apply our method to texture and motion segmentation. Experiments on benchmark datasets show that a continuum of scales leads to better segmentation accuracy over discrete scales and other competing methods.

  20. Coarse-to-Fine Segmentation with Shape-Tailored Continuum Scale Spaces

    KAUST Repository

    Khan, Naeemullah; Hong, Byung-Woo; Yezzi, Anthony; Sundaramoorthi, Ganesh

    2017-01-01

    We formulate an energy for segmentation that is designed to have preference for segmenting the coarse over fine structure of the image, without smoothing across boundaries of regions. The energy is formulated by integrating a continuum of scales from a scale space computed from the heat equation within regions. We show that the energy can be optimized without computing a continuum of scales, but instead from a single scale. This makes the method computationally efficient in comparison to energies using a discrete set of scales. We apply our method to texture and motion segmentation. Experiments on benchmark datasets show that a continuum of scales leads to better segmentation accuracy over discrete scales and other competing methods.

  1. MRI-based brain structure volumes in temporal lobe epilepsy patients and their unaffected siblings: a preliminary study.

    LENUS (Irish Health Repository)

    Scanlon, Cathy

    2013-01-01

    Investigating the heritability of brain structure may be useful in simplifying complicated genetic studies in temporal lobe epilepsy (TLE). A preliminary study is presented to determine if volume deficits of candidate brain structures present at a higher rate in unaffected siblings than controls subjects.

  2. Coarse-grained molecular simulations of allosteric cooperativity

    Energy Technology Data Exchange (ETDEWEB)

    Nandigrami, Prithviraj; Portman, John J. [Department of Physics, Kent State University, Kent, Ohio 44242 (United States)

    2016-03-14

    Interactions between a protein and a ligand are often accompanied by a redistribution of the population of thermally accessible conformations. This dynamic response of the protein’s functional energy landscape enables a protein to modulate binding affinities and control binding sensitivity to ligand concentration. In this paper, we investigate the structural origins of binding affinity and allosteric cooperativity of binding two Ca{sup 2+} ions to each domain of Calmodulin (CaM) through simulations of a simple coarse-grained model. In this model, the protein’s conformational transitions between open and closed conformational ensembles are simulated explicitly and ligand binding and unbinding are treated implicitly within the grand canonical ensemble. Ligand binding is cooperative because the binding sites are coupled through a shift in the dominant conformational ensemble upon binding. The classic Monod-Wyman-Changeux model of allostery with appropriate binding free energies to the open and closed ensembles accurately describes the simulated binding thermodynamics. The simulations predict that the two domains of CaM have distinct binding affinity and cooperativity. In particular, the C-terminal domain binds Ca{sup 2+} with higher affinity and greater cooperativity than the N-terminal domain. From a structural point of view, the affinity of an individual binding loop depends sensitively on the loop’s structural compatibility with the ligand in the bound ensemble, as well as the conformational flexibility of the binding site in the unbound ensemble.

  3. Analysis in temporal regime of dispersive invisible structures designed from transformation optics

    Science.gov (United States)

    Gralak, B.; Arismendi, G.; Avril, B.; Diatta, A.; Guenneau, S.

    2016-03-01

    A simple invisible structure made of two anisotropic homogeneous layers is analyzed theoretically in temporal regime. The frequency dispersion is introduced and analytic expression of the transient part of the field is derived for large times when the structure is illuminated by a causal excitation. This expression shows that the limiting amplitude principle applies with transient fields decaying as the power -3 /4 of the time. The quality of the cloak is then reduced at short times and remains preserved at large times. The one-dimensional theoretical analysis is supplemented with full-wave numerical simulations in two-dimensional situations which confirm the effect of dispersion.

  4. MT-ADRES: Multithreading on Coarse-Grained Reconfigurable Architecture

    DEFF Research Database (Denmark)

    Wu, Kehuai; Kanstein, Andreas; Madsen, Jan

    2007-01-01

    The coarse-grained reconfigurable architecture ADRES (Architecture for Dynamically Reconfigurable Embedded Systems) and its compiler offer high instruction-level parallelism (ILP) to applications by means of a sparsely interconnected array of functional units and register files. As high-ILP archi......The coarse-grained reconfigurable architecture ADRES (Architecture for Dynamically Reconfigurable Embedded Systems) and its compiler offer high instruction-level parallelism (ILP) to applications by means of a sparsely interconnected array of functional units and register files. As high......-ILP architectures achieve only low parallelism when executing partially sequential code segments, which is also known as Amdahl’s law, this paper proposes to extend ADRES to MT-ADRES (Multi-Threaded ADRES) to also exploit thread-level parallelism. On MT-ADRES architectures, the array can be partitioned in multiple...

  5. Influence of uncoated and coated plastic waste coarse aggregates to concrete compressive strength

    Directory of Open Access Journals (Sweden)

    Purnomo Heru

    2017-01-01

    Full Text Available The use of plastic waste as coarse aggregates in concrete is part of efforts to reduce environmental pollution. In one hand the use of plastic as aggregates can provide lighter weight of the concrete than concrete using natural aggregates, but on the other hand bond between plastic coarse aggregates and hard matrix give low concrete compressive strength. Improvement of the bond between plastic coarse aggregate and hard matrix through a sand coating to plastic coarse aggregate whole surface is studied. Sand used to coat the plastic aggregates are Merapi volcanic sand which are taken in Magelang. Three mixtures of polypropylene (PP coarse plastic aggregates, Cimangkok river sand as fine aggregates, water and Portland Cement Composite with a water-cement ratio of 0.28, 0.3 and 0.35 are conducted. Compression test are performed on concrete cylindrical specimens with a diameter of 10 cm and a height of 20 cm. The results in general show that concrete specimens using plastic aggregates coated with sand have higher compressive strength compared to those of concrete specimens using plastic aggregates without sand coating. The bond improvement is indirectly indicated by the betterment of concrete compressive strength.

  6. Coarse Grained Molecular Dynamics Simulations of Transmembrane Protein-Lipid Systems

    Directory of Open Access Journals (Sweden)

    Peter Spijker

    2010-06-01

    Full Text Available Many biological cellular processes occur at the micro- or millisecond time scale. With traditional all-atom molecular modeling techniques it is difficult to investigate the dynamics of long time scales or large systems, such as protein aggregation or activation. Coarse graining (CG can be used to reduce the number of degrees of freedom in such a system, and reduce the computational complexity. In this paper the first version of a coarse grained model for transmembrane proteins is presented. This model differs from other coarse grained protein models due to the introduction of a novel angle potential as well as a hydrogen bonding potential. These new potentials are used to stabilize the backbone. The model has been validated by investigating the adaptation of the hydrophobic mismatch induced by the insertion of WALP-peptides into a lipid membrane, showing that the first step in the adaptation is an increase in the membrane thickness, followed by a tilting of the peptide.

  7. Effects of coarse-graining on the scaling behavior of long-range correlated and anti-correlated signals

    OpenAIRE

    Xu, Yinlin; Ma, Qianli D.Y.; Schmitt, Daniel T.; Bernaola-Galván, Pedro; Ivanov, Plamen Ch.

    2011-01-01

    We investigate how various coarse-graining methods affect the scaling properties of long-range power-law correlated and anti-correlated signals, quantified by the detrended fluctuation analysis. Specifically, for coarse-graining in the magnitude of a signal, we consider (i) the Floor, (ii) the Symmetry and (iii) the Centro-Symmetry coarse-graining methods. We find, that for anti-correlated signals coarse-graining in the magnitude leads to a crossover to random behavior at large scales, and th...

  8. Chemodectomas arising in temporal bone structures

    International Nuclear Information System (INIS)

    Dickens, W.J.; Million, R.R.; Cassisi, N.J.; Singleton, G.T.

    1982-01-01

    Eighteen patients with chemodectomas arising in temporal bone structures were evaluated and treated at the University of Florida. Seventeen patients have each been followed a minimum of 3 years. Patients were retrospectively staged as having ''local'' or ''advanced'' disease, depending on the presence or absence of bone destruction and/or cranial nerve involvement. Fourteen of the patients received radiation therapy as all or part of their therapy; 6 patients were treated with radiation therapy alone, 3 patients were irradiated immediately postoperatively for residual disease, and 5 patients had radiation therapy for recurrence after operation. They were treated with cobalt-60 radiation with doses ranging from 3760 to 5640 rad. All irradiated patients demonstrated evidence of tumor regression, and none have had tumor recurrence with followup of 3-12 years. Of the 8 patients with cranial nerve paralysis prior to therapy, 5 had return of function of 1 or more cranial nerves. One of 6 patients treated initially with radiation therapy had a complication, while 6 of 8 patients irradiated postoperatively had complications. None of the complications were fatal. Three patients treated by operation for early disease limited to the hypotympanum had the disease controlled for 11-12 years. Guidelines for the selection of initial therapy are discussed

  9. Effects of Nb on microstructure and continuous cooling transformation of coarse grain heat-affected zone in 610 MPa class high-strength low-alloy structural steels

    International Nuclear Information System (INIS)

    Zhang, Y.Q.; Zhang, H.Q.; Liu, W.M.; Hou, H.

    2009-01-01

    Continuous cooling transformation diagrams of the coarse grain heat-affected zone and microstructure after continuous cooling were investigated for 610 MPa class high-strength low-alloy (HSLA) structural steels with and without niobium. For the steel without Nb, grain boundary ferrite, degenerate pearlite and acicular ferrite are produced at slower cooling rates. Bainite phase is formed at faster cooling rates. However, for the steel with Nb, granular bainite is dominant at a large range of cooling rates. At cooling rates 32 K/s, Nb addition has no obvious influence on transformation start temperature, but it influences microstructure transformation significantly. Martensite is observed in steel with Nb at faster cooling rates, but not produced in steel without Nb

  10. Development of new test procedures for measuring fine and coarse aggregates specific gravity.

    Science.gov (United States)

    2009-09-01

    The objective of the research is to develop and evaluate new test methods at determining the specific gravity and absorption of both fine and coarse aggregates. Current methods at determining the specific gravity and absorption of fine and coarse agg...

  11. Coarse-grain modelling of protein-protein interactions

    NARCIS (Netherlands)

    Baaden, Marc; Marrink, Siewert J.

    2013-01-01

    Here, we review recent advances towards the modelling of protein-protein interactions (PPI) at the coarse-grained (CG) level, a technique that is now widely used to understand protein affinity, aggregation and self-assembly behaviour. PPI models of soluble proteins and membrane proteins are

  12. STABILITY AND DYNAMICS OF SPATIO-TEMPORAL STRUCTURES

    Energy Technology Data Exchange (ETDEWEB)

    Hermann Riecke

    2005-10-21

    This document constitutes the final report for the grant. It provides a complete list of publications and presentations that arose from the project as well as a brief description of the highlights of the research results. The research funded by this grant has provided insights into the spontaneous formation of structures of increasing complexity in systems driven far from thermodynamic equilibrium. A classic example of such a system is thermally driven convection in a horizontal fluid layer. Highlights of the research are: (1) explanation of the localized traveling wave pulses observed in binary-mixture convection, (2) explanation of the localized waves in electroconvection, (3) introduction of a new diagnostics for spatially and temporally chaotic states, which is based on the statistics of defect trajectories, (4) prediction of complex states in thermally driven convection in rotating systems. Additional contributions provided insight into the localization mechanism for oscillons, the prediction of a new localization mechanism for traveling waves based on a resonant periodic forcing, and an analysis of the stability of quasi-periodic patterns.

  13. Reactor calculation in coarse mesh by finite element method applied to matrix response method

    International Nuclear Information System (INIS)

    Nakata, H.

    1982-01-01

    The finite element method is applied to the solution of the modified formulation of the matrix-response method aiming to do reactor calculations in coarse mesh. Good results are obtained with a short running time. The method is applicable to problems where the heterogeneity is predominant and to problems of evolution in coarse meshes where the burnup is variable in one same coarse mesh, making the cross section vary spatially with the evolution. (E.G.) [pt

  14. General asymmetric neutral networks and structure design by genetic algorithms: A learning rule for temporal patterns

    Energy Technology Data Exchange (ETDEWEB)

    Bornholdt, S. [Heidelberg Univ., (Germany). Inst., fuer Theoretische Physik; Graudenz, D. [Lawrence Berkeley Lab., CA (United States)

    1993-07-01

    A learning algorithm based on genetic algorithms for asymmetric neural networks with an arbitrary structure is presented. It is suited for the learning of temporal patterns and leads to stable neural networks with feedback.

  15. General asymmetric neutral networks and structure design by genetic algorithms: A learning rule for temporal patterns

    International Nuclear Information System (INIS)

    Bornholdt, S.

    1993-07-01

    A learning algorithm based on genetic algorithms for asymmetric neural networks with an arbitrary structure is presented. It is suited for the learning of temporal patterns and leads to stable neural networks with feedback

  16. Effects of Elevated Temperature on Concrete with Recycled Coarse Aggregates

    Science.gov (United States)

    Salau, M. A.; Oseafiana, O. J.; Oyegoke, T. O.

    2015-11-01

    This paper discusses the effects of heating temperatures of 200°C, 400°C and 600°C each for 2 hours at a heating rate of 2.5°C/min on concrete with the content of Natural Coarse Aggregates (NCA) partially replaced with Recycled Coarse Aggregates (RCA), obtained from demolished building in the ratio of 0%, 15% and 30%.There was an initial drop in strength from 100°C to 200°C which is suspected to be due to the relatively weak interfacial bond between the RCA and the hardened paste within the concrete matrix;a gradual increase in strength continued from 200°C to 450°C and steady drop occurred again as it approached 600°C.With replacement proportion of 0%, 15% and 30% of NCA and exposure to peak temperature of 600°C, a relative concrete strength of 23.6MPa, 25.3MPa and 22.2MPa respectively can be achieved for 28 days curing age. Furthermore, RAC with 15% NCA replacement when exposed to optimum temperature of 450°C yielded high compressive strength comparable to that of control specimen (normal concrete). In addition, for all concrete samples only slight surface hairline cracks were noticed as the temperature approached 400°C. Thus, the RAC demonstrated behavior just like normal concrete and may be considered fit for structural use.

  17. On the Effect of Sphere-Overlap on Super Coarse-Grained Models of Protein Assemblies

    Science.gov (United States)

    Degiacomi, Matteo T.

    2018-05-01

    Ion mobility mass spectrometry (IM/MS) can provide structural information on intact protein complexes. Such data, including connectivity and collision cross sections (CCS) of assemblies' subunits, can in turn be used as a guide to produce representative super coarse-grained models. These models are constituted by ensembles of overlapping spheres, each representing a protein subunit. A model is considered plausible if the CCS and sphere-overlap levels of its subunits fall within predetermined confidence intervals. While the first is determined by experimental error, the latter is based on a statistical analysis on a range of protein dimers. Here, we first propose a new expression to describe the overlap between two spheres. Then we analyze the effect of specific overlap cutoff choices on the precision and accuracy of super coarse-grained models. Finally, we propose a method to determine overlap cutoff levels on a per-case scenario, based on collected CCS data, and show that it can be applied to the characterization of the assembly topology of symmetrical homo-multimers. [Figure not available: see fulltext.

  18. Comparison of coarse-grained (MARTINI) and atomistic molecular ...

    Indian Academy of Sciences (India)

    Rajat Desikan

    as the root mean square deviation (RMSD) histograms and the inner pore radius profiles from ... ever coarse-grained simulations of membrane-proteins ..... from the MARTINI simulations show greater fluctuations than the all-atom simulations.

  19. Coarse grainings and irreversibility in quantum field theory

    International Nuclear Information System (INIS)

    Anastopoulos, C.

    1997-01-01

    In this paper we are interested in studying coarse graining in field theories using the language of quantum open systems. Motivated by the ideas of Hu and Calzetta on correlation histories we employ the Zwanzig projection technique to obtain evolution equations for relevant observables in self-interacting scalar field theories. Our coarse-graining operation consists in concentrating solely on the evolution of the correlation functions of degree less than n, a treatment which corresponds to the familiar truncation of the BBKGY hierarchy at the nth level. We derive the equations governing the evolution of mean-field and two-point functions thus identifying the terms corresponding to dissipation and noise. We discuss possible applications of our formalism, the emergence of classical behavior, and the connection to the decoherent histories framework. copyright 1997 The American Physical Society

  20. Pollination Biology and Spatio-Temporal Structuring of Some Major Acacia Species (Leguminosae) of the Arabian Peninsula

    International Nuclear Information System (INIS)

    Adgaba, N.; Alghamidi, A.; Tadesse, Y.; Getachew, A.; Ansari, M. J.

    2016-01-01

    Acacias are the dominant woody plant species distributed over the vast tracts of land throughout the Arabian Peninsula. However, information on spatio-temporal structuring and pollination biology of the species is not precisely available. To determine whether any variations exist among the Acacia species in their temporal distribution, their flowering period was determined through monitoring the commencing, peaking and ending of flowering of each species. Moreover, if any variations exist in release of floral rewards among the different co-existing and co-flowering species as mechanisms of partitioning of pollinators, to minimize competition for pollination, the progress of their anthesis over time was recorded by scoring polyads to anthers ratio at different hours of a day. In addition, the amount and dynamics of nectar sugar per inflorescence (N =225/species) was determined following flower nectar sugar washing technique. Types and frequencies of flower visitors and their preferences were determined by recording the visitors 6 times a day. The current study revealed that the Acacia species of the Arabian Peninsula are spatio-temporally structured: some species co-exist yet have different flowering seasons, whereas others co-exist, flowering concurrently yet exhibit a shift in their time of peak flowering and in the time at which the peak pollen is released during the day. This study demonstrates that all Acacia species examined secrete a considerable amount of nectar (2.24+-1.72 -10.02+-4.0mg/inflorescence) which serves as a floral reward for pollinators. Insects of the Order Hymenoptera are the most prevalent visitors to Acacia species in the region. The variations in spatio-temporal structuring of the Acaciaspecies could be due to their adaptation of reducing competition for pollinators and minimizing hetero-specific pollen transfer. (author)

  1. Coarse grained model for semiquantitative lipid simulations

    NARCIS (Netherlands)

    Marrink, SJ; de Vries, AH; Mark, AE

    2004-01-01

    This paper describes the parametrization of a new coarse grained (CG) model for lipid and surfactant systems. Reduction of the number of degrees of freedom together with the use of short range potentials makes it computationally very efficient. Compared to atomistic models a gain of 3-4 orders of

  2. The spatio-temporal structure of electrostatic turbulence in the WEGA stellarator

    Energy Technology Data Exchange (ETDEWEB)

    Marsen, Stefan

    2008-03-15

    The main object of this work is to provide a detailed characterisation of electrostatic turbulence in WEGA and to identify the underlying instability mechanism driving turbulence. The spatio-temporal structure of turbulence is studied using multiple Langmuir probes providing a sufficiently high spatial and temporal resolution. Turbulence in WEGA is dominated by drift wave dynamics. The phase shift between density and potential fluctuations is close to zero, fluctuations are mainly driven by the density gradient, and the phase velocity of turbulent structures points in the direction of the electron diamagnetic drift. The structure of turbulence is studied mainly in the plasma edge region inside the last closed flux surface. WEGA can be operated in two regimes differing in the magnetic field strength by almost one order of magnitude (57 mT and 500 mT, respectively). At 57 mT large structures with a poloidal extent comparable to the machine dimensions are observed, whereas at 500 mT turbulent structures are much smaller. The poloidal structure size scales nearly linearly with the inverse magnetic field strength. This scaling may be argued to be related to the drift wave dispersion scale, {rho}{sub s}={radical}(m{sub i}k{sub B}T{sub e})/(qB). However, the structure size remains unchanged when the ion mass is changed by using different discharge gases. Inside the last closed flux surface the poloidal E x B drift in WEGA is negligible. The three-dimensional structure is studied in detail using probes which are toroidally separated but aligned along connecting magnetic field lines. A small but finite parallel wavenumber is found. The ratio between the average parallel and perpendicular wavenumber is in the order of anti {kappa} {sub parallel} / anti {kappa}{sub {theta}} {approx} 10{sup -2}. The parallel phase velocity of turbulent structures is in-between the ion sound velocity and the Alfven velocity. In the parallel dynamics a fundamental difference between the two

  3. Coarse-grained Simulations of Substrate Export through Multidrug Efflux Transporter AcrB

    Science.gov (United States)

    Jewel, Yead; Dutta, Prashanta; Liu, Jin

    2017-11-01

    The treatment of bacterial infectious diseases hampered by the overexpression of multidrug resistance (MDR) systems. The MDR system actively pumps the antibiotic drugs as well as other toxic compounds out of the cells. During the pumping, AcrB (one of the key MDR components) undergoes a series of large-scale proton/substrate dependent conformational changes. In this work, we implement a hybrid coarse-grained PACE force field that couples the united-atom protein model with the coarse-grained MARTINI water/lipid, to investigate the conformational changes of AcrB. We first develop the substrate force field which is compatible with PACE, then we implement the force field to explore large scale structural changes of AcrB in microsecond simulations. The effects of the substrate and the protonation states of two key residues: Asp407 and Asp408, are investigated. Our results show that the drug export through AcrB is proton as well as substrate dependent. Our simulations explain molecular mechanisms of substrate transport through AcrB complex, as well as provide valuable insights for designing proper antibiotic drugs. Research reported in this publication was supported by the National Institute of General Medical Sciences of the National Institutes of Health under Award Number R01GM122081.

  4. Coarse-grained stochastic processes and kinetic Monte Carlo simulators for the diffusion of interacting particles

    Science.gov (United States)

    Katsoulakis, Markos A.; Vlachos, Dionisios G.

    2003-11-01

    We derive a hierarchy of successively coarse-grained stochastic processes and associated coarse-grained Monte Carlo (CGMC) algorithms directly from the microscopic processes as approximations in larger length scales for the case of diffusion of interacting particles on a lattice. This hierarchy of models spans length scales between microscopic and mesoscopic, satisfies a detailed balance, and gives self-consistent fluctuation mechanisms whose noise is asymptotically identical to the microscopic MC. Rigorous, detailed asymptotics justify and clarify these connections. Gradient continuous time microscopic MC and CGMC simulations are compared under far from equilibrium conditions to illustrate the validity of our theory and delineate the errors obtained by rigorous asymptotics. Information theory estimates are employed for the first time to provide rigorous error estimates between the solutions of microscopic MC and CGMC, describing the loss of information during the coarse-graining process. Simulations under periodic boundary conditions are used to verify the information theory error estimates. It is shown that coarse-graining in space leads also to coarse-graining in time by q2, where q is the level of coarse-graining, and overcomes in part the hydrodynamic slowdown. Operation counting and CGMC simulations demonstrate significant CPU savings in continuous time MC simulations that vary from q3 for short potentials to q4 for long potentials. Finally, connections of the new coarse-grained stochastic processes to stochastic mesoscopic and Cahn-Hilliard-Cook models are made.

  5. Coarse particles-water mixtures flow in pipes

    Czech Academy of Sciences Publication Activity Database

    Vlasák, Pavel

    2017-01-01

    Roč. 225, č. 2017 (2017), s. 338-341 ISSN 2411-3336 R&D Projects: GA ČR GAP105/10/1574 Institutional support: RVO:67985874 Keywords : hydrotransport * coarse particles pipeline installation * pressure drop * pipe inclination Subject RIV: BK - Fluid Dynamics OBOR OECD: Fluids and plasma physics (including surface physics)

  6. Coarse-grained simulation of polymer-filler blends

    Science.gov (United States)

    Legters, Gregg; Kuppa, Vikram; Beaucage, Gregory; Univ of Dayton Collaboration; Univ of Cincinnati Collaboration

    The practical use of polymers often relies on additives that improve the property of the mixture. Examples of such complex blends include tires, pigments, blowing agents and other reactive additives in thermoplastics, and recycled polymers. Such systems usually exhibit a complex partitioning of the components. Most prior work has either focused on fine-grained details such as molecular modeling of chains at interfaces, or on coarse, heuristic, trial-and-error approaches to compounding (eg: tire industry). Thus, there is a significant gap in our understanding of how complex hierarchical structure (across several decades in length) develops in these multicomponent systems. This research employs dissipative particle thermodynamics in conjunction with a pseudo-thermodynamic parameter derived from scattering experiments to represent polymer-filler interactions. DPD simulations will probe how filler dispersion and hierarchical morphology develops in these complex blends, and are validated against experimental (scattering) data. The outcome of our approach is a practical solution to compounding issues, based on a mutually validating experimental and simulation methodology. Support from the NSF (CMMI-1636036/1635865) is gratefully acknowledged.

  7. The temporal structure of resting-state brain activity in the medial prefrontal cortex predicts self-consciousness.

    Science.gov (United States)

    Huang, Zirui; Obara, Natsuho; Davis, Henry Hap; Pokorny, Johanna; Northoff, Georg

    2016-02-01

    Recent studies have demonstrated an overlap between the neural substrate of resting-state activity and self-related processing in the cortical midline structures (CMS). However, the neural and psychological mechanisms mediating this so-called "rest-self overlap" remain unclear. To investigate the neural mechanisms, we estimated the temporal structure of spontaneous/resting-state activity, e.g. its long-range temporal correlations or self-affinity across time as indexed by the power-law exponent (PLE). The PLE was obtained in resting-state activity in the medial prefrontal cortex (MPFC) and the posterior cingulate cortex (PCC) in 47 healthy subjects by functional magnetic resonance imaging (fMRI). We performed correlation analyses of the PLE and Revised Self-Consciousness Scale (SCSR) scores, which enabled us to access different dimensions of self-consciousness and specified rest-self overlap in a psychological regard. The PLE in the MPFC's resting-state activity correlated with private self-consciousness scores from the SCSR. Conversely, we found no correlation between the PLE and the other subscales of the SCSR (public, social) or between other resting-state measures, including functional connectivity, and the SCSR subscales. This is the first evidence for the association between the scale-free dynamics of resting-state activity in the CMS and the private dimension of self-consciousness. This finding implies the relationship of especially the private dimension of self with the temporal structure of resting-state activity. Copyright © 2016 Elsevier Ltd. All rights reserved.

  8. Representing the Marginal Stability of Peptides in Coarse Grained Models

    Science.gov (United States)

    Sayar, Mehmet; Dalgicdir, Cahit; Ramezanghorbani, Farhad

    Tertiary structure of proteins is only marginally stable; such that the folded structure is separated from local minima by as little as 10 kcal/mol. In particular for intrinsically disordered peptides, this marginal stability is key to understanding their complex behavior. Bottom-up coarse grained (CG) models for proteins/peptides which rely on structural and/or thermodynamic reference data from experiments or all atom simulations inherently focus on the equilibrium structure and fail to capture the conformational dynamics of the molecule. In this study, we present a CG model for a synthetic peptide, LK, which successfully captures the conformational flexibility of the molecule in different environments. LK peptide is composed of leucine and lysine residues and displays a stark conformational transition from a degenerate conformation in dilute solution to a fully stable alpha-helix at macroscopic and molecular interfaces. In this study we demonstrate that by carefully combining atomistic references from both the unfolded and folded states, one can create a CG model that can represent not only the folded state, but also the conformational transitions that the peptide exhibits in response to changes in the environment. M. Sayar thanks TÜBİTAK (Grant No. 212T184) and TÜBA Distinguished Young Scientist Award (2012 awardee) for financial support.

  9. Transferable coarse-grained model for perfluorosulfonic acid polymer membranes

    Science.gov (United States)

    Kuo, An-Tsung; Okazaki, Susumu; Shinoda, Wataru

    2017-09-01

    Perfluorosulfonic acid (PFSA) polymer membranes are widely used as proton exchange membranes. Because the structure of the aqueous domain within the PFSA membrane is expected to directly influence proton conductance, many coarse-grained (CG) simulation studies have been performed to investigate the membrane morphology; these studies mostly used phenomenological models, such as dissipative particle dynamics. However, a chemically accurate CG model is required to investigate the morphology in realistic membranes and to provide a concrete molecular design. Here, we attempt to construct a predictive CG model for the structure and morphology of PFSA membranes that is compatible with the Sinoda-DeVane-Klein (SDK) CG water model [Shinoda et al., Mol. Simul. 33, 27 (2007)]. First, we extended the parameter set for the SDK CG force field to examine a hydrated PFSA membrane based on thermodynamic and structural data from experiments and all-atom (AA) molecular dynamics (MD) simulations. However, a noticeable degradation of the morphology motivated us to improve the structural properties by using the iterative Boltzmann inversion (IBI) approach. Thus, we explored a possible combination of the SDK and IBI approaches to describe the nonbonded interaction. The hybrid SDK/IBI model improved the structural issues of SDK, showing a better agreement with AA-MD in the radial distribution functions. The hybrid SDK/IBI model was determined to reasonably reproduce both the thermodynamic and structural properties of the PFSA membrane for all examined water contents. In addition, the model demonstrated good transferability and has considerable potential for application to realistic long-chained PFSA membranes.

  10. Systematic methods for defining coarse-grained maps in large biomolecules.

    Science.gov (United States)

    Zhang, Zhiyong

    2015-01-01

    Large biomolecules are involved in many important biological processes. It would be difficult to use large-scale atomistic molecular dynamics (MD) simulations to study the functional motions of these systems because of the computational expense. Therefore various coarse-grained (CG) approaches have attracted rapidly growing interest, which enable simulations of large biomolecules over longer effective timescales than all-atom MD simulations. The first issue in CG modeling is to construct CG maps from atomic structures. In this chapter, we review the recent development of a novel and systematic method for constructing CG representations of arbitrarily complex biomolecules, in order to preserve large-scale and functionally relevant essential dynamics (ED) at the CG level. In this ED-CG scheme, the essential dynamics can be characterized by principal component analysis (PCA) on a structural ensemble, or elastic network model (ENM) of a single atomic structure. Validation and applications of the method cover various biological systems, such as multi-domain proteins, protein complexes, and even biomolecular machines. The results demonstrate that the ED-CG method may serve as a very useful tool for identifying functional dynamics of large biomolecules at the CG level.

  11. Coarse-mesh discretized low-order quasi-diffusion equations for subregion averaged scalar fluxes

    International Nuclear Information System (INIS)

    Anistratov, D. Y.

    2004-01-01

    In this paper we develop homogenization procedure and discretization for the low-order quasi-diffusion equations on coarse grids for core-level reactor calculations. The system of discretized equations of the proposed method is formulated in terms of the subregion averaged group scalar fluxes. The coarse-mesh solution is consistent with a given fine-mesh discretization of the transport equation in the sense that it preserves a set of average values of the fine-mesh transport scalar flux over subregions of coarse-mesh cells as well as the surface currents, and eigenvalue. The developed method generates numerical solution that mimics the large-scale behavior of the transport solution within assemblies. (authors)

  12. Characteristics of fine and coarse particles of natural and urban aerosols of Brazil

    International Nuclear Information System (INIS)

    Orsini, C.M.Q.; Tabacniks, M.H.; Artaxo Netto, P.E.; Andrade, M.F.; Kerr, A.

    1986-02-01

    Fine and coarse particles have been sampled from 1982 to 1985 in one natural forest seacoast site (Jureia) and five urban-industrial cities (Vitoria, Salvador, Porto Alegre, Sao Paulo, and Belo Horizonte). The time variations of concentrations in air and the relative elemental compositions of fine and coarse particle fractions, sampled by Nuclepore stacked filter units (SFU), have been determined gravimetrically and by PIXE analysis, respectively. Enrichment factors and correlation coefficients of the trace elements measured lead to unambiguous characterization of soil dust and sea salt, both major aerosol sources that emit coarse particles, and soil dust is also a significant source of fine particles. (Author) [pt

  13. Episodic reinstatement in the medial temporal lobe.

    Science.gov (United States)

    Staresina, Bernhard P; Henson, Richard N A; Kriegeskorte, Nikolaus; Alink, Arjen

    2012-12-12

    The essence of episodic memory is our ability to reexperience past events in great detail, even in the absence of external stimulus cues. Does the phenomenological reinstatement of past experiences go along with reinstating unique neural representations in the brain? And if so, how is this accomplished by the medial temporal lobe (MTL), a brain region intimately linked to episodic memory? Computational models suggest that such reinstatement (also termed "pattern completion") in cortical regions is mediated by the hippocampus, a key region of the MTL. Although recent functional magnetic resonance imaging studies demonstrated reinstatement of coarse item properties like stimulus category or task context across different brain regions, it has not yet been shown whether reinstatement can be observed at the level of individual, discrete events-arguably the defining feature of episodic memory-nor whether MTL structures like the hippocampus support this "true episodic" reinstatement. Here we show that neural activity patterns for unique word-scene combinations encountered during encoding are reinstated in human parahippocampal cortex (PhC) during retrieval. Critically, this reinstatement occurs when word-scene combinations are successfully recollected (even though the original scene is not visually presented) and does not encompass other stimulus domains (such as word-color associations). Finally, the degree of PhC reinstatement across retrieval events correlated with hippocampal activity, consistent with a role of the hippocampus in coordinating pattern completion in cortical regions.

  14. Temporal variance reverses the impact of high mean intensity of stress in climate change experiments.

    Science.gov (United States)

    Benedetti-Cecchi, Lisandro; Bertocci, Iacopo; Vaselli, Stefano; Maggi, Elena

    2006-10-01

    Extreme climate events produce simultaneous changes to the mean and to the variance of climatic variables over ecological time scales. While several studies have investigated how ecological systems respond to changes in mean values of climate variables, the combined effects of mean and variance are poorly understood. We examined the response of low-shore assemblages of algae and invertebrates of rocky seashores in the northwest Mediterranean to factorial manipulations of mean intensity and temporal variance of aerial exposure, a type of disturbance whose intensity and temporal patterning of occurrence are predicted to change with changing climate conditions. Effects of variance were often in the opposite direction of those elicited by changes in the mean. Increasing aerial exposure at regular intervals had negative effects both on diversity of assemblages and on percent cover of filamentous and coarsely branched algae, but greater temporal variance drastically reduced these effects. The opposite was observed for the abundance of barnacles and encrusting coralline algae, where high temporal variance of aerial exposure either reversed a positive effect of mean intensity (barnacles) or caused a negative effect that did not occur under low temporal variance (encrusting algae). These results provide the first experimental evidence that changes in mean intensity and temporal variance of climatic variables affect natural assemblages of species interactively, suggesting that high temporal variance may mitigate the ecological impacts of ongoing and predicted climate changes.

  15. Effects of coarse-graining on the scaling behavior of long-range correlated and anti-correlated signals.

    Science.gov (United States)

    Xu, Yinlin; Ma, Qianli D Y; Schmitt, Daniel T; Bernaola-Galván, Pedro; Ivanov, Plamen Ch

    2011-11-01

    We investigate how various coarse-graining (signal quantization) methods affect the scaling properties of long-range power-law correlated and anti-correlated signals, quantified by the detrended fluctuation analysis. Specifically, for coarse-graining in the magnitude of a signal, we consider (i) the Floor, (ii) the Symmetry and (iii) the Centro-Symmetry coarse-graining methods. We find that for anti-correlated signals coarse-graining in the magnitude leads to a crossover to random behavior at large scales, and that with increasing the width of the coarse-graining partition interval Δ, this crossover moves to intermediate and small scales. In contrast, the scaling of positively correlated signals is less affected by the coarse-graining, with no observable changes when Δ 1 a crossover appears at small scales and moves to intermediate and large scales with increasing Δ. For very rough coarse-graining (Δ > 3) based on the Floor and Symmetry methods, the position of the crossover stabilizes, in contrast to the Centro-Symmetry method where the crossover continuously moves across scales and leads to a random behavior at all scales; thus indicating a much stronger effect of the Centro-Symmetry compared to the Floor and the Symmetry method. For coarse-graining in time, where data points are averaged in non-overlapping time windows, we find that the scaling for both anti-correlated and positively correlated signals is practically preserved. The results of our simulations are useful for the correct interpretation of the correlation and scaling properties of symbolic sequences.

  16. Spatio-Temporal Story Mapping Animation Based On Structured Causal Relationships Of Historical Events

    Science.gov (United States)

    Inoue, Y.; Tsuruoka, K.; Arikawa, M.

    2014-04-01

    In this paper, we proposed a user interface that displays visual animations on geographic maps and timelines for depicting historical stories by representing causal relationships among events for time series. We have been developing an experimental software system for the spatial-temporal visualization of historical stories for tablet computers. Our proposed system makes people effectively learn historical stories using visual animations based on hierarchical structures of different scale timelines and maps.

  17. Fine-coarse semantic processing in schizophrenia: a reversed pattern of hemispheric dominance.

    Science.gov (United States)

    Zeev-Wolf, Maor; Goldstein, Abraham; Levkovitz, Yechiel; Faust, Miriam

    2014-04-01

    Left lateralization for language processing is a feature of neurotypical brains. In individuals with schizophrenia, lack of left lateralization is associated with the language impairments manifested in this population. Beeman׳s fine-coarse semantic coding model asserts left hemisphere specialization in fine (i.e., conventionalized) semantic coding and right hemisphere specialization in coarse (i.e., non-conventionalized) semantic coding. Applying this model to schizophrenia would suggest that language impairments in this population are a result of greater reliance on coarse semantic coding. We investigated this hypothesis and examined whether a reversed pattern of hemispheric involvement in fine-coarse semantic coding along the time course of activation could be detected in individuals with schizophrenia. Seventeen individuals with schizophrenia and 30 neurotypical participants were presented with two word expressions of four types: literal, conventional metaphoric, unrelated (exemplars of fine semantic coding) and novel metaphoric (an exemplar of coarse semantic coding). Expressions were separated by either a short (250 ms) or long (750 ms) delay. Findings indicate that whereas during novel metaphor processing, controls displayed a left hemisphere advantage at 250 ms delay and right hemisphere advantage at 750 ms, individuals with schizophrenia displayed the opposite. For conventional metaphoric and unrelated expressions, controls showed left hemisphere advantage across times, while individuals with schizophrenia showed a right hemisphere advantage. Furthermore, whereas individuals with schizophrenia were less accurate than control at judging literal, conventional metaphoric and unrelated expressions they were more accurate when judging novel metaphors. Results suggest that individuals with schizophrenia display a reversed pattern of lateralization for semantic coding which causes them to rely more heavily on coarse semantic coding. Thus, for individuals with

  18. Multiscale Modeling at Nanointerfaces: Polymer Thin Film Materials Discovery via Thermomechanically Consistent Coarse Graining

    Science.gov (United States)

    Hsu, David D.

    Due to high nanointerfacial area to volume ratio, the properties of "nanoconfined" polymer thin films, blends, and composites become highly altered compared to their bulk homopolymer analogues. Understanding the structure-property mechanisms underlying this effect is an active area of research. However, despite extensive work, a fundamental framework for predicting the local and system-averaged thermomechanical properties as a function of configuration and polymer species has yet to be established. Towards bridging this gap, here, we present a novel, systematic coarse-graining (CG) method which is able to capture quantitatively, the thermomechanical properties of real polymer systems in bulk and in nanoconfined geometries. This method, which we call thermomechanically consistent coarse-graining (TCCG), is a two-bead-per-monomer CG hybrid approach through which bonded interactions are optimized to match the atomistic structure via the Iterative Boltzmann Inversion method (IBI), and nonbonded interactions are tuned to macroscopic targets through parametric studies. We validate the TCCG method by systematically developing coarse-grain models for a group of five specialized methacrylate-based polymers including poly(methyl methacrylate) (PMMA). Good correlation with bulk all-atom (AA) simulations and experiments is found for the temperature-dependent glass transition temperature (Tg) Flory-Fox scaling relationships, self-diffusion coefficients of liquid monomers, and modulus of elasticity. We apply this TCCG method also to bulk polystyrene (PS) using a comparable coarse-grain CG bead mapping strategy. The model demonstrates chain stiffness commensurate with experiments, and we utilize a density-correction term to improve the transferability of the elastic modulus over a 500 K range. Additionally, PS and PMMA models capture the unexplained, characteristically dissimilar scaling of Tg with the thickness of free-standing films as seen in experiments. Using vibrational

  19. The Temporal Organization of Syllabic Structure

    Science.gov (United States)

    Shaw, Jason A.

    2010-01-01

    This dissertation develops analytical tools which enable rigorous evaluation of competing syllabic parses on the basis of temporal patterns in speech production data. The data come from the articulographic tracking of fleshpoints on target speech organs, e.g., tongue, lips, jaw, in experiments with native speakers of American English and Moroccan…

  20. Formulation of coarse mesh finite difference to calculate mathematical adjoint flux

    International Nuclear Information System (INIS)

    Pereira, Valmir; Martinez, Aquilino Senra; Silva, Fernando Carvalho da

    2002-01-01

    The objective of this work is the obtention of the mathematical adjoint flux, having as its support the nodal expansion method (NEM) for coarse mesh problems. Since there are difficulties to evaluate this flux by using NEM. directly, a coarse mesh finite difference program was developed to obtain this adjoint flux. The coarse mesh finite difference formulation (DFMG) adopted uses results of the direct calculation (node average flux and node face averaged currents) obtained by NEM. These quantities (flux and currents) are used to obtain the correction factors which modify the classical finite differences formulation . Since the DFMG formulation is also capable of calculating the direct flux it was also tested to obtain this flux and it was verified that it was able to reproduce with good accuracy both the flux and the currents obtained via NEM. In this way, only matrix transposition is needed to calculate the mathematical adjoint flux. (author)

  1. Coarse mode aerosols in the High Arctic

    Science.gov (United States)

    Baibakov, K.; O'Neill, N. T.; Chaubey, J. P.; Saha, A.; Duck, T. J.; Eloranta, E. W.

    2014-12-01

    Fine mode (submicron) aerosols in the Arctic have received a fair amount of scientific attention in terms of smoke intrusions during the polar summer and Arctic haze pollution during the polar winter. Relatively little is known about coarse mode (supermicron) aerosols, notably dust, volcanic ash and sea salt. Asian dust is a regular springtime event whose optical and radiative forcing effects have been fairly well documented at the lower latitudes over North America but rarely reported for the Arctic. Volcanic ash, whose socio-economic importance has grown dramatically since the fear of its effects on aircraft engines resulted in the virtual shutdown of European civil aviation in the spring of 2010 has rarely been reported in the Arctic in spite of the likely probability that ash from Iceland and the Aleutian Islands makes its way into the Arctic and possibly the high Arctic. Little is known about Arctic sea salt aerosols and we are not aware of any literature on the optical measurement of these aerosols. In this work we present preliminary results of the combined sunphotometry-lidar analysis at two High Arctic stations in North America: PEARL (80°N, 86°W) for 2007-2011 and Barrow (71°N,156°W) for 2011-2014. The multi-years datasets were analyzed to single out potential coarse mode incursions and study their optical characteristics. In particular, CIMEL sunphotometers provided coarse mode optical depths as well as information on particle size and refractive index. Lidar measurements from High Spectral Resolution lidars (AHSRL at PEARL and NSHSRL at Barrow) yielded vertically resolved aerosol profiles and gave an indication of particle shape and size from the depolarization ratio and color ratio profiles. Additionally, we employed supplementary analyses of HYSPLIT backtrajectories, OMI aerosol index, and NAAPS (Navy Aerosol Analysis and Prediction System) outputs to study the spatial context of given events.

  2. Coarse mesh code development

    Energy Technology Data Exchange (ETDEWEB)

    Lieberoth, J.

    1975-06-15

    The numerical solution of the neutron diffusion equation plays a very important role in the analysis of nuclear reactors. A wide variety of numerical procedures has been proposed, at which most of the frequently used numerical methods are fundamentally based on the finite- difference approximation where the partial derivatives are approximated by the finite difference. For complex geometries, typical of the practical reactor problems, the computational accuracy of the finite-difference method is seriously affected by the size of the mesh width relative to the neutron diffusion length and by the heterogeneity of the medium. Thus, a very large number of mesh points are generally required to obtain a reasonably accurate approximate solution of the multi-dimensional diffusion equation. Since the computation time is approximately proportional to the number of mesh points, a detailed multidimensional analysis, based on the conventional finite-difference method, is still expensive even with modern large-scale computers. Accordingly, there is a strong incentive to develop alternatives that can reduce the number of mesh-points and still retain accuracy. One of the promising alternatives is the finite element method, which consists of the expansion of the neutron flux by piecewise polynomials. One of the advantages of this procedure is its flexibility in selecting the locations of the mesh points and the degree of the expansion polynomial. The small number of mesh points of the coarse grid enables to store the results of several of the least outer iterations and to calculate well extrapolated values of them by comfortable formalisms. This holds especially if only one energy distribution of fission neutrons is assumed for all fission processes in the reactor, because the whole information of an outer iteration is contained in a field of fission rates which has the size of all mesh points of the coarse grid.

  3. In pursuit of an accurate spatial and temporal model of biomolecules at the atomistic level: a perspective on computer simulation.

    Science.gov (United States)

    Gray, Alan; Harlen, Oliver G; Harris, Sarah A; Khalid, Syma; Leung, Yuk Ming; Lonsdale, Richard; Mulholland, Adrian J; Pearson, Arwen R; Read, Daniel J; Richardson, Robin A

    2015-01-01

    Despite huge advances in the computational techniques available for simulating biomolecules at the quantum-mechanical, atomistic and coarse-grained levels, there is still a widespread perception amongst the experimental community that these calculations are highly specialist and are not generally applicable by researchers outside the theoretical community. In this article, the successes and limitations of biomolecular simulation and the further developments that are likely in the near future are discussed. A brief overview is also provided of the experimental biophysical methods that are commonly used to probe biomolecular structure and dynamics, and the accuracy of the information that can be obtained from each is compared with that from modelling. It is concluded that progress towards an accurate spatial and temporal model of biomacromolecules requires a combination of all of these biophysical techniques, both experimental and computational.

  4. Spatial and temporal variation in population genetic structure of wild Nile tilapia (Oreochromis niloticus across Africa

    Directory of Open Access Journals (Sweden)

    Bezault Etienne

    2011-12-01

    Full Text Available Abstract Background Reconstructing the evolutionary history of a species is challenging. It often depends not only on the past biogeographic and climatic events but also the contemporary and ecological factors, such as current connectivity and habitat heterogeneity. In fact, these factors might interact with each other and shape the current species distribution. However, to what extent the current population genetic structure reflects the past and the contemporary factors is largely unknown. Here we investigated spatio-temporal genetic structures of Nile tilapia (Oreochromis niloticus populations, across their natural distribution in Africa. While its large biogeographic distribution can cause genetic differentiation at the paleo-biogeographic scales, its restricted dispersal capacity might induce a strong genetic structure at micro-geographic scales. Results Using nine microsatellite loci and 350 samples from ten natural populations, we found the highest genetic differentiation among the three ichthyofaunal provinces and regions (Ethiopian, Nilotic and Sudano-Sahelian (RST = 0.38 - 0.69. This result suggests the predominant effect of paleo-geographic events at macro-geographic scale. In addition, intermediate divergences were found between rivers and lakes within the regions, presumably reflecting relatively recent interruptions of gene flow between hydrographic basins (RST = 0.24 - 0.32. The lowest differentiations were observed among connected populations within a basin (RST = 0.015 in the Volta basin. Comparison of temporal sample series revealed subtle changes in the gene pools in a few generations (F = 0 - 0.053. The estimated effective population sizes were 23 - 143 and the estimated migration rate was moderate (m ~ 0.094 - 0.097 in the Volta populations. Conclusions This study revealed clear hierarchical patterns of the population genetic structuring of O. niloticus in Africa. The effects of paleo-geographic and climatic events were

  5. Coarse-mesh method for multidimensional, mixed-lattice diffusion calculations

    International Nuclear Information System (INIS)

    Dodds, H.L. Jr.; Honeck, H.C.; Hostetler, D.E.

    1977-01-01

    A coarse-mesh finite difference method has been developed for multidimensional, mixed-lattice reactor diffusion calculations, both statics and kinetics, in hexagonal geometry. Results obtained with the coarse-mesh (CM) method have been compared with a conventional mesh-centered finite difference method and with experiment. The results of this comparison indicate that the accuracy of the CM method for highly heterogeneous (mixed) lattices using one point per hexagonal mesh element (''hex'') is about the same as the conventional method with six points per hex. Furthermore, the computing costs (i.e., central processor unit time and core storage requirements) of the CM method with one point per hex are about the same as the conventional method with one point per hex

  6. MT-ADRES: multi-threading on coarse-grained reconfigurable architecture

    DEFF Research Database (Denmark)

    Wu, Kehuai; Kanstein, Andreas; Madsen, Jan

    2008-01-01

    The coarse-grained reconfigurable architecture ADRES (architecture for dynamically reconfigurable embedded systems) and its compiler offer high instruction-level parallelism (ILP) to applications by means of a sparsely interconnected array of functional units and register files. As high-ILP archi......The coarse-grained reconfigurable architecture ADRES (architecture for dynamically reconfigurable embedded systems) and its compiler offer high instruction-level parallelism (ILP) to applications by means of a sparsely interconnected array of functional units and register files. As high......-ILP architectures achieve only low parallelism when executing partially sequential code segments, which is also known as Amdahl's law, this article proposes to extend ADRES to MT-ADRES (multi-threaded ADRES) to also exploit thread-level parallelism. On MT-ADRES architectures, the array can be partitioned...

  7. Blind identification of full-field vibration modes of output-only structures from uniformly-sampled, possibly temporally-aliased (sub-Nyquist), video measurements

    Science.gov (United States)

    Yang, Yongchao; Dorn, Charles; Mancini, Tyler; Talken, Zachary; Nagarajaiah, Satish; Kenyon, Garrett; Farrar, Charles; Mascareñas, David

    2017-03-01

    Enhancing the spatial and temporal resolution of vibration measurements and modal analysis could significantly benefit dynamic modelling, analysis, and health monitoring of structures. For example, spatially high-density mode shapes are critical for accurate vibration-based damage localization. In experimental or operational modal analysis, higher (frequency) modes, which may be outside the frequency range of the measurement, contain local structural features that can improve damage localization as well as the construction and updating of the modal-based dynamic model of the structure. In general, the resolution of vibration measurements can be increased by enhanced hardware. Traditional vibration measurement sensors such as accelerometers have high-frequency sampling capacity; however, they are discrete point-wise sensors only providing sparse, low spatial sensing resolution measurements, while dense deployment to achieve high spatial resolution is expensive and results in the mass-loading effect and modification of structure's surface. Non-contact measurement methods such as scanning laser vibrometers provide high spatial and temporal resolution sensing capacity; however, they make measurements sequentially that requires considerable acquisition time. As an alternative non-contact method, digital video cameras are relatively low-cost, agile, and provide high spatial resolution, simultaneous, measurements. Combined with vision based algorithms (e.g., image correlation or template matching, optical flow, etc.), video camera based measurements have been successfully used for experimental and operational vibration measurement and subsequent modal analysis. However, the sampling frequency of most affordable digital cameras is limited to 30-60 Hz, while high-speed cameras for higher frequency vibration measurements are extremely costly. This work develops a computational algorithm capable of performing vibration measurement at a uniform sampling frequency lower than

  8. Superplastic behavior of coarse-grained aluminum alloys

    NARCIS (Netherlands)

    Chezan, AR; De Hosson, JTM

    2005-01-01

    In this paper we concentrate on the superplastic behavior and the microstructural evolution of two coarse-grained Al alloys: Al-4.4w/oMg and Al-4.4w/oMg-0.4w/oCu. The values for the strain rate sensitivity index and activation energy suggest that solute drag on dislocation motion is an important

  9. Radiosurgery for Medial Temporal Lobe Epilepsy Resulting from Mesial Temporal Sclerosis.

    Science.gov (United States)

    Gianaris, Thomas; Witt, Thomas; Barbaro, Nicholas M

    2016-01-01

    Medial temporal lobe epilepsy associated with mesial temporal sclerosis (MTS) is perhaps the most well-defined epilepsy syndrome that is responsive to structural interventions such as surgery. Several minimally invasive techniques have arisen that provide additional options for the treatment of MTS while potentially avoiding many of open surgery's associated risks. By evading these risks, they also open up treatment options to patients who otherwise are poor surgical candidates. Radiosurgery is one of the most intensively studied of these alternatives and has found a growing role in the treatment of medial temporal lobe epilepsy. Copyright © 2016 Elsevier Inc. All rights reserved.

  10. Symmetries and the coarse-mesh method

    International Nuclear Information System (INIS)

    Makai, M.

    1980-10-01

    This report approaches the basic problem of the coarse-mesh method from a new side. Group theory is used for the determination of the space dependency of the flux. The result is a method called ANANAS after the analytic-analytic solution. This method was tested on two benchmark problems: one given by Melice and the IAEA benchmark. The ANANAS program is an experimental one. The method was intended for use in hexagonal geometry. (Auth.)

  11. Enhancement of properties of recycled coarse aggregate concrete using bacteria

    Science.gov (United States)

    Sahoo; Arakha; Sarkar; P; Jha

    2016-01-01

    Due to rapid construction, necessity for raw materials of concrete, especially coarse aggregate, tends to increase the danger of early exhaustion of the natural resources. An alternative source of raw materials would perhaps delay the advent of this early exhaustion. Recycled coarse aggregate (RCA) plays a great role as an alternative raw material that can replace the natural coarse aggregate (NCA) for concrete. Previous studies show that the properties of RCA concrete are inferior in quality compared to NCA concrete. This article attempts to study the improvement of properties of RCA concrete with the addition of bacteria named as Bacillus subtilis. The experimental investigation was carried out to evaluate the improvement of the compressive strength, capillary water absorption, and drying shrinkage of RCA concrete incorporating bacteria. The compressive strength of RCA concrete is found to be increased by about 20% when the cell concentration of B. subtilis is 106 cells/ml. The capillary water absorption as well as drying shrinkage of RCA are reduced when bacteria is incorporated. The improvement of RCA concrete is confirmed to be due to the calcium carbonate precipitation as observed from the microstructure studies carried out on it such as EDX, SEM, and XRD.

  12. A detection of the coarse water droplets in steam turbines

    Directory of Open Access Journals (Sweden)

    Bartoš Ondřej

    2014-03-01

    Full Text Available The aim of this paper is to introduce a novel method for the detection of coarse water droplets in a low pressure part of steam turbines. The photogrammetry method has been applied for the measurement of coarse droplets in the low-pressure part of a steam turbine. A new probe based on this measurement technique was developed and tested in the laboratory and in a steam turbine in the Počerady power-plant. The probe was equipped with state-of-the-art instrumentation. The paper contains results from laboratory tests and the first preliminary measurements in a steam turbine. Possible applications of this method have been examined.

  13. Modification of the MORSE code for Monte Carlo eigenvalue problems by coarse-mesh rebalance acceleration

    International Nuclear Information System (INIS)

    Nishida, Takahiko; Horikami, Kunihiko; Suzuki, Tadakazu; Nakahara, Yasuaki; Taji, Yukichi

    1975-09-01

    The coarse-mesh rebalancing technique is introduced into the general-purpose neutron and gamma-ray Monte Carlo transport code MORSE, to accelerate the convergence rate of the iteration process for eigenvalue calculation in a nuclear reactor system. Two subroutines are thus attached to the code. One is bookkeeping routine 'COARSE' for obtaining the quantities related with the neutron balance in each coarse mesh cell, such as the number of neutrons absorbed in the cell, from random walks of neutrons in a batch. The other is rebalance factor calculation routine 'REBAL' for obtaining the scaling factor whereby the neutron flux in the cell is multiplied to attain the neutron balance. The two subroutines and algorithm of the coarse mesh rebalancing acceleration in a Monte Carlo game are described. (auth.)

  14. Martini Coarse-Grained Force Field : Extension to Carbohydrates

    NARCIS (Netherlands)

    Lopez, Cesar A.; Rzepiela, Andrzej J.; de Vries, Alex H.; Dijkhuizen, Lubbert; Huenenberger, Philippe H.; Marrink, Siewert J.

    2009-01-01

    We present an extension of the Martini coarse-grained force field to carbohydrates. The parametrization follows the same philosophy as was used previously for lipids and proteins, focusing on the reproduction of partitioning free energies of small compounds between polar and nonpolar phases. The

  15. Temporal and Spatial Impact of Human Cadaver Decomposition on Soil Bacterial and Arthropod Community Structure and Function

    Science.gov (United States)

    Singh, Baneshwar; Minick, Kevan J.; Strickland, Michael S.; Wickings, Kyle G.; Crippen, Tawni L.; Tarone, Aaron M.; Benbow, M. Eric; Sufrin, Ness; Tomberlin, Jeffery K.; Pechal, Jennifer L.

    2018-01-01

    As vertebrate carrion decomposes, there is a release of nutrient-rich fluids into the underlying soil, which can impact associated biological community structure and function. How these changes alter soil biogeochemical cycles is relatively unknown and may prove useful in the identification of carrion decomposition islands that have long lasting, focal ecological effects. This study investigated the spatial (0, 1, and 5 m) and temporal (3–732 days) dynamics of human cadaver decomposition on soil bacterial and arthropod community structure and microbial function. We observed strong evidence of a predictable response to cadaver decomposition that varies over space for soil bacterial and arthropod community structure, carbon (C) mineralization and microbial substrate utilization patterns. In the presence of a cadaver (i.e., 0 m samples), the relative abundance of Bacteroidetes and Firmicutes was greater, while the relative abundance of Acidobacteria, Chloroflexi, Gemmatimonadetes, and Verrucomicrobia was lower when compared to samples at 1 and 5 m. Micro-arthropods were more abundant (15 to 17-fold) in soils collected at 0 m compared to either 1 or 5 m, but overall, micro-arthropod community composition was unrelated to either bacterial community composition or function. Bacterial community structure and microbial function also exhibited temporal relationships, whereas arthropod community structure did not. Cumulative precipitation was more effective in predicting temporal variations in bacterial abundance and microbial activity than accumulated degree days. In the presence of the cadaver (i.e., 0 m samples), the relative abundance of Actinobacteria increased significantly with cumulative precipitation. Furthermore, soil bacterial communities and C mineralization were sensitive to the introduction of human cadavers as they diverged from baseline levels and did not recover completely in approximately 2 years. These data are valuable for understanding ecosystem

  16. Temporal and Spatial Impact of Human Cadaver Decomposition on Soil Bacterial and Arthropod Community Structure and Function

    Directory of Open Access Journals (Sweden)

    Baneshwar Singh

    2018-01-01

    Full Text Available As vertebrate carrion decomposes, there is a release of nutrient-rich fluids into the underlying soil, which can impact associated biological community structure and function. How these changes alter soil biogeochemical cycles is relatively unknown and may prove useful in the identification of carrion decomposition islands that have long lasting, focal ecological effects. This study investigated the spatial (0, 1, and 5 m and temporal (3–732 days dynamics of human cadaver decomposition on soil bacterial and arthropod community structure and microbial function. We observed strong evidence of a predictable response to cadaver decomposition that varies over space for soil bacterial and arthropod community structure, carbon (C mineralization and microbial substrate utilization patterns. In the presence of a cadaver (i.e., 0 m samples, the relative abundance of Bacteroidetes and Firmicutes was greater, while the relative abundance of Acidobacteria, Chloroflexi, Gemmatimonadetes, and Verrucomicrobia was lower when compared to samples at 1 and 5 m. Micro-arthropods were more abundant (15 to 17-fold in soils collected at 0 m compared to either 1 or 5 m, but overall, micro-arthropod community composition was unrelated to either bacterial community composition or function. Bacterial community structure and microbial function also exhibited temporal relationships, whereas arthropod community structure did not. Cumulative precipitation was more effective in predicting temporal variations in bacterial abundance and microbial activity than accumulated degree days. In the presence of the cadaver (i.e., 0 m samples, the relative abundance of Actinobacteria increased significantly with cumulative precipitation. Furthermore, soil bacterial communities and C mineralization were sensitive to the introduction of human cadavers as they diverged from baseline levels and did not recover completely in approximately 2 years. These data are valuable for understanding

  17. Understanding structure of urban traffic network based on spatial-temporal correlation analysis

    Science.gov (United States)

    Yang, Yanfang; Jia, Limin; Qin, Yong; Han, Shixiu; Dong, Honghui

    2017-08-01

    Understanding the structural characteristics of urban traffic network comprehensively can provide references for improving road utilization rate and alleviating traffic congestion. This paper focuses on the spatial-temporal correlations between different pairs of traffic series and proposes a complex network-based method of constructing the urban traffic network. In the network, the nodes represent road segments, and an edge between a pair of nodes is added depending on the result of significance test for the corresponding spatial-temporal correlation. Further, a modified PageRank algorithm, named the geographical weight-based PageRank algorithm (GWPA), is proposed to analyze the spatial distribution of important segments in the road network. Finally, experiments are conducted by using three kinds of traffic series collected from the urban road network in Beijing. Experimental results show that the urban traffic networks constructed by three traffic variables all indicate both small-world and scale-free characteristics. Compared with the results of PageRank algorithm, GWPA is proved to be valid in evaluating the importance of segments and identifying the important segments with small degree.

  18. POTENTIAL OF MULTI-TEMPORAL OBLIQUE AIRBORNE IMAGERY FOR STRUCTURAL DAMAGE ASSESSMENT

    Directory of Open Access Journals (Sweden)

    A. Vetrivel

    2016-06-01

    Full Text Available Quick post-disaster actions demand automated, rapid and detailed building damage assessment. Among the available technologies, post-event oblique airborne images have already shown their potential for this task. However, existing methods usually compensate the lack of pre-event information with aprioristic assumptions of building shapes and textures that can lead to uncertainties and misdetections. However, oblique images have been already captured over many cities of the world, and the exploitation of pre- and post-event data as inputs to damage assessment is readily feasible in urban areas. In this paper, we investigate the potential of multi-temporal oblique imagery for detailed damage assessment focusing on two methodologies: the first method aims at detecting severe structural damages related to geometrical deformation by combining the complementary information provided by photogrammetric point clouds and oblique images. The developed method detected 87% of damaged elements. The failed detections are due to varying noise levels within the point cloud which hindered the recognition of some structural elements. We observed, in general that the façade regions are very noisy in point clouds. To address this, we propose our second method which aims to detect damages to building façades using the oriented oblique images. The results show that the proposed methodology can effectively differentiate among the three proposed categories: collapsed/highly damaged, lower levels of damage and undamaged buildings, using a computationally light-weight approach. We describe the implementations of the above mentioned methods in detail and present the promising results achieved using multi-temporal oblique imagery over the city of L’Aquila (Italy.

  19. On the genesis of spatio-temporal self-organized structures in plasma devices

    International Nuclear Information System (INIS)

    Talasman, S.J.; Sanduloviciu, M.

    1995-01-01

    The genesis of luminous sharply defined nearly spherical space charges structures formed in an Argon plasma column was experimental investigated. The results reveal spatio-temporal characteristics proper to systems resulting after a self-organization process. Their phenomenology involves electrical charges separation produced by symmetry breaking and spatial separation of the excitation and ionization cross sections functions in a region where electrons are accelerated and, as a result, the appearance of electrostatic forces that, acting as long range correlations, assures, together with dissipative effects, its stability. (Author) 8 Figs., 31 Refs

  20. Representing environment-induced helix-coil transitions in a coarse grained peptide model

    Science.gov (United States)

    Dalgicdir, Cahit; Globisch, Christoph; Sayar, Mehmet; Peter, Christine

    2016-10-01

    Coarse grained (CG) models are widely used in studying peptide self-assembly and nanostructure formation. One of the recurrent challenges in CG modeling is the problem of limited transferability, for example to different thermodynamic state points and system compositions. Understanding transferability is generally a prerequisite to knowing for which problems a model can be reliably used and predictive. For peptides, one crucial transferability question is whether a model reproduces the molecule's conformational response to a change in its molecular environment. This is of particular importance since CG peptide models often have to resort to auxiliary interactions that aid secondary structure formation. Such interactions take care of properties of the real system that are per se lost in the coarse graining process such as dihedral-angle correlations along the backbone or backbone hydrogen bonding. These auxiliary interactions may then easily overstabilize certain conformational propensities and therefore destroy the ability of the model to respond to stimuli and environment changes, i.e. they impede transferability. In the present paper we have investigated a short peptide with amphiphilic EALA repeats which undergoes conformational transitions between a disordered and a helical state upon a change in pH value or due to the presence of a soft apolar/polar interface. We designed a base CG peptide model that does not carry a specific (backbone) bias towards a secondary structure. This base model was combined with two typical approaches of ensuring secondary structure formation, namely a C α -C α -C α -C α pseudodihedral angle potential or a virtual site interaction that mimics hydrogen bonding. We have investigated the ability of the two resulting CG models to represent the environment-induced conformational changes in the helix-coil equilibrium of EALA. We show that with both approaches a CG peptide model can be obtained that is environment-transferable and that

  1. Texture coarseness responsive neurons and their mapping in layer 2–3 of the rat barrel cortex in vivo

    Science.gov (United States)

    Garion, Liora; Dubin, Uri; Rubin, Yoav; Khateb, Mohamed; Schiller, Yitzhak; Azouz, Rony; Schiller, Jackie

    2014-01-01

    Texture discrimination is a fundamental function of somatosensory systems, yet the manner by which texture is coded and spatially represented in the barrel cortex are largely unknown. Using in vivo two-photon calcium imaging in the rat barrel cortex during artificial whisking against different surface coarseness or controlled passive whisker vibrations simulating different coarseness, we show that layer 2–3 neurons within barrel boundaries differentially respond to specific texture coarsenesses, while only a minority of neurons responded monotonically with increased or decreased surface coarseness. Neurons with similar preferred texture coarseness were spatially clustered. Multi-contact single unit recordings showed a vertical columnar organization of texture coarseness preference in layer 2–3. These findings indicate that layer 2–3 neurons perform high hierarchical processing of tactile information, with surface coarseness embodied by distinct neuronal subpopulations that are spatially mapped onto the barrel cortex. DOI: http://dx.doi.org/10.7554/eLife.03405.001 PMID:25233151

  2. Spatio-temporal structure, path characteristics and perceptual grouping in immediate serial spatial recall

    Directory of Open Access Journals (Sweden)

    Carlo De Lillo

    2016-11-01

    Full Text Available Immediate serial spatial recall measures the ability to retain sequences of locations in short-term memory and is considered the spatial equivalent of digit span. It is tested by requiring participants to reproduce sequences of movements performed by an experimenter or displayed on a monitor. Different organizational factors dramatically affect serial spatial recall but they are often confounded or underspecified. Untangling them is crucial for the characterization of working-memory models and for establishing the contribution of structure and memory capacity to spatial span. We report five experiments assessing the relative role and independence of factors that have been reported in the literature. Experiment 1 disentangled the effects of spatial clustering and path-length by manipulating the distance of items displayed on a touchscreen monitor. Long-path sequences segregated by spatial clusters were compared with short-path sequences not segregated by clusters. Recall was more accurate for sequences segregated by clusters independently from path-length. Experiment 2 featured conditions where temporal pauses were introduced between or within cluster boundaries during the presentation of sequences with the same paths. Thus, the temporal structure of the sequences was either consistent or inconsistent with a hierarchical representation based on segmentation by spatial clusters but the effect of structure could not be confounded with effects of path-characteristics. Pauses at cluster boundaries yielded more accurate recall, as predicted by a hierarchical model. In Experiment 3, the systematic manipulation of sequence structure, path-length and presence of path-crossings of sequences showed that structure explained most of the variance, followed by the presence/absence of path-crossings, and path-length. Experiments 4 and 5 replicated the results of the previous experiments in immersive virtual reality navigation tasks where the viewpoint of the

  3. Principles of Temporal Processing Across the Cortical Hierarchy.

    Science.gov (United States)

    Himberger, Kevin D; Chien, Hsiang-Yun; Honey, Christopher J

    2018-05-02

    The world is richly structured on multiple spatiotemporal scales. In order to represent spatial structure, many machine-learning models repeat a set of basic operations at each layer of a hierarchical architecture. These iterated spatial operations - including pooling, normalization and pattern completion - enable these systems to recognize and predict spatial structure, while robust to changes in the spatial scale, contrast and noisiness of the input signal. Because our brains also process temporal information that is rich and occurs across multiple time scales, might the brain employ an analogous set of operations for temporal information processing? Here we define a candidate set of temporal operations, and we review evidence that they are implemented in the mammalian cerebral cortex in a hierarchical manner. We conclude that multiple consecutive stages of cortical processing can be understood to perform temporal pooling, temporal normalization and temporal pattern completion. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

  4. Coarsely resolved topography along protein folding pathways

    Science.gov (United States)

    Fernández, Ariel; Kostov, Konstantin S.; Berry, R. Stephen

    2000-03-01

    The kinetic data from the coarse representation of polypeptide torsional dynamics described in the preceding paper [Fernandez and Berry, J. Chem. Phys. 112, 5212 (2000), preceding paper] is inverted by using detailed balance to obtain a topographic description of the potential-energy surface (PES) along the dominant folding pathway of the bovine pancreatic trypsin inhibitor (BPTI). The topography is represented as a sequence of minima and effective saddle points. The dominant folding pathway displays an overall monotonic decrease in energy with a large number of staircaselike steps, a clear signature of a good structure-seeker. The diversity and availability of alternative folding pathways is analyzed in terms of the Shannon entropy σ(t) associated with the time-dependent probability distribution over the kinetic ensemble of contact patterns. Several stages in the folding process are evident. Initially misfolded states form and dismantle revealing no definite pattern in the topography and exhibiting high Shannon entropy. Passage down a sequence of staircase steps then leads to the formation of a nativelike intermediate, for which σ(t) is much lower and fairly constant. Finally, the structure of the intermediate is refined to produce the native state of BPTI. We also examine how different levels of tolerance to mismatches of side chain contacts influence the folding kinetics, the topography of the dominant folding pathway, and the Shannon entropy. This analysis yields upper and lower bounds of the frustration tolerance required for the expeditious and robust folding of BPTI.

  5. Coupling a nano-particle with isothermal fluctuating hydrodynamics: Coarse-graining from microscopic to mesoscopic dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Español, Pep [Dept. Física Fundamental, Universidad Nacional de Educación a Distancia, Aptdo. 60141, E-28080 Madrid (Spain); Donev, Aleksandar [Dept. Física Fundamental, Universidad Nacional de Educación a Distancia, Aptdo. 60141, E-28080 Madrid (Spain); Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, New York, New York 10012 (United States)

    2015-12-21

    We derive a coarse-grained description of the dynamics of a nanoparticle immersed in an isothermal simple fluid by performing a systematic coarse graining of the underlying microscopic dynamics. As coarse-grained or relevant variables, we select the position of the nanoparticle and the total mass and momentum density field of the fluid, which are locally conserved slow variables because they are defined to include the contribution of the nanoparticle. The theory of coarse graining based on the Zwanzing projection operator leads us to a system of stochastic ordinary differential equations that are closed in the relevant variables. We demonstrate that our discrete coarse-grained equations are consistent with a Petrov-Galerkin finite-element discretization of a system of formal stochastic partial differential equations which resemble previously used phenomenological models based on fluctuating hydrodynamics. Key to this connection between our “bottom-up” and previous “top-down” approaches is the use of the same dual orthogonal set of linear basis functions familiar from finite element methods (FEMs), both as a way to coarse-grain the microscopic degrees of freedom and as a way to discretize the equations of fluctuating hydrodynamics. Another key ingredient is the use of a “linear for spiky” weak approximation which replaces microscopic “fields” with a linear FE interpolant inside expectation values. For the irreversible or dissipative dynamics, we approximate the constrained Green-Kubo expressions for the dissipation coefficients with their equilibrium averages. Under suitable approximations, we obtain closed approximations of the coarse-grained dynamics in a manner which gives them a clear physical interpretation and provides explicit microscopic expressions for all of the coefficients appearing in the closure. Our work leads to a model for dilute nanocolloidal suspensions that can be simulated effectively using feasibly short molecular dynamics

  6. Using of Porcelinite as Coarse Aggregate in Concrete

    Directory of Open Access Journals (Sweden)

    Haifa Saleh

    2015-02-01

    Full Text Available In this research the ability of using porcelinite as coarse aggregate to produce light weight concrete was investigated.  The experimental program consists of preparing and testing a mixes to investigate mechanical properties of concrete, with a total of 15 cubes (100×100×100 mm, 30 cylinders (100×200 mm. The tests include compressive strength, splitting tensile strength, fresh and hardened density of  light weight concrete for different porcelinite percentages ranged between(0% to 100% of the coarse aggregate weight. The obtained results for tested specimens were compared to control one. Test results indicated that using of porcelinite in concrete mix reduces the strength of concrete Porcelinite aggregate represents a reduction in density ranging between (10%-36% of normal weight concrete, therefore there is an advantage  using this type of light weight aggregate in this country where soil bearing capacity is low in most construction sites.

  7. METHOD FOR THE ANALYSIS OF TEMPORAL CHANGE OF PHYSICAL STRUCTURE IN THE INSTRUMENTATION AND CONTROL LIFE-CYCLE

    Directory of Open Access Journals (Sweden)

    MARKUS GÖRING

    2013-10-01

    On one hand, this paper proposes the restructuring of the sequential IEC 61513 I&C life-cycle according to the V-model, so as to adequately integrate the concept of verification and validation. On the other hand, based on a metamodel for the modeling of I&C systems, this paper introduces a method for the modeling and analysis of the effects with respect to the superposition of failure combinations and event sequences on the I&C system design, i.e. the temporal change of physical structure is analyzed. In the first step, the method is concerned with the modeling of the I&C systems. In the second step, the method considers the analysis of temporal change of physical structure, which integrates the concepts of the diversity and defense-in-depth analysis, fault tree analysis, event tree analysis, and failure mode and effects analysis.

  8. Development of a stranded oil in coarse sediment (SOCS) model

    International Nuclear Information System (INIS)

    Humphrey, B.; Owens, E.; Sergy, G.

    1993-01-01

    Oil spills in Canadian waters have a high probability of impacting coarse sediment beaches, yet the ability to predict oil fate and estimate natural self-cleaning rates is less than adequate. Data is lacking to understand fully many oil sediment interactions. Historically, shoreline interactions have been considered using fairly simple concepts. The authors examined the processes that may occur on a coarse sediment beach, selected those which are important, and developed a fate and persistence model for stranded oil. The processes were divided into stages relative to the spill event, and the factors which affect each stage were evaluated. Three areas of special interest were the capacity of a beach to hold oil, the residual capacity of a beach for oil, and the long-term fate of the oil. After developing model algorithms, the outputs were compared to a data base of information collected during the Exxon Valdez oil spill. The stranded oil in coarse sediment model will provide information at two levels: a general level for planning and sensitivity mapping and a more detailed level intended for the prediction of oil fate on specific known beaches. The strengths and weaknesses of the model have been assessed in terms of data deficiencies. The type and nature of the data which are most useful to, and which need to be collected for, spill planning and spill monitoring were identified. The model shows that the important factors directing the fate of oil on coarse sediment beaches are porosity and permeability, determined by grain size and oil properties (composition, viscosity, etc.). The natural rate of removal of oil, modeled as a first-order (exponential) removal, is dependent on the stage of the spill process and on wave energy

  9. The attachment of α -synuclein to a fiber: A coarse-grain approach

    Science.gov (United States)

    Ilie, Ioana M.; den Otter, Wouter K.; Briels, Wim J.

    2017-03-01

    We present simulations of the amyloidogenic core of α-synuclein, the protein causing Parkinson's disease, as a short chain of coarse-grain patchy particles. Each particle represents a sequence of about a dozen amino acids. The fluctuating secondary structure of this intrinsically disordered protein is modelled by dynamic variations of the shape and interaction characteristics of the patchy particles, ranging from spherical with weak isotropic attractions for the disordered state to spherocylindrical with strong directional interactions for a β-sheet. Flexible linkers between the particles enable sampling of the tertiary structure. This novel model is applied here to study the growth of an amyloid fibril, by calculating the free energy profile of a protein attaching to the end of a fibril. The simulation results suggest that the attaching protein readily becomes trapped in a mis-folded state, thereby inhibiting further growth of the fibril until the protein has readjusted to conform to the fibril structure, in line with experimental findings and previous simulations on small fragments of other proteins.

  10. Can temporal fine structure represent the fundamental frequency of unresolved harmonics?

    Science.gov (United States)

    Oxenham, Andrew J; Micheyl, Christophe; Keebler, Michael V

    2009-04-01

    At least two modes of pitch perception exist: in one, the fundamental frequency (F0) of harmonic complex tones is estimated using the temporal fine structure (TFS) of individual low-order resolved harmonics; in the other, F0 is derived from the temporal envelope of high-order unresolved harmonics that interact in the auditory periphery. Pitch is typically more accurate in the former than in the latter mode. Another possibility is that pitch can sometimes be coded via the TFS from unresolved harmonics. A recent study supporting this third possibility [Moore et al. (2006a). J. Acoust. Soc. Am. 119, 480-490] based its conclusion on a condition where phase interaction effects (implying unresolved harmonics) accompanied accurate F0 discrimination (implying TFS processing). The present study tests whether these results were influenced by audible distortion products. Experiment 1 replicated the original results, obtained using a low-level background noise. However, experiments 2-4 found no evidence for the use of TFS cues with unresolved harmonics when the background noise level was raised, or the stimulus level was lowered, to render distortion inaudible. Experiment 5 measured the presence and phase dependence of audible distortion products. The results provide no evidence that TFS cues are used to code the F0 of unresolved harmonics.

  11. Temporal motifs in time-dependent networks

    International Nuclear Information System (INIS)

    Kovanen, Lauri; Karsai, Márton; Kaski, Kimmo; Kertész, János; Saramäki, Jari

    2011-01-01

    Temporal networks are commonly used to represent systems where connections between elements are active only for restricted periods of time, such as telecommunication, neural signal processing, biochemical reaction and human social interaction networks. We introduce the framework of temporal motifs to study the mesoscale topological–temporal structure of temporal networks in which the events of nodes do not overlap in time. Temporal motifs are classes of similar event sequences, where the similarity refers not only to topology but also to the temporal order of the events. We provide a mapping from event sequences to coloured directed graphs that enables an efficient algorithm for identifying temporal motifs. We discuss some aspects of temporal motifs, including causality and null models, and present basic statistics of temporal motifs in a large mobile call network

  12. Selective amygdalohippocampectomy via trans-superior temporal gyrus keyhole approach.

    Science.gov (United States)

    Mathon, Bertrand; Clemenceau, Stéphane

    2016-04-01

    Hippocampal sclerosis is the most common cause of drug-resistant epilepsy amenable for surgical treatment and seizure control. The rationale of the selective amygdalohippocampectomy is to spare cerebral tissue not included in the seizure generator. Describe the selective amygdalohippocampectomy through the trans-superior temporal gyrus keyhole approach. Selective amygdalohippocampectomy for temporal lobe epilepsy is performed when the data (semiology, neuroimaging, electroencephalography) point to the mesial temporal structures. The trans-superior temporal gyrus keyhole approach is a minimally invasive and safe technique that allows disconnection of the temporal stem and resection of temporomesial structures.

  13. Theoretical analysis of the spatio-temporal structure of bone multicellular units

    International Nuclear Information System (INIS)

    Buenzli, P R; Pivonka, P; Gardiner, B S; Smith, D W; Dunstan, C R; Mundy, G R

    2010-01-01

    Bone multicellular units (BMUs) maintain the viability of the skeletal tissue by coordinating locally the sequence of bone resorption and bone formation performed by cells of the osteoclastic and osteoblastic lineage. Understanding the emergence and the net bone balance of such structured microsystems out of the complex network of biochemical interactions between bone cells is fundamental for many bone-related diseases and the evaluation of fracture risk. Based on current experimental knowledge, we propose a spatio-temporal continuum model describing the interactions of osteoblastic and osteoclastic cells. We show that this model admits travelling-wave-like solutions with well-confined cell profiles upon specifying external conditions mimicking the environment encountered in cortical bone remodelling. The shapes of the various cell concentration profiles within this travelling structure are intrinsically linked to the parameters of the model such as differentiation, proliferation, and apoptosis rates of bone cells. The internal structure of BMUs is reproduced, allowing for experimental calibration. The spatial distribution of the key regulatory factors can also be exhibited, which in diseased states could give hints as to the biochemical agent most accountable for the disorder.

  14. Separation and collection of coarse aggregate from waste concrete by electric pulsed power

    Science.gov (United States)

    Shigeishi, Mitsuhiro

    2017-09-01

    Waste concrete accounts for a substantial fraction of construction waste, and the recycling of waste concrete as concrete aggregate for construction is an important challenge associated with the rapid increase in the amount of waste concrete and the tight supply of natural aggregate. In this study, we propose a technique based on the use of high-voltage pulsed electric discharge into concrete underwater for separating and collecting aggregate from waste concrete with minimal deterioration of quality. By using this technique, the quality of the coarse aggregate separated and collected from concrete test specimens is comparable to that of coarse aggregate recycled by heating and grinding methods, thus satisfying the criteria in Japan Industrial Standard (JIS) A 5021 for the oven-dry density and the water absorption of coarse aggregate by advanced recycling.

  15. Recycled concrete with coarse recycled aggregate. An overview and analysis

    Directory of Open Access Journals (Sweden)

    B. González-Fonteboa

    2018-04-01

    Full Text Available The construction field has contributed to environmental degradation, producing a high amount of construction and demolition waste (C&D waste and consuming large volumes of natural resources. In this context, recycled concrete (RC has been recognised as a means to preserve natural resources and reduce space for waste storage. During the last decades, many researchers have developed works studying different recycled concrete properties. This review focuses on structural RC made with coarse recycled aggregate from concrete waste. The main objective is to provide a state of the art report on RC’s properties and an analysis on how to predict them taking into account relevant research works. Moreover, the study tries to collect and update RC findings, proposing equations to define RC’s performance, in terms of mechanical strength, modulus of elasticity, stress-strain, creep and shrinkage.

  16. Computed tomography of temporal bone fractures and temporal region anatomy in horses.

    Science.gov (United States)

    Pownder, S; Scrivani, P V; Bezuidenhout, A; Divers, T J; Ducharme, N G

    2010-01-01

    In people, specific classifications of temporal bone fractures are associated with clinical signs and prognosis. In horses, similar classifications have not been evaluated and might be useful establishing prognosis or understanding pathogenesis of certain types of trauma. We hypothesized associations between temporal bone fracture location and orientation in horses detected during computed tomography (CT) and frequency of facial nerve (CN7) deficit, vestibulocochlear nerve (CN8) deficit, or temporohyoid osteoarthropathy (THO). Complex temporal region anatomy may confound fracture identification, and consequently a description of normal anatomy was included. All horses undergoing temporal region CT at our hospital between July 1998 and May 2008. Data were collected retrospectively, examiners were blinded, and relationships were investigated among temporal bone fractures, ipsilateral THO, ipsilateral CN7, or ipsilateral CN8 deficits by Chi-square or Fischer's exact tests. Seventy-nine horses had CT examinations of the temporal region (158 temporal bones). Sixteen temporal bone fractures were detected in 14 horses. Cranial nerve deficits were seen with fractures in all parts of the temporal bone (petrosal, squamous, and temporal) and, temporal bone fractures were associated with CN7 and CN8 deficits and THO. No investigated fracture classification scheme, however, was associated with specific cranial nerve deficits. Without knowledge of the regional anatomy, normal structures may be mistaken for a temporal bone fracture or vice versa. Although no fracture classification scheme was associated with the assessed clinical signs, simple descriptive terminology (location and orientation) is recommended for reporting and facilitating future comparisons.

  17. Aberrant topological patterns of brain structural network in temporal lobe epilepsy.

    Science.gov (United States)

    Yasuda, Clarissa Lin; Chen, Zhang; Beltramini, Guilherme Coco; Coan, Ana Carolina; Morita, Marcia Elisabete; Kubota, Bruno; Bergo, Felipe; Beaulieu, Christian; Cendes, Fernando; Gross, Donald William

    2015-12-01

    Although altered large-scale brain network organization in patients with temporal lobe epilepsy (TLE) has been shown using morphologic measurements such as cortical thickness, these studies, have not included critical subcortical structures (such as hippocampus and amygdala) and have had relatively small sample sizes. Here, we investigated differences in topological organization of the brain volumetric networks between patients with right TLE (RTLE) and left TLE (LTLE) with unilateral hippocampal atrophy. We performed a cross-sectional analysis of 86 LTLE patients, 70 RTLE patients, and 116 controls. RTLE and LTLE groups were balanced for gender (p = 0.64), seizure frequency (Mann-Whitney U test, p = 0.94), age (p = 0.39), age of seizure onset (p = 0.21), and duration of disease (p = 0.69). Brain networks were constructed by thresholding correlation matrices of volumes from 80 cortical/subcortical regions (parcellated with Freesurfer v5.3 https://surfer.nmr.mgh.harvard.edu/) that were then analyzed using graph theoretical approaches. We identified reduced cortical/subcortical connectivity including bilateral hippocampus in both TLE groups, with the most significant interregional correlation increases occurring within the limbic system in LTLE and contralateral hemisphere in RTLE. Both TLE groups demonstrated less optimal topological organization, with decreased global efficiency and increased local efficiency and clustering coefficient. LTLE also displayed a more pronounced network disruption. Contrary to controls, hub nodes in both TLE groups were not distributed across whole brain, but rather found primarily in the paralimbic/limbic and temporal association cortices. Regions with increased centrality were concentrated in occipital lobes for LTLE and contralateral limbic/temporal areas for RTLE. These findings provide first evidence of altered topological organization of the whole brain volumetric network in TLE, with disruption of the coordinated patterns of

  18. Exact CTP renormalization group equation for the coarse-grained effective action

    International Nuclear Information System (INIS)

    Dalvit, D.A.; Mazzitelli, F.D.

    1996-01-01

    We consider a scalar field theory in Minkowski spacetime and define a coarse-grained closed time path (CTP) effective action by integrating quantum fluctuations of wavelengths shorter than a critical value. We derive an exact CTP renormalization group equation for the dependence of the effective action on the coarse-graining scale. We solve this equation using a derivative expansion approach. Explicit calculation is performed for the λφ 4 theory. We discuss the relevance of the CTP average action in the study of nonequilibrium aspects of phase transitions in quantum field theory. copyright 1996 The American Physical Society

  19. Structural alterations of the superior temporal gyrus in schizophrenia: Detailed subregional differences.

    Science.gov (United States)

    Ohi, K; Matsuda, Y; Shimada, T; Yasuyama, T; Oshima, K; Sawai, K; Kihara, H; Nitta, Y; Okubo, H; Uehara, T; Kawasaki, Y

    2016-05-01

    Reduced gray matter volumes in the superior temporal gyrus (STG) have been reported in patients with schizophrenia. Such volumetric abnormalities might denote alterations in cortical thickness, surface area, local gyrification or all of these factors. The STG can be anatomically divided into five subregions using automatic parcellation in FreeSurfer: lateral aspect of the STG, anterior transverse temporal gyrus of Heschl gyrus (HG), planum polare (PP) of the STG, planum temporale (PT) of the STG and transverse temporal sulcus. We acquired magnetic resonance imaging (MRI) 3T scans from 40 age- and sex-matched patients with schizophrenia and 40 healthy subjects, and the scans were automatically processed using FreeSurfer. General linear models were used to assess group differences in regional volumes and detailed thickness, surface area and local gyrification. As expected, patients with schizophrenia had significantly smaller bilateral STG volumes than healthy subjects. Of the five subregions in the STG, patients with schizophrenia showed significantly and marginally reduced volumes in the lateral aspect of the STG and PT of the STG bilaterally compared with healthy subjects. The volumetric alteration in bilateral lateral STG was derived from both the cortical thickness and surface area but not local gyrification. There was no significant laterality of the alteration in the lateral STG between patients and controls and no correlation among the structures and clinical characteristics. These findings suggest that of five anatomical subregions in the STG, the lateral STG is one of the most meaningful regions for brain pathophysiology in schizophrenia. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

  20. Temporal stability in the genetic structure of Sarcoptes scabiei under the host-taxon law: empirical evidences from wildlife-derived Sarcoptes mite in Asturias, Spain

    Directory of Open Access Journals (Sweden)

    Rossi Luca

    2011-07-01

    Full Text Available Abstract Background Implicitly, parasite molecular studies assume temporal genetic stability. In this study we tested, for the first time to our knowledge, the extent of changes in genetic diversity and structure of Sarcoptes mite populations from Pyrenean chamois (Rupicapra pyrenaica in Asturias (Spain, using one multiplex of 9 microsatellite markers and Sarcoptes samples from sympatric Pyrenean chamois, red deer (Cervus elaphus, roe deer (Capreolus capreolus and red fox (Vulpes vulpes. Results The analysis of an 11-years interval period found little change in the genetic diversity (allelic diversity, and observed and expected heterozygosity. The temporal stability in the genetic diversity was confirmed by population structure analysis, which was not significantly variable over time. Population structure analysis revealed temporal stability in the genetic diversity of Sarcoptes mite under the host-taxon law (herbivore derived- and carnivore derived-Sarcoptes mite among the sympatric wild animals from Asturias. Conclusions The confirmation of parasite temporal genetic stability is of vital interest to allow generalizations to be made, which have further implications regarding the genetic structure, epidemiology and monitoring protocols of the ubiquitous Sarcoptes mite. This could eventually be applied to other parasite species.

  1. Temporal Organization of Sound Information in Auditory Memory

    Directory of Open Access Journals (Sweden)

    Kun Song

    2017-06-01

    Full Text Available Memory is a constructive and organizational process. Instead of being stored with all the fine details, external information is reorganized and structured at certain spatiotemporal scales. It is well acknowledged that time plays a central role in audition by segmenting sound inputs into temporal chunks of appropriate length. However, it remains largely unknown whether critical temporal structures exist to mediate sound representation in auditory memory. To address the issue, here we designed an auditory memory transferring study, by combining a previously developed unsupervised white noise memory paradigm with a reversed sound manipulation method. Specifically, we systematically measured the memory transferring from a random white noise sound to its locally temporal reversed version on various temporal scales in seven experiments. We demonstrate a U-shape memory-transferring pattern with the minimum value around temporal scale of 200 ms. Furthermore, neither auditory perceptual similarity nor physical similarity as a function of the manipulating temporal scale can account for the memory-transferring results. Our results suggest that sounds are not stored with all the fine spectrotemporal details but are organized and structured at discrete temporal chunks in long-term auditory memory representation.

  2. Temporal Organization of Sound Information in Auditory Memory.

    Science.gov (United States)

    Song, Kun; Luo, Huan

    2017-01-01

    Memory is a constructive and organizational process. Instead of being stored with all the fine details, external information is reorganized and structured at certain spatiotemporal scales. It is well acknowledged that time plays a central role in audition by segmenting sound inputs into temporal chunks of appropriate length. However, it remains largely unknown whether critical temporal structures exist to mediate sound representation in auditory memory. To address the issue, here we designed an auditory memory transferring study, by combining a previously developed unsupervised white noise memory paradigm with a reversed sound manipulation method. Specifically, we systematically measured the memory transferring from a random white noise sound to its locally temporal reversed version on various temporal scales in seven experiments. We demonstrate a U-shape memory-transferring pattern with the minimum value around temporal scale of 200 ms. Furthermore, neither auditory perceptual similarity nor physical similarity as a function of the manipulating temporal scale can account for the memory-transferring results. Our results suggest that sounds are not stored with all the fine spectrotemporal details but are organized and structured at discrete temporal chunks in long-term auditory memory representation.

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

    Science.gov (United States)

    Genheden, Samuel

    2017-10-01

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

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

    Science.gov (United States)

    Genheden, Samuel

    2017-10-01

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

  5. Recycled tires as coarse aggregate in concrete pavement mixtures.

    Science.gov (United States)

    2013-07-01

    The reuse potential of tire chips as coarse aggregates in pavement concrete was examined in this research by : investigating the effects of low- and high-volume tire chips on fresh and hardened concrete properties. One concrete : control mixture was ...

  6. Control of periodic surface structures on silicon by combined temporal and polarization shaping of femtosecond laser pulses

    Science.gov (United States)

    Fraggelakis, F.; Stratakis, E.; Loukakos, P. A.

    2018-06-01

    We demonstrate the capability to exercise advanced control on the laser-induced periodic surface structures (LIPSS) on silicon by combining the effect of temporal shaping, via tuning the interpulse temporal delay between double femtosecond laser pulses, along with the independent manipulation of the polarization state of each of the individual pulses. For this, cross-polarized (CP) as well as counter-rotating (CR) double circularly polarized pulses have been utilized. The pulse duration was 40 fs and the central wavelength of 790 nm. The linearly polarized double pulses are generated by a modified Michelson interferometer allowing the temporal delay between the pulses to vary from Δτ = -80 ps to Δτ = +80 ps with an accuracy of 0.2 fs. We show the significance of fluence balance between the two pulse components and its interplay with the interpulse delay and with the order of arrival of the individually polarized pulse components of the double pulse sequence on the final surface morphology. For the case of CR pulses we found that when the pulses are temporally well separated the surface morphology attains no axial symmetry. But strikingly, when the two CP pulses temporally overlap, we demonstrate, for the first time in our knowledge, the detrimental effect that the phase delay has on the ripple orientation. Our results provide new insight showing that temporal pulse shaping in combination with polarization control gives a powerful tool for drastically controlling the surface nanostructure morphology.

  7. Non-Steady Oscillatory Flow in Coarse Granular Materials

    DEFF Research Database (Denmark)

    Andersen, O. H.; Gent, M. R. A. van; Meer, J. W. van der

    1992-01-01

    Stationary and oscillatory flow through coarse granular materials have been investigated experimentally at Delft Hydraulics in their oscillating water tunnel with the objective of determining the coefficients of the extended Forchheimer equation. Cylinders, spheres and different types of rock have....... Further, for the non-stationary term, the virtual mass coefficient will be derived....

  8. Loop overhead reduction techniques for coarse grained reconfigurable architectures

    NARCIS (Netherlands)

    Vadivel, K.; Wijtvliet, M.; Jordans, R.; Corporaal, H.

    2017-01-01

    Due to their flexibility and high performance, Coarse Grained Reconfigurable Array (CGRA) are a topic of increasing research interest. However, CGRAs also have the potential to achieve very high energy efficiency in comparison to other reconfigurable architectures when hardware optimizations are

  9. Coarse root topology of Norway spruce (Picea abies) and its effects on slope stability

    Science.gov (United States)

    Lith, Aniek; Schmaltz, Elmar; Bogaard, Thom; Keesstra, Saskia

    2017-04-01

    The structural distribution of coarse roots and its beneficial effects on soil reinforcement has widely been assessed. However, it is still not fully understood how topological features of coarse roots (e.g. branching patterns) are affected by slope inclination and further influence the ability of young trees to reinforce soil. This study aims to analyse empirically the impact of slope gradient on the topological development of coarse roots and thus to assess its effects on soil reinforcement. We performed root system excavations on two young Picea abies: tree A on a gently inclined plane (β ≈ 12°) where slope failures are not expected; tree B on a slope (β ≈ 35°) with failure potential. The diameter (d) of the segments between distinct root nodes (root ends, branching locations, direction changes and attachments to stem) of coarse roots (d > 2mm) were measured in situ. The spatial coordinates (x,y,z) of the nodes and surface were measured on a plane raster grid, from which segment length (ls), direction and inclination towards the surface (βr) were derived. Roots and segments were classified into laterals (βr classifications (FSC), to obtain quantitative relations between the topological order and number of segments, total and average ls. The maximal root cohesion (cr) of each segment was assessed using material specific tensile forces (Tr), root area ratio (RAR) and βr, assuming that a potential slip surface would cross the root system parallel to the slope. Laterals depicted the majority of roots (57 %) for tree A orientated rather in upslope direction (76.8 %), whereas tree B showed mostly obliques (54 %) orientated rather in downslope direction (55.4 %). Vertical roots were scarcely observable for both trees. DSC showed a high r2 (> 0.84) for the segments and ls. FSC showed high r2 (> 0.95) for the number of segments and the total length. RAR values of tree B are distributed rather upslope (76.8 % of RARtot), compared to 44.5 % of RARtot for tree A

  10. A coarse-to-fine approach for pericardial effusion localization and segmentation in chest CT scans

    Science.gov (United States)

    Liu, Jiamin; Chellamuthu, Karthik; Lu, Le; Bagheri, Mohammadhadi; Summers, Ronald M.

    2018-02-01

    Pericardial effusion on CT scans demonstrates very high shape and volume variability and very low contrast to adjacent structures. This inhibits traditional automated segmentation methods from achieving high accuracies. Deep neural networks have been widely used for image segmentation in CT scans. In this work, we present a two-stage method for pericardial effusion localization and segmentation. For the first step, we localize the pericardial area from the entire CT volume, providing a reliable bounding box for the more refined segmentation step. A coarse-scaled holistically-nested convolutional networks (HNN) model is trained on entire CT volume. The resulting HNN per-pixel probability maps are then threshold to produce a bounding box covering the pericardial area. For the second step, a fine-scaled HNN model is trained only on the bounding box region for effusion segmentation to reduce the background distraction. Quantitative evaluation is performed on a dataset of 25 CT scans of patient (1206 images) with pericardial effusion. The segmentation accuracy of our two-stage method, measured by Dice Similarity Coefficient (DSC), is 75.59+/-12.04%, which is significantly better than the segmentation accuracy (62.74+/-15.20%) of only using the coarse-scaled HNN model.

  11. Enhanced Visual Temporal Resolution in Autism Spectrum Disorders

    NARCIS (Netherlands)

    Falter, Christine M.; Elliott, Mark A.; Bailey, Anthony J.

    2012-01-01

    Cognitive functions that rely on accurate sequencing of events, such as action planning and execution, verbal and nonverbal communication, and social interaction rely on well-tuned coding of temporal event-structure. Visual temporal event-structure coding was tested in 17 high-functioning

  12. Hierarchical coarse-graining transform.

    Science.gov (United States)

    Pancaldi, Vera; King, Peter R; Christensen, Kim

    2009-03-01

    We present a hierarchical transform that can be applied to Laplace-like differential equations such as Darcy's equation for single-phase flow in a porous medium. A finite-difference discretization scheme is used to set the equation in the form of an eigenvalue problem. Within the formalism suggested, the pressure field is decomposed into an average value and fluctuations of different kinds and at different scales. The application of the transform to the equation allows us to calculate the unknown pressure with a varying level of detail. A procedure is suggested to localize important features in the pressure field based only on the fine-scale permeability, and hence we develop a form of adaptive coarse graining. The formalism and method are described and demonstrated using two synthetic toy problems.

  13. Temporal Lobe Epilepsy Surgery Failures: A Review

    Science.gov (United States)

    Harroud, Adil; Bouthillier, Alain; Weil, Alexander G.; Nguyen, Dang Khoa

    2012-01-01

    Patients with temporal lobe epilepsy (TLE) are refractory to antiepileptic drugs in about 30% of cases. Surgical treatment has been shown to be beneficial for the selected patients but fails to provide a seizure-free outcome in 20–30% of TLE patients. Several reasons have been identified to explain these surgical failures. This paper will address the five most common causes of TLE surgery failure (a) insufficient resection of epileptogenic mesial temporal structures, (b) relapse on the contralateral mesial temporal lobe, (c) lateral temporal neocortical epilepsy, (d) coexistence of mesial temporal sclerosis and a neocortical lesion (dual pathology); and (e) extratemporal lobe epilepsy mimicking TLE or temporal plus epilepsy. Persistence of epileptogenic mesial structures in the posterior temporal region and failure to distinguish mesial and lateral temporal epilepsy are possible causes of seizure persistence after TLE surgery. In cases of dual pathology, failure to identify a subtle mesial temporal sclerosis or regions of cortical microdysgenesis is a likely explanation for some surgical failures. Extratemporal epilepsy syndromes masquerading as or coexistent with TLE result in incomplete resection of the epileptogenic zone and seizure relapse after surgery. In particular, the insula may be an important cause of surgical failure in patients with TLE. PMID:22934162

  14. Ancient sedimentary structures in the Mars, that resemble macroscopic morphology, spatial associations, and temporal succession in terrestrial microbialites.

    Science.gov (United States)

    Noffke, Nora

    2015-02-01

    Sandstone beds of the Mars have been interpreted as evidence of an ancient playa lake environment. On Earth, such environments have been sites of colonization by microbial mats from the early Archean to the present time. Terrestrial microbial mats in playa lake environments form microbialites known as microbially induced sedimentary structures (MISS). On Mars, three lithofacies of the Gillespie Lake Member sandstone display centimeter- to meter-scale structures similar in macroscopic morphology to terrestrial MISS that include "erosional remnants and pockets," "mat chips," "roll-ups," "desiccation cracks," and "gas domes." The microbially induced sedimentary-like structures identified in Curiosity rover mission images do not have a random distribution. Rather, they were found to be arranged in spatial associations and temporal successions that indicate they changed over time. On Earth, if such MISS occurred with this type of spatial association and temporal succession, they would be interpreted as having recorded the growth of a microbially dominated ecosystem that thrived in pools that later dried completely: erosional pockets, mat chips, and roll-ups resulted from water eroding an ancient microbial mat-covered sedimentary surface; during the course of subsequent water recess, channels would have cut deep into the microbial mats, leaving erosional remnants behind; desiccation cracks and gas domes would have occurred during a final period of subaerial exposure of the microbial mats. In this paper, the similarities of the macroscopic morphologies, spatial associations, and temporal succession of sedimentary structures on Mars to MISS preserved on Earth has led to the following hypothesis: The sedimentary structures in the Mars are ancient MISS produced by interactions between microbial mats and their environment. Proposed here is a strategy for detecting, identifying, confirming, and differentiating possible MISS during current and future Mars missions.

  15. Climatic regions as an indicator of forest coarse and fine woody debris carbon stocks in the United States

    Directory of Open Access Journals (Sweden)

    Liknes Greg C

    2008-06-01

    Full Text Available Abstract Background Coarse and fine woody debris are substantial forest ecosystem carbon stocks; however, there is a lack of understanding how these detrital carbon stocks vary across forested landscapes. Because forest woody detritus production and decay rates may partially depend on climatic conditions, the accumulation of coarse and fine woody debris carbon stocks in forests may be correlated with climate. This study used a nationwide inventory of coarse and fine woody debris in the United States to examine how these carbon stocks vary by climatic regions and variables. Results Mean coarse and fine woody debris forest carbon stocks vary by Köppen's climatic regions across the United States. The highest carbon stocks were found in regions with cool summers while the lowest carbon stocks were found in arid desert/steppes or temperate humid regions. Coarse and fine woody debris carbon stocks were found to be positively correlated with available moisture and negatively correlated with maximum temperature. Conclusion It was concluded with only medium confidence that coarse and fine woody debris carbon stocks may be at risk of becoming net emitter of carbon under a global climate warming scenario as increases in coarse or fine woody debris production (sinks may be more than offset by increases in forest woody detritus decay rates (emission. Given the preliminary results of this study and the rather tenuous status of coarse and fine woody debris carbon stocks as either a source or sink of CO2, further research is suggested in the areas of forest detritus decay and production.

  16. The Role of Temporal Envelope and Fine Structure in Mandarin Lexical Tone Perception in Auditory Neuropathy Spectrum Disorder.

    Directory of Open Access Journals (Sweden)

    Shuo Wang

    Full Text Available Temporal information in a signal can be partitioned into temporal envelope (E and fine structure (FS. Fine structure is important for lexical tone perception for normal-hearing (NH listeners, and listeners with sensorineural hearing loss (SNHL have an impaired ability to use FS in lexical tone perception due to the reduced frequency resolution. The present study was aimed to assess which of the acoustic aspects (E or FS played a more important role in lexical tone perception in subjects with auditory neuropathy spectrum disorder (ANSD and to determine whether it was the deficit in temporal resolution or frequency resolution that might lead to more detrimental effects on FS processing in pitch perception. Fifty-eight native Mandarin Chinese-speaking subjects (27 with ANSD, 16 with SNHL, and 15 with NH were assessed for (1 their ability to recognize lexical tones using acoustic E or FS cues with the "auditory chimera" technique, (2 temporal resolution as measured with temporal gap detection (TGD threshold, and (3 frequency resolution as measured with the Q(10dB values of the psychophysical tuning curves. Overall, 26.5%, 60.2%, and 92.1% of lexical tone responses were consistent with FS cues for tone perception for listeners with ANSD, SNHL, and NH, respectively. The mean TGD threshold was significantly higher for listeners with ANSD (11.9 ms than for SNHL (4.0 ms; p < 0.001 and NH (3.9 ms; p < 0.001 listeners, with no significant difference between SNHL and NH listeners. In contrast, the mean Q(10dB for listeners with SNHL (1.8 ± 0.4 was significantly lower than that for ANSD (3.5 ± 1.0; p < 0.001 and NH (3.4 ± 0.9; p < 0.001 listeners, with no significant difference between ANSD and NH listeners. These results suggest that reduced temporal resolution, as opposed to reduced frequency selectivity, in ANSD subjects leads to greater degradation of FS processing for pitch perception.

  17. Sampling of temporal networks: Methods and biases

    Science.gov (United States)

    Rocha, Luis E. C.; Masuda, Naoki; Holme, Petter

    2017-11-01

    Temporal networks have been increasingly used to model a diversity of systems that evolve in time; for example, human contact structures over which dynamic processes such as epidemics take place. A fundamental aspect of real-life networks is that they are sampled within temporal and spatial frames. Furthermore, one might wish to subsample networks to reduce their size for better visualization or to perform computationally intensive simulations. The sampling method may affect the network structure and thus caution is necessary to generalize results based on samples. In this paper, we study four sampling strategies applied to a variety of real-life temporal networks. We quantify the biases generated by each sampling strategy on a number of relevant statistics such as link activity, temporal paths and epidemic spread. We find that some biases are common in a variety of networks and statistics, but one strategy, uniform sampling of nodes, shows improved performance in most scenarios. Given the particularities of temporal network data and the variety of network structures, we recommend that the choice of sampling methods be problem oriented to minimize the potential biases for the specific research questions on hand. Our results help researchers to better design network data collection protocols and to understand the limitations of sampled temporal network data.

  18. The influence of coarse aggregate size and volume on the fracture behavior and brittleness of self-compacting concrete

    International Nuclear Information System (INIS)

    Beygi, Morteza H.A.; Kazemi, Mohammad Taghi; Nikbin, Iman M.; Vaseghi Amiri, Javad; Rabbanifar, Saeed; Rahmani, Ebrahim

    2014-01-01

    This paper presents the results of an experimental investigation on fracture characteristics and brittleness of self-compacting concrete (SCC), involving the tests of 185 three point bending beams with different coarse aggregate size and content. Generally, the parameters were analyzed by the work of fracture method (WFM) and the size effect method (SEM). The results showed that with increase of size and content of coarse aggregate, (a) the fracture energy increases which is due to the change in fractal dimensions, (b) behavior of SCC beams approaches strength criterion, (c) characteristic length, which is deemed as an index of brittleness, increases linearly. It was found with decrease of w/c ratio that fracture energy increases which may be explained by the improvement in structure of aggregate-paste transition zone. Also, the results showed that there is a correlation between the fracture energy measured by WFM (G F ) and the value measured through SEM (G f ) (G F = 3.11G f )

  19. The influence of coarse aggregate size and volume on the fracture behavior and brittleness of self-compacting concrete

    Energy Technology Data Exchange (ETDEWEB)

    Beygi, Morteza H.A., E-mail: M.beygi@nit.ac.ir [Department of Civil Engineering, Babol University of Technology (Iran, Islamic Republic of); Kazemi, Mohammad Taghi, E-mail: Kazemi@sharif.edu [Department of Civil Engineering, Sharif University of Technology, P.O. Box 11155-9313 (Iran, Islamic Republic of); Nikbin, Iman M., E-mail: nikbin@iaurasht.ac.ir [Faculty of Civil Engineering, Islamic Azad University, Rasht Branch, Rasht (Iran, Islamic Republic of); Vaseghi Amiri, Javad, E-mail: Vaseghi@nit.ac.ir [Department of Civil Engineering, Babol University of Technology (Iran, Islamic Republic of); Rabbanifar, Saeed, E-mail: Saeed.rabbanifar@yahoo.com [Department of Civil Engineering, Babol University of Technology (Iran, Islamic Republic of); Rahmani, Ebrahim, E-mail: Ebrahim.rahmani84@gmail.com [Department of Civil Engineering, Babol University of Technology (Iran, Islamic Republic of)

    2014-12-15

    This paper presents the results of an experimental investigation on fracture characteristics and brittleness of self-compacting concrete (SCC), involving the tests of 185 three point bending beams with different coarse aggregate size and content. Generally, the parameters were analyzed by the work of fracture method (WFM) and the size effect method (SEM). The results showed that with increase of size and content of coarse aggregate, (a) the fracture energy increases which is due to the change in fractal dimensions, (b) behavior of SCC beams approaches strength criterion, (c) characteristic length, which is deemed as an index of brittleness, increases linearly. It was found with decrease of w/c ratio that fracture energy increases which may be explained by the improvement in structure of aggregate-paste transition zone. Also, the results showed that there is a correlation between the fracture energy measured by WFM (G{sub F}) and the value measured through SEM (G{sub f}) (G{sub F} = 3.11G{sub f})

  20. On the representability problem and the physical meaning of coarse-grained models

    Energy Technology Data Exchange (ETDEWEB)

    Wagner, Jacob W.; Dama, James F.; Durumeric, Aleksander E. P.; Voth, Gregory A., E-mail: gavoth@uchicago.edu [Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, and Computation Institute, The University of Chicago, Chicago, Illinois 60637 (United States)

    2016-07-28

    In coarse-grained (CG) models where certain fine-grained (FG, i.e., atomistic resolution) observables are not directly represented, one can nonetheless identify indirect the CG observables that capture the FG observable’s dependence on CG coordinates. Often, in these cases it appears that a CG observable can be defined by analogy to an all-atom or FG observable, but the similarity is misleading and significantly undermines the interpretation of both bottom-up and top-down CG models. Such problems emerge especially clearly in the framework of the systematic bottom-up CG modeling, where a direct and transparent correspondence between FG and CG variables establishes precise conditions for consistency between CG observables and underlying FG models. Here we present and investigate these representability challenges and illustrate them via the bottom-up conceptual framework for several simple analytically tractable polymer models. The examples provide special focus on the observables of configurational internal energy, entropy, and pressure, which have been at the root of controversy in the CG literature, as well as discuss observables that would seem to be entirely missing in the CG representation but can nonetheless be correlated with CG behavior. Though we investigate these problems in the framework of systematic coarse-graining, the lessons apply to top-down CG modeling also, with crucial implications for simulation at constant pressure and surface tension and for the interpretations of structural and thermodynamic correlations for comparison to experiment.

  1. Free-energy coarse-grained potential for C60

    International Nuclear Information System (INIS)

    Edmunds, D. M.; Tangney, P.; Vvedensky, D. D.; Foulkes, W. M. C.

    2015-01-01

    We propose a new deformable free energy method for generating a free-energy coarse-graining potential for C 60 . Potentials generated from this approach exhibit a strong temperature dependence and produce excellent agreement with benchmark fully atomistic molecular dynamics simulations. Parameter sets for analytical fits to this potential are provided at four different temperatures

  2. Systematic coarse-graining of the dynamics of entangled polymer melts: the road from chemistry to rheology

    International Nuclear Information System (INIS)

    Padding, J T; Briels, W J

    2011-01-01

    For optimal processing and design of entangled polymeric materials it is important to establish a rigorous link between the detailed molecular composition of the polymer and the viscoelastic properties of the macroscopic melt. We review current and past computer simulation techniques and critically assess their ability to provide such a link between chemistry and rheology. We distinguish between two classes of coarse-graining levels, which we term coarse-grained molecular dynamics (CGMD) and coarse-grained stochastic dynamics (CGSD). In CGMD the coarse-grained beads are still relatively hard, thus automatically preventing bond crossing. This also implies an upper limit on the number of atoms that can be lumped together (up to five backbone carbon atoms) and therefore on the longest chain lengths that can be studied. To reach a higher degree of coarse-graining, in CGSD many more atoms are lumped together (more than ten backbone carbon atoms), leading to relatively soft beads. In that case friction and stochastic forces dominate the interactions, and action must be undertaken to prevent bond crossing. We also review alternative methods that make use of the tube model of polymer dynamics, by obtaining the entanglement characteristics through a primitive path analysis and by simulation of a primitive chain network. We finally review super-coarse-grained methods in which an entire polymer is represented by a single particle, and comment on ways to include memory effects and transient forces. (topical review)

  3. Spatial and Temporal Variations of Aerosol Optical Properties during KORUS-AQ

    Science.gov (United States)

    Choi, Y.; Ghim, Y. S.; Segal-Rosenhaimer, M.; Redemann, J.

    2017-12-01

    As part of the KORUS-AQ campaign, Aerosol Robotic Networks (AERONET) Cimel sunphotometers were deployed at more than 20 sites over Korea including the Seoul Metropolitan Area (SMA) and rural/background areas. We analyzed hourly mean values of fine and coarse mode aerosol optical depths (AODs), and fine mode fraction (FMF) from spectral deconvolution algorithm retrievals. The AERONET sites over Korea were classified into four groups - those in SMA, southeastern and southwestern parts of Korea, and background sites, which distribute similar results from particulate matter (PM) stations in Korea. Temporal and spatial variations of aerosol optical properties (AOPs) from the four groups were further examined using AODs from the Spectrometer for Sky-Scanning, Sun-Tracking Atmospheric Research (4STAR), which can provide denser spatial resolution than AERONET sites and PM stations. AOPs from more than 30 flights over SMA were also investigated to distinguish the characteristics of diurnal variations upwind and downwind of SMA. The spatial and temporal homogeneity and/or heterogeneity of AOPs are discussed in terms of meteorological variables, other pollutants and nearby emission sources.

  4. Linear mixing model applied to coarse resolution satellite data

    Science.gov (United States)

    Holben, Brent N.; Shimabukuro, Yosio E.

    1992-01-01

    A linear mixing model typically applied to high resolution data such as Airborne Visible/Infrared Imaging Spectrometer, Thematic Mapper, and Multispectral Scanner System is applied to the NOAA Advanced Very High Resolution Radiometer coarse resolution satellite data. The reflective portion extracted from the middle IR channel 3 (3.55 - 3.93 microns) is used with channels 1 (0.58 - 0.68 microns) and 2 (0.725 - 1.1 microns) to run the Constrained Least Squares model to generate fraction images for an area in the west central region of Brazil. The derived fraction images are compared with an unsupervised classification and the fraction images derived from Landsat TM data acquired in the same day. In addition, the relationship betweeen these fraction images and the well known NDVI images are presented. The results show the great potential of the unmixing techniques for applying to coarse resolution data for global studies.

  5. Temporal subtraction of dual-energy chest radiographs

    International Nuclear Information System (INIS)

    Armato, Samuel G. III; Doshi, Devang J.; Engelmann, Roger; Caligiuri, Philip; MacMahon, Heber

    2006-01-01

    Temporal subtraction and dual-energy imaging are two enhanced radiography techniques that are receiving increased attention in chest radiography. Temporal subtraction is an image processing technique that facilitates the visualization of pathologic change across serial chest radiographic images acquired from the same patient; dual-energy imaging exploits the differential relative attenuation of x-ray photons exhibited by soft-tissue and bony structures at different x-ray energies to generate a pair of images that accentuate those structures. Although temporal subtraction images provide a powerful mechanism for enhancing visualization of subtle change, misregistration artifacts in these images can mimic or obscure abnormalities. The purpose of this study was to evaluate whether dual-energy imaging could improve the quality of temporal subtraction images. Temporal subtraction images were generated from 100 pairs of temporally sequential standard radiographic chest images and from the corresponding 100 pairs of dual-energy, soft-tissue radiographic images. The registration accuracy demonstrated in the resulting temporal subtraction images was evaluated subjectively by two radiologists. The registration accuracy of the soft-tissue-based temporal subtraction images was rated superior to that of the conventional temporal subtraction images. Registration accuracy also was evaluated objectively through an automated method, which achieved an area-under-the-ROC-curve value of 0.92 in the distinction between temporal subtraction images that demonstrated clinically acceptable and clinically unacceptable registration accuracy. By combining dual-energy soft-tissue images with temporal subtraction, misregistration artifacts can be reduced and superior image quality can be obtained

  6. Multi-temporal LiDAR and Landsat quantification of fire-induced changes to forest structure

    Science.gov (United States)

    McCarley, T. Ryan; Kolden, Crystal A.; Vaillant, Nicole M.; Hudak, Andrew T.; Smith, Alistair M.S.; Wing, Brian M.; Kellogg, Bryce; Kreitler, Jason R.

    2017-01-01

    Measuring post-fire effects at landscape scales is critical to an ecological understanding of wildfire effects. Predominantly this is accomplished with either multi-spectral remote sensing data or through ground-based field sampling plots. While these methods are important, field data is usually limited to opportunistic post-fire observations, and spectral data often lacks validation with specific variables of change. Additional uncertainty remains regarding how best to account for environmental variables influencing fire effects (e.g., weather) for which observational data cannot easily be acquired, and whether pre-fire agents of change such as bark beetle and timber harvest impact model accuracy. This study quantifies wildfire effects by correlating changes in forest structure derived from multi-temporal Light Detection and Ranging (LiDAR) acquisitions to multi-temporal spectral changes captured by the Landsat Thematic Mapper and Operational Land Imager for the 2012 Pole Creek Fire in central Oregon. Spatial regression modeling was assessed as a methodology to account for spatial autocorrelation, and model consistency was quantified across areas impacted by pre-fire mountain pine beetle and timber harvest. The strongest relationship (pseudo-r2 = 0.86, p LiDAR-derived estimate of canopy cover change. Relationships between percentage of LiDAR returns in forest strata and spectral indices generally increased in strength with strata height. Structural measurements made closer to the ground were not well correlated. The spatial regression approach improved all relationships, demonstrating its utility, but model performance declined across pre-fire agents of change, suggesting that such studies should stratify by pre-fire forest condition. This study establishes that spectral indices such as d74 and dNBR are most sensitive to wildfire-caused structural changes such as reduction in canopy cover and perform best when that structure has not been reduced pre-fire.

  7. Time evolution as refining, coarse graining and entangling

    International Nuclear Information System (INIS)

    Dittrich, Bianca; Steinhaus, Sebastian

    2014-01-01

    We argue that refining, coarse graining and entangling operators can be obtained from time evolution operators. This applies in particular to geometric theories, such as spin foams. We point out that this provides a construction principle for the physical vacuum in quantum gravity theories and more generally allows construction of a (cylindrically) consistent continuum limit of the theory. (paper)

  8. Time evolution as refining, coarse graining and entangling

    Science.gov (United States)

    Dittrich, Bianca; Steinhaus, Sebastian

    2014-12-01

    We argue that refining, coarse graining and entangling operators can be obtained from time evolution operators. This applies in particular to geometric theories, such as spin foams. We point out that this provides a construction principle for the physical vacuum in quantum gravity theories and more generally allows construction of a (cylindrically) consistent continuum limit of the theory.

  9. Mechanical Properties of Lightweight Concrete Using Recycled Cement-Sand Brick as Coarse Aggregates Replacement

    Science.gov (United States)

    Joohari, Ilya; Farhani Ishak, Nor; Amin, Norliyati Mohd

    2018-03-01

    This paper presents the result of replacing natural course aggregate with recycled cement-sand brick (CSB) towards the mechanical properties of concrete. Natural aggregates were used in this study as a control sample to compare with recycled coarse aggregates. This study was also carried to determine the optimum proportion of coarse aggregates replacement to produce lightweight concrete. Besides, this study was conducted to observe the crack and its behaviour development during the mechanical testing. Through this study, four types of concrete mixed were prepared, which were the control sample, 25%, 50% and 75% replacement of CSB. The test conducted to determine the effectiveness of recycled CSB as coarse aggregates replacement in this study were slump test, density measurement, compression test, and flexural test and. The strength of concrete was tested at 7 days and 28 days of curing. From the results obtained, the optimum proportion which produced the highest strength is 25% replacement of recycled CSB. The compressive and flexural strength has decreased by 10%-12% and 4%-34% respectively compared to the control sample. The presence of recycled coarse aggregates in sample has decreased the density of concrete by 0.8%-3% compared to the control sample.

  10. Local free energies for the coarse-graining of adsorption phenomena: The interacting pair approximation

    Science.gov (United States)

    Pazzona, Federico G.; Pireddu, Giovanni; Gabrieli, Andrea; Pintus, Alberto M.; Demontis, Pierfranco

    2018-05-01

    We investigate the coarse-graining of host-guest systems under the perspective of the local distribution of pore occupancies, along with the physical meaning and actual computability of the coarse-interaction terms. We show that the widely accepted approach, in which the contributions to the free energy given by the molecules located in two neighboring pores are estimated through Monte Carlo simulations where the two pores are kept separated from the rest of the system, leads to inaccurate results at high sorbate densities. In the coarse-graining strategy that we propose, which is based on the Bethe-Peierls approximation, density-independent interaction terms are instead computed according to local effective potentials that take into account the correlations between the pore pair and its surroundings by means of mean-field correction terms without the need for simulating the pore pair separately. Use of the interaction parameters obtained this way allows the coarse-grained system to reproduce more closely the equilibrium properties of the original one. Results are shown for lattice-gases where the local free energy can be computed exactly and for a system of Lennard-Jones particles under the effect of a static confining field.

  11. Boltzmann rovibrational collisional coarse-grained model for internal energy excitation and dissociation in hypersonic flows.

    Science.gov (United States)

    Munafò, A; Panesi, M; Magin, T E

    2014-02-01

    A Boltzmann rovibrational collisional coarse-grained model is proposed to reduce a detailed kinetic mechanism database developed at NASA Ames Research Center for internal energy transfer and dissociation in N(2)-N interactions. The coarse-grained model is constructed by lumping the rovibrational energy levels of the N(2) molecule into energy bins. The population of the levels within each bin is assumed to follow a Boltzmann distribution at the local translational temperature. Excitation and dissociation rate coefficients for the energy bins are obtained by averaging the elementary rate coefficients. The energy bins are treated as separate species, thus allowing for non-Boltzmann distributions of their populations. The proposed coarse-grained model is applied to the study of nonequilibrium flows behind normal shock waves and within converging-diverging nozzles. In both cases, the flow is assumed inviscid and steady. Computational results are compared with those obtained by direct solution of the master equation for the rovibrational collisional model and a more conventional multitemperature model. It is found that the proposed coarse-grained model is able to accurately resolve the nonequilibrium dynamics of internal energy excitation and dissociation-recombination processes with only 20 energy bins. Furthermore, the proposed coarse-grained model provides a superior description of the nonequilibrium phenomena occurring in shock heated and nozzle flows when compared with the conventional multitemperature models.

  12. Bottom-up coarse-grained models with predictive accuracy and transferability for both structural and thermodynamic properties of heptane-toluene mixtures

    Energy Technology Data Exchange (ETDEWEB)

    Dunn, Nicholas J. H.; Noid, W. G., E-mail: wnoid@chem.psu.edu [Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802 (United States)

    2016-05-28

    This work investigates the promise of a “bottom-up” extended ensemble framework for developing coarse-grained (CG) models that provide predictive accuracy and transferability for describing both structural and thermodynamic properties. We employ a force-matching variational principle to determine system-independent, i.e., transferable, interaction potentials that optimally model the interactions in five distinct heptane-toluene mixtures. Similarly, we employ a self-consistent pressure-matching approach to determine a system-specific pressure correction for each mixture. The resulting CG potentials accurately reproduce the site-site rdfs, the volume fluctuations, and the pressure equations of state that are determined by all-atom (AA) models for the five mixtures. Furthermore, we demonstrate that these CG potentials provide similar accuracy for additional heptane-toluene mixtures that were not included their parameterization. Surprisingly, the extended ensemble approach improves not only the transferability but also the accuracy of the calculated potentials. Additionally, we observe that the required pressure corrections strongly correlate with the intermolecular cohesion of the system-specific CG potentials. Moreover, this cohesion correlates with the relative “structure” within the corresponding mapped AA ensemble. Finally, the appendix demonstrates that the self-consistent pressure-matching approach corresponds to minimizing an appropriate relative entropy.

  13. Felder-Soloman's Index of Learning Styles: internal consistency, temporal stability, and factor structure.

    Science.gov (United States)

    Hosford, Charles C; Siders, William A

    2010-10-01

    Strategies to facilitate learning include using knowledge of students' learning style preferences to inform students and their teachers. Aims of this study were to evaluate the factor structure, internal consistency, and temporal stability of medical student responses to the Index of Learning Styles (ILS) and determine its appropriateness as an instrument for medical education. The ILS assesses preferences on four dimensions: sensing/intuitive information perceiving, visual/verbal information receiving, active/reflective information processing, and sequential/global information understanding. Students entering the 2002-2007 classes completed the ILS; some completed the ILS again after 2 and 4 years. Analyses of responses supported the ILS's intended structure and moderate reliability. Students had moderate preferences for sensing and visual learning. This study provides evidence supporting the appropriateness of the ILS for assessing learning style preferences in medical students.

  14. Spatio-temporal networks: reachability, centrality and robustness.

    Science.gov (United States)

    Williams, Matthew J; Musolesi, Mirco

    2016-06-01

    Recent advances in spatial and temporal networks have enabled researchers to more-accurately describe many real-world systems such as urban transport networks. In this paper, we study the response of real-world spatio-temporal networks to random error and systematic attack, taking a unified view of their spatial and temporal performance. We propose a model of spatio-temporal paths in time-varying spatially embedded networks which captures the property that, as in many real-world systems, interaction between nodes is non-instantaneous and governed by the space in which they are embedded. Through numerical experiments on three real-world urban transport systems, we study the effect of node failure on a network's topological, temporal and spatial structure. We also demonstrate the broader applicability of this framework to three other classes of network. To identify weaknesses specific to the behaviour of a spatio-temporal system, we introduce centrality measures that evaluate the importance of a node as a structural bridge and its role in supporting spatio-temporally efficient flows through the network. This exposes the complex nature of fragility in a spatio-temporal system, showing that there is a variety of failure modes when a network is subject to systematic attacks.

  15. Coarse-graining complex dynamics

    DEFF Research Database (Denmark)

    Sibani, Paolo

    2013-01-01

    Continuous Time Random Walks (CTRW) are widely used to coarse-grain the evolution of systems jumping from a metastable sub-set of their configuration space, or trap, to another via rare intermittent events. The multi-scaled behavior typical of complex dynamics is provided by a fat...... macroscopic variables all produce identical long time relaxation behaviors. Hence, CTRW shed no light on the link between microscopic and macroscopic dynamics. We then highlight how a more recent approach, Record Dynamics (RD) provides a viable alternative, based on a very different set of physical ideas......: while CTRW make use of a renewal process involving identical traps of infinite size, RD embodies a dynamical entrenchment into a hierarchy of traps which are finite in size and possess different degrees of meta-stability. We show in particular how RD produces the stretched exponential, power...

  16. Hierarchical temporal structure in music, speech and animal vocalizations: jazz is like a conversation, humpbacks sing like hermit thrushes.

    Science.gov (United States)

    Kello, Christopher T; Bella, Simone Dalla; Médé, Butovens; Balasubramaniam, Ramesh

    2017-10-01

    Humans talk, sing and play music. Some species of birds and whales sing long and complex songs. All these behaviours and sounds exhibit hierarchical structure-syllables and notes are positioned within words and musical phrases, words and motives in sentences and musical phrases, and so on. We developed a new method to measure and compare hierarchical temporal structures in speech, song and music. The method identifies temporal events as peaks in the sound amplitude envelope, and quantifies event clustering across a range of timescales using Allan factor (AF) variance. AF variances were analysed and compared for over 200 different recordings from more than 16 different categories of signals, including recordings of speech in different contexts and languages, musical compositions and performances from different genres. Non-human vocalizations from two bird species and two types of marine mammals were also analysed for comparison. The resulting patterns of AF variance across timescales were distinct to each of four natural categories of complex sound: speech, popular music, classical music and complex animal vocalizations. Comparisons within and across categories indicated that nested clustering in longer timescales was more prominent when prosodic variation was greater, and when sounds came from interactions among individuals, including interactions between speakers, musicians, and even killer whales. Nested clustering also was more prominent for music compared with speech, and reflected beat structure for popular music and self-similarity across timescales for classical music. In summary, hierarchical temporal structures reflect the behavioural and social processes underlying complex vocalizations and musical performances. © 2017 The Author(s).

  17. Information Theoretic Tools for Parameter Fitting in Coarse Grained Models

    KAUST Repository

    Kalligiannaki, Evangelia; Harmandaris, Vagelis; Katsoulakis, Markos A.; Plechac, Petr

    2015-01-01

    We study the application of information theoretic tools for model reduction in the case of systems driven by stochastic dynamics out of equilibrium. The model/dimension reduction is considered by proposing parametrized coarse grained dynamics

  18. Abrasion and algal fouling of coarse material on the Murman littoral

    Directory of Open Access Journals (Sweden)

    Malavenda S. V.

    2017-03-01

    Full Text Available On the Murmansk coast of the Barents Sea the boulder littoral zone is widely spread mostly covered by Fucus communities. This is one of the most productive benthic communities of the Barents Sea. The studies of intertidal communities have the long history, but the dynamics of intertidal ecosystems due to surf and storms is not clear. The goal of the work is to identify the leading factors that determine the rate of abrasion of coarse material and fouling algae-macrophytes of the intertidal zone of Murman. The study has been conducted in the Zelenetskaya Bay of the Barents Sea on the basis of the biological station of the MMBI KSC RAS. The rate of abrasion has been carried out during 2004–2013, phyto-overgrowing – 2009–2013. In three pilot landfills 12 samples of coarse material have been exposed during the year (from July to next July. The weight change of the sample as well as species composition and biomass of algae of fouling communities have been investigated. The influence of the surf intensity, temperature of water and air has been analyzed (univariate analysis of variance ANOVA has been applied. It has been shown that on the littoral of the Murmansk coast the abrasion of coarse material is determined primarily by the number of storms, so the storm rate has been proposed. It has been revealed that the density of fouling boulders with macroalgae depends primarily on the intensity of the surf and the average gradient of air temperature. The basis for the emerging communities of annual species are green (Acrosiphonia arcta, Blidingia minima, Spongomorpha aeruginosa and brown algae (Pylaiella littoralis, Dictyosiphon chordaria. These algae groups are found everywhere in Fucus communities of the boulder intertidal zone of the Murman coast and probably they are the intermediate stage of fouling the coarse-grained material

  19. Premelting, fluctuations, and coarse-graining of water-ice interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Limmer, David T., E-mail: dlimmer@princeton.edu [Princeton Center for Theoretical Science, Princeton University, Princeton, New Jersey 08540 (United States); Chandler, David [Department of Chemistry, University of California, Berkeley, California 94609 (United States)

    2014-11-14

    Using statistical field theory supplemented with molecular dynamics simulations, we consider premelting on the surface of ice as a generic consequence of broken hydrogen bonds at the boundary between the condensed and gaseous phases. A procedure for coarse-graining molecular configurations onto a continuous scalar order parameter field is discussed, which provides a convenient representation of the interface between locally crystal-like and locally liquid-like regions. A number of interfacial properties are straightforwardly evaluated using this procedure such as the average premelting thickness and surface tension. The temperature and system size dependence of the premelting layer thickness calculated in this way confirms the characteristic logarithmic growth expected for the scalar field theory that the system is mapped onto through coarse-graining, though remains finite due to long-ranged interactions. Finally, from explicit simulations the existence of a premelting layer is shown to be insensitive to bulk lattice geometry, exposed crystal face, and curvature.

  20. Premelting, fluctuations, and coarse-graining of water-ice interfaces

    Science.gov (United States)

    Limmer, David T.; Chandler, David

    2014-11-01

    Using statistical field theory supplemented with molecular dynamics simulations, we consider premelting on the surface of ice as a generic consequence of broken hydrogen bonds at the boundary between the condensed and gaseous phases. A procedure for coarse-graining molecular configurations onto a continuous scalar order parameter field is discussed, which provides a convenient representation of the interface between locally crystal-like and locally liquid-like regions. A number of interfacial properties are straightforwardly evaluated using this procedure such as the average premelting thickness and surface tension. The temperature and system size dependence of the premelting layer thickness calculated in this way confirms the characteristic logarithmic growth expected for the scalar field theory that the system is mapped onto through coarse-graining, though remains finite due to long-ranged interactions. Finally, from explicit simulations the existence of a premelting layer is shown to be insensitive to bulk lattice geometry, exposed crystal face, and curvature.

  1. Premelting, fluctuations, and coarse-graining of water-ice interfaces

    International Nuclear Information System (INIS)

    Limmer, David T.; Chandler, David

    2014-01-01

    Using statistical field theory supplemented with molecular dynamics simulations, we consider premelting on the surface of ice as a generic consequence of broken hydrogen bonds at the boundary between the condensed and gaseous phases. A procedure for coarse-graining molecular configurations onto a continuous scalar order parameter field is discussed, which provides a convenient representation of the interface between locally crystal-like and locally liquid-like regions. A number of interfacial properties are straightforwardly evaluated using this procedure such as the average premelting thickness and surface tension. The temperature and system size dependence of the premelting layer thickness calculated in this way confirms the characteristic logarithmic growth expected for the scalar field theory that the system is mapped onto through coarse-graining, though remains finite due to long-ranged interactions. Finally, from explicit simulations the existence of a premelting layer is shown to be insensitive to bulk lattice geometry, exposed crystal face, and curvature

  2. Premelting, fluctuations, and coarse-graining of water-ice interfaces.

    Science.gov (United States)

    Limmer, David T; Chandler, David

    2014-11-14

    Using statistical field theory supplemented with molecular dynamics simulations, we consider premelting on the surface of ice as a generic consequence of broken hydrogen bonds at the boundary between the condensed and gaseous phases. A procedure for coarse-graining molecular configurations onto a continuous scalar order parameter field is discussed, which provides a convenient representation of the interface between locally crystal-like and locally liquid-like regions. A number of interfacial properties are straightforwardly evaluated using this procedure such as the average premelting thickness and surface tension. The temperature and system size dependence of the premelting layer thickness calculated in this way confirms the characteristic logarithmic growth expected for the scalar field theory that the system is mapped onto through coarse-graining, though remains finite due to long-ranged interactions. Finally, from explicit simulations the existence of a premelting layer is shown to be insensitive to bulk lattice geometry, exposed crystal face, and curvature.

  3. Coarse mesh finite element method for boiling water reactor physics analysis

    International Nuclear Information System (INIS)

    Ellison, P.G.

    1983-01-01

    A coarse mesh method is formulated for the solution of Boiling Water Reactor physics problems using two group diffusion theory. No fuel assembly cross-section homogenization is required; water gaps, control blades and fuel pins of varying enrichments are treated explicitly. The method combines constrained finite element discretization with infinite lattice super cell trial functions to obtain coarse mesh solutions for which the only approximations are along the boundaries between fuel assemblies. The method is applied to bench mark Boiling Water Reactor problems to obtain both the eigenvalue and detailed flux distributions. The solutions to these problems indicate the method is useful in predicting detailed power distributions and eigenvalues for Boiling Water Reactor physics problems

  4. Signal processing for ultrasonic testing of stainless steel with coarse structure

    International Nuclear Information System (INIS)

    Dahlgren, Sven; Ericsson, Lars

    2000-03-01

    Ultrasonic testing of materials with coarse grains often gives poor signal-to-noise-ratio due to backscattering from the grain boundaries. The influence of the back-scattering, being strongly dependent on the size of the grains and the wavelength used, can be reduced by suitable choice of inspection frequencies used. The actual choice can be made flexible using broad band probes in combination with digital signal processing. Furthermore, with such an approach it might be possible both to detect and size defects from the same scan. One well-known signal processing method is Split Spectrum Processing (SSP). This method can significantly reduce grain noise, but finding the optimal choice of parameters involved is difficult. The introduction of the Consecutive Polarity Coincidence (CPC) as SSP target extraction algorithm more or less solved this problem but other draw-backs such as reduced temporal resolution is inherent in SSP. Based on the experiences with SSP a new approach to grain noise reduction, based on non coherent detection (NCD), was developed at Uppsala University. The technique is evaluated, in this investigation. The NCD algorithm has for a long time been used within the field of telecommunication and is based upon detection of bandpass signals in additive Gaussian noise. To adapt the algorithm for use in NDE a two parameter transient model is used. The construction of an NCD filter includes three steps: estimation of the autocorrelation of the noise; specification of the two parameters, lower and upper frequency, of the signal prototype; computation of the filter. During the project two algorithms, based on signal entropy and signal-to-noise-ratio enhancement (SNRE), have been developed to determine the two parameters in an automated procedure. UTdata to evaluate the NCD algorithm were collected in three phases: Phase 1: Manual scanning was performed on CSS-block with ideal reflectors (laboratory environment). Tuning of the two NCD parameters was done

  5. Temporal network epidemiology

    CERN Document Server

    Holme, Petter

    2017-01-01

    This book covers recent developments in epidemic process models and related data on temporally varying networks. It is widely recognized that contact networks are indispensable for describing, understanding, and intervening to stop the spread of infectious diseases in human and animal populations; “network epidemiology” is an umbrella term to describe this research field. More recently, contact networks have been recognized as being highly dynamic. This observation, also supported by an increasing amount of new data, has led to research on temporal networks, a rapidly growing area. Changes in network structure are often informed by epidemic (or other) dynamics, in which case they are referred to as adaptive networks. This volume gathers contributions by prominent authors working in temporal and adaptive network epidemiology, a field essential to understanding infectious diseases in real society.

  6. Intra-temporal facial nerve centerline segmentation for navigated temporal bone surgery

    Science.gov (United States)

    Voormolen, Eduard H. J.; van Stralen, Marijn; Woerdeman, Peter A.; Pluim, Josien P. W.; Noordmans, Herke J.; Regli, Luca; Berkelbach van der Sprenkel, Jan W.; Viergever, Max A.

    2011-03-01

    Approaches through the temporal bone require surgeons to drill away bone to expose a target skull base lesion while evading vital structures contained within it, such as the sigmoid sinus, jugular bulb, and facial nerve. We hypothesize that an augmented neuronavigation system that continuously calculates the distance to these structures and warns if the surgeon drills too close, will aid in making safe surgical approaches. Contemporary image guidance systems are lacking an automated method to segment the inhomogeneous and complexly curved facial nerve. Therefore, we developed a segmentation method to delineate the intra-temporal facial nerve centerline from clinically available temporal bone CT images semi-automatically. Our method requires the user to provide the start- and end-point of the facial nerve in a patient's CT scan, after which it iteratively matches an active appearance model based on the shape and texture of forty facial nerves. Its performance was evaluated on 20 patients by comparison to our gold standard: manually segmented facial nerve centerlines. Our segmentation method delineates facial nerve centerlines with a maximum error along its whole trajectory of 0.40+/-0.20 mm (mean+/-standard deviation). These results demonstrate that our model-based segmentation method can robustly segment facial nerve centerlines. Next, we can investigate whether integration of this automated facial nerve delineation with a distance calculating neuronavigation interface results in a system that can adequately warn surgeons during temporal bone drilling, and effectively diminishes risks of iatrogenic facial nerve palsy.

  7. In pursuit of an accurate spatial and temporal model of biomolecules at the atomistic level: a perspective on computer simulation

    Energy Technology Data Exchange (ETDEWEB)

    Gray, Alan [The University of Edinburgh, Edinburgh EH9 3JZ, Scotland (United Kingdom); Harlen, Oliver G. [University of Leeds, Leeds LS2 9JT (United Kingdom); Harris, Sarah A., E-mail: s.a.harris@leeds.ac.uk [University of Leeds, Leeds LS2 9JT (United Kingdom); University of Leeds, Leeds LS2 9JT (United Kingdom); Khalid, Syma; Leung, Yuk Ming [University of Southampton, Southampton SO17 1BJ (United Kingdom); Lonsdale, Richard [Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr (Germany); Philipps-Universität Marburg, Hans-Meerwein Strasse, 35032 Marburg (Germany); Mulholland, Adrian J. [University of Bristol, Bristol BS8 1TS (United Kingdom); Pearson, Arwen R. [University of Leeds, Leeds LS2 9JT (United Kingdom); University of Hamburg, Hamburg (Germany); Read, Daniel J.; Richardson, Robin A. [University of Leeds, Leeds LS2 9JT (United Kingdom); The University of Edinburgh, Edinburgh EH9 3JZ, Scotland (United Kingdom)

    2015-01-01

    The current computational techniques available for biomolecular simulation are described, and the successes and limitations of each with reference to the experimental biophysical methods that they complement are presented. Despite huge advances in the computational techniques available for simulating biomolecules at the quantum-mechanical, atomistic and coarse-grained levels, there is still a widespread perception amongst the experimental community that these calculations are highly specialist and are not generally applicable by researchers outside the theoretical community. In this article, the successes and limitations of biomolecular simulation and the further developments that are likely in the near future are discussed. A brief overview is also provided of the experimental biophysical methods that are commonly used to probe biomolecular structure and dynamics, and the accuracy of the information that can be obtained from each is compared with that from modelling. It is concluded that progress towards an accurate spatial and temporal model of biomacromolecules requires a combination of all of these biophysical techniques, both experimental and computational.

  8. Visual cortex responses reflect temporal structure of continuous quasi-rhythmic sensory stimulation.

    Science.gov (United States)

    Keitel, Christian; Thut, Gregor; Gross, Joachim

    2017-02-01

    Neural processing of dynamic continuous visual input, and cognitive influences thereon, are frequently studied in paradigms employing strictly rhythmic stimulation. However, the temporal structure of natural stimuli is hardly ever fully rhythmic but possesses certain spectral bandwidths (e.g. lip movements in speech, gestures). Examining periodic brain responses elicited by strictly rhythmic stimulation might thus represent ideal, yet isolated cases. Here, we tested how the visual system reflects quasi-rhythmic stimulation with frequencies continuously varying within ranges of classical theta (4-7Hz), alpha (8-13Hz) and beta bands (14-20Hz) using EEG. Our findings substantiate a systematic and sustained neural phase-locking to stimulation in all three frequency ranges. Further, we found that allocation of spatial attention enhances EEG-stimulus locking to theta- and alpha-band stimulation. Our results bridge recent findings regarding phase locking ("entrainment") to quasi-rhythmic visual input and "frequency-tagging" experiments employing strictly rhythmic stimulation. We propose that sustained EEG-stimulus locking can be considered as a continuous neural signature of processing dynamic sensory input in early visual cortices. Accordingly, EEG-stimulus locking serves to trace the temporal evolution of rhythmic as well as quasi-rhythmic visual input and is subject to attentional bias. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  9. The effect of STDP temporal kernel structure on the learning dynamics of single excitatory and inhibitory synapses.

    Directory of Open Access Journals (Sweden)

    Yotam Luz

    Full Text Available Spike-Timing Dependent Plasticity (STDP is characterized by a wide range of temporal kernels. However, much of the theoretical work has focused on a specific kernel - the "temporally asymmetric Hebbian" learning rules. Previous studies linked excitatory STDP to positive feedback that can account for the emergence of response selectivity. Inhibitory plasticity was associated with negative feedback that can balance the excitatory and inhibitory inputs. Here we study the possible computational role of the temporal structure of the STDP. We represent the STDP as a superposition of two processes: potentiation and depression. This allows us to model a wide range of experimentally observed STDP kernels, from Hebbian to anti-Hebbian, by varying a single parameter. We investigate STDP dynamics of a single excitatory or inhibitory synapse in purely feed-forward architecture. We derive a mean-field-Fokker-Planck dynamics for the synaptic weight and analyze the effect of STDP structure on the fixed points of the mean field dynamics. We find a phase transition along the Hebbian to anti-Hebbian parameter from a phase that is characterized by a unimodal distribution of the synaptic weight, in which the STDP dynamics is governed by negative feedback, to a phase with positive feedback characterized by a bimodal distribution. The critical point of this transition depends on general properties of the STDP dynamics and not on the fine details. Namely, the dynamics is affected by the pre-post correlations only via a single number that quantifies its overlap with the STDP kernel. We find that by manipulating the STDP temporal kernel, negative feedback can be induced in excitatory synapses and positive feedback in inhibitory. Moreover, there is an exact symmetry between inhibitory and excitatory plasticity, i.e., for every STDP rule of inhibitory synapse there exists an STDP rule for excitatory synapse, such that their dynamics is identical.

  10. On the Spatial and Temporal Sampling Errors of Remotely Sensed Precipitation Products

    Directory of Open Access Journals (Sweden)

    Ali Behrangi

    2017-11-01

    Full Text Available Observation with coarse spatial and temporal sampling can cause large errors in quantification of the amount, intensity, and duration of precipitation events. In this study, the errors resulting from temporal and spatial sampling of precipitation events were quantified and examined using the latest version (V4 of the Global Precipitation Measurement (GPM mission integrated multi-satellite retrievals for GPM (IMERG, which is available since spring of 2014. Relative mean square error was calculated at 0.1° × 0.1° every 0.5 h between the degraded (temporally and spatially and original IMERG products. The temporal and spatial degradation was performed by producing three-hour (T3, six-hour (T6, 0.5° × 0.5° (S5, and 1.0° × 1.0° (S10 maps. The results show generally larger errors over land than ocean, especially over mountainous regions. The relative error of T6 is almost 20% larger than T3 over tropical land, but is smaller in higher latitudes. Over land relative error of T6 is larger than S5 across all latitudes, while T6 has larger relative error than S10 poleward of 20°S–20°N. Similarly, the relative error of T3 exceeds S5 poleward of 20°S–20°N, but does not exceed S10, except in very high latitudes. Similar results are also seen over ocean, but the error ratios are generally less sensitive to seasonal changes. The results also show that the spatial and temporal relative errors are not highly correlated. Overall, lower correlations between the spatial and temporal relative errors are observed over ocean than over land. Quantification of such spatiotemporal effects provides additional insights into evaluation studies, especially when different products are cross-compared at a range of spatiotemporal scales.

  11. The geometry of generalized force matching and related information metrics in coarse-graining of molecular systems

    International Nuclear Information System (INIS)

    Kalligiannaki, Evangelia; Harmandaris, Vagelis; Katsoulakis, Markos A.; Plecháč, Petr

    2015-01-01

    Using the probabilistic language of conditional expectations, we reformulate the force matching method for coarse-graining of molecular systems as a projection onto spaces of coarse observables. A practical outcome of this probabilistic description is the link of the force matching method with thermodynamic integration. This connection provides a way to systematically construct a local mean force and to optimally approximate the potential of mean force through force matching. We introduce a generalized force matching condition for the local mean force in the sense that allows the approximation of the potential of mean force under both linear and non-linear coarse graining mappings (e.g., reaction coordinates, end-to-end length of chains). Furthermore, we study the equivalence of force matching with relative entropy minimization which we derive for general non-linear coarse graining maps. We present in detail the generalized force matching condition through applications to specific examples in molecular systems

  12. The geometry of generalized force matching and related information metrics in coarse-graining of molecular systems

    Energy Technology Data Exchange (ETDEWEB)

    Kalligiannaki, Evangelia, E-mail: ekalligian@tem.uoc.gr [Department of Mathematics and Applied Mathematics, University of Crete, 70013 Heraklion (Greece); Harmandaris, Vagelis, E-mail: harman@uoc.gr [Department of Mathematics and Applied Mathematics, University of Crete, 70013 Heraklion (Greece); Institute of Applied and Computational Mathematics (IACM), Foundation for Research and Technology Hellas (FORTH), IACM/FORTH, GR-71110 Heraklion (Greece); Katsoulakis, Markos A., E-mail: markos@math.umass.edu [Department of Mathematics and Statistics, University of Massachusetts, Amherst, Massachusetts 01003 (United States); Plecháč, Petr, E-mail: plechac@math.udel.edu [Department of Mathematical Sciences, University of Delaware, Newark, Delaware 19716 (United States)

    2015-08-28

    Using the probabilistic language of conditional expectations, we reformulate the force matching method for coarse-graining of molecular systems as a projection onto spaces of coarse observables. A practical outcome of this probabilistic description is the link of the force matching method with thermodynamic integration. This connection provides a way to systematically construct a local mean force and to optimally approximate the potential of mean force through force matching. We introduce a generalized force matching condition for the local mean force in the sense that allows the approximation of the potential of mean force under both linear and non-linear coarse graining mappings (e.g., reaction coordinates, end-to-end length of chains). Furthermore, we study the equivalence of force matching with relative entropy minimization which we derive for general non-linear coarse graining maps. We present in detail the generalized force matching condition through applications to specific examples in molecular systems.

  13. Coarse Point Cloud Registration by Egi Matching of Voxel Clusters

    Science.gov (United States)

    Wang, Jinhu; Lindenbergh, Roderik; Shen, Yueqian; Menenti, Massimo

    2016-06-01

    Laser scanning samples the surface geometry of objects efficiently and records versatile information as point clouds. However, often more scans are required to fully cover a scene. Therefore, a registration step is required that transforms the different scans into a common coordinate system. The registration of point clouds is usually conducted in two steps, i.e. coarse registration followed by fine registration. In this study an automatic marker-free coarse registration method for pair-wise scans is presented. First the two input point clouds are re-sampled as voxels and dimensionality features of the voxels are determined by principal component analysis (PCA). Then voxel cells with the same dimensionality are clustered. Next, the Extended Gaussian Image (EGI) descriptor of those voxel clusters are constructed using significant eigenvectors of each voxel in the cluster. Correspondences between clusters in source and target data are obtained according to the similarity between their EGI descriptors. The random sampling consensus (RANSAC) algorithm is employed to remove outlying correspondences until a coarse alignment is obtained. If necessary, a fine registration is performed in a final step. This new method is illustrated on scan data sampling two indoor scenarios. The results of the tests are evaluated by computing the point to point distance between the two input point clouds. The presented two tests resulted in mean distances of 7.6 mm and 9.5 mm respectively, which are adequate for fine registration.

  14. Estimating the acute health effects of coarse particulate matter accounting for exposure measurement error.

    Science.gov (United States)

    Chang, Howard H; Peng, Roger D; Dominici, Francesca

    2011-10-01

    In air pollution epidemiology, there is a growing interest in estimating the health effects of coarse particulate matter (PM) with aerodynamic diameter between 2.5 and 10 μm. Coarse PM concentrations can exhibit considerable spatial heterogeneity because the particles travel shorter distances and do not remain suspended in the atmosphere for an extended period of time. In this paper, we develop a modeling approach for estimating the short-term effects of air pollution in time series analysis when the ambient concentrations vary spatially within the study region. Specifically, our approach quantifies the error in the exposure variable by characterizing, on any given day, the disagreement in ambient concentrations measured across monitoring stations. This is accomplished by viewing monitor-level measurements as error-prone repeated measurements of the unobserved population average exposure. Inference is carried out in a Bayesian framework to fully account for uncertainty in the estimation of model parameters. Finally, by using different exposure indicators, we investigate the sensitivity of the association between coarse PM and daily hospital admissions based on a recent national multisite time series analysis. Among Medicare enrollees from 59 US counties between the period 1999 and 2005, we find a consistent positive association between coarse PM and same-day admission for cardiovascular diseases.

  15. Temporal lobe sclerosis associated with hippocampal sclerosis in temporal lobe epilepsy: neuropathological features.

    Science.gov (United States)

    Thom, Maria; Eriksson, Sofia; Martinian, Lillian; Caboclo, Luis O; McEvoy, Andrew W; Duncan, John S; Sisodiya, Sanjay M

    2009-08-01

    Widespread changes involving neocortical and mesial temporal lobe structures can be present in patients with temporal lobe epilepsy and hippocampal sclerosis. The incidence, pathology, and clinical significance of neocortical temporal lobe sclerosis (TLS) are not well characterized. We identified TLS in 30 of 272 surgically treated cases of hippocampal sclerosis. Temporal lobe sclerosis was defined by variable reduction of neurons from cortical layers II/III and laminar gliosis; it was typically accompanied by additional architectural abnormalities of layer II, that is, abnormal neuronal orientation and aggregation. Quantitative analysis including tessellation methods for the distribution of layer II neurons supported these observations. In 40% of cases, there was a gradient of TLS with more severe involvement toward the temporal pole, possibly signifying involvement of hippocampal projection pathways. There was a history of a febrile seizure as an initial precipitating injury in 73% of patients with TLS compared with 36% without TLS; no other clinical differences between TLS and non-TLS cases were identified. Temporal lobe sclerosis was not evident preoperatively by neuroimaging. No obvious effect of TLS on seizure outcome was noted after temporal lobe resection; 73% became seizure-free at 2-year follow-up. In conclusion, approximately 11% of surgically treated hippocampal sclerosis is accompanied by TLS. Temporal lobe sclerosis is likely an acquired process with accompanying reorganizational dysplasia and an extension of mesial temporal sclerosis rather than a separate pathological entity.

  16. Fatigue damage in coarse-grained lean duplex stainless steels

    Energy Technology Data Exchange (ETDEWEB)

    Strubbia, R., E-mail: strubbia@ifir-conicet.gov.ar; Hereñú, S.; Marinelli, M.C.; Alvarez-Armas, I.

    2016-04-06

    The present investigation is focused on assessing the effect of a thermal treatment for grain coarsening on the low cycle fatigue damage evolution in two types of Lean Duplex Stainless Steels (LDSSs). The dislocation structure developed during cycling is observed by transmission electron microscopy (TEM). Additionally, a detailed analysis of short crack initiated and grown during low cycle fatigue (LCF) is performed by means of optical and scanning electron (SEM) microscopy in combination with automated electron back-scattered diffraction (EBSD) technique. Though in both coarse-grained LDSSs the short cracks nucleate in the ferrite phase, in each steels its origin is different. The embrittlement caused by the Cr{sub 2}N precipitation and the plastic activity sustained by each phase can explain this difference. The propagation behavior of the short cracks present two alternative growing mechanisms: the crack grows along a favorable slip plane with high Schmid Factor (SF) or the crack alternates between two slip systems. In both cases, the crack follows the path with the smallest tilt angle (β) at a grain boundary.

  17. Medial temporal lobe structure and cognition in individuals with schizophrenia and in their non-psychotic siblings.

    Science.gov (United States)

    Karnik-Henry, Meghana S; Wang, Lei; Barch, Deanna M; Harms, Michael P; Campanella, Carolina; Csernansky, John G

    2012-07-01

    Medial temporal lobe (MTL) structures play a central role in episodic memory. Prior studies suggest that individuals with schizophrenia have deficits in episodic memory as well as structural abnormalities of the medial temporal lobe (MTL). While correlations have been reported between MTL volume loss and episodic memory deficits in such individuals, it is not clear whether such correlations reflect the influence of the disease state or of underlying genetic influences that might contribute to risk. We used high resolution magnetic resonance imaging and probabilistic algorithms for image analysis to determine whether MTL structure, episodic memory performance and the relationship between the two differed among groups of 47 healthy control subjects, 50 control siblings, 39 schizophrenia subjects, and 33 siblings of schizophrenia subjects. High-dimensional large deformation brain mapping was used to obtain volume measures of the hippocampus. Cortical distance mapping was used to obtain volume and thickness measures of the parahippocampal gyrus (PHG) and its substructures: the entorhinal cortex (ERC), the perirhinal cortex (PRC), and the parahippocampal cortex (PHC). Neuropsychological data was used to establish an episodic memory domain score for each subject. Both schizophrenia subjects and their siblings displayed abnormalities in episodic memory performance. Siblings of individuals with schizophrenia, and to a lesser extent, individuals with schizophrenia themselves, displayed abnormalities in measures of MTL structure (volume loss or cortical thinning) as compared to control groups. Further, we observed correlations between structural measures and memory performance in both schizophrenia subjects and their siblings, but not in their respective control groups. These findings suggest that disease-specific genetic factors present in both patients and their relatives may be responsible for correlated abnormalities of MTL structure and memory impairment. The observed

  18. Intraglomerular inhibition shapes the strength and temporal structure of glomerular output.

    Science.gov (United States)

    Shao, Zuoyi; Puche, Adam C; Liu, Shaolin; Shipley, Michael T

    2012-08-01

    Odor signals are transmitted to the olfactory bulb by olfactory nerve (ON) synapses onto mitral/tufted cells (MCs) and external tufted cells (ETCs). ETCs, in turn, provide feedforward excitatory input to MCs. MC and ETCs are also regulated by inhibition: intraglomerular and interglomerular inhibitory circuits act at MC and ETC apical dendrites; granule cells (GCs) inhibit MC lateral dendrites via the MC→GC→MC circuit. We investigated the contribution of intraglomerular inhibition to MC and ETCs responses to ON input. ON input evokes initial excitation followed by early, strongly summating inhibitory postsynaptic currents (IPSCs) in MCs; this is followed by prolonged, intermittent IPSCs. The N-methyl-d-aspartate receptor antagonist dl-amino-5-phosphovaleric acid, known to suppress GABA release by GCs, reduced late IPSCs but had no effect on early IPSCs. In contrast, selective intraglomerular block of GABA(A) receptors eliminated all early IPSCs and caused a 5-fold increase in ON-evoked MC spiking and a 10-fold increase in response duration. ETCs also receive intraglomerular inhibition; blockade of inhibition doubled ETC spike responses. By reducing ETC excitatory drive and directly inhibiting MCs, intraglomerular inhibition is a key factor shaping the strength and temporal structure of MC responses to sensory input. Sensory input generates an intraglomerular excitation-inhibition sequence that limits MC spike output to a brief temporal window. Glomerular circuits may dynamically regulate this input-output window to optimize MC encoding across sniff-sampled inputs.

  19. Marine protected areas increase temporal stability of community structure, but not density or diversity, of tropical seagrass fish communities.

    Directory of Open Access Journals (Sweden)

    Elisa Alonso Aller

    Full Text Available Marine protected areas (MPAs have been shown to increase long-term temporal stability of fish communities and enhance ecosystem resilience to anthropogenic disturbance. Yet, the potential ability of MPAs to buffer effects of environmental variability at shorter time scales remains widely unknown. In the tropics, the yearly monsoon cycle is a major natural force affecting marine organisms in tropical regions, and its timing and severity are predicted to change over the coming century, with potentially severe effects on marine organisms, ecosystems and ecosystem services. Here, we assessed the ability of MPAs to buffer effects of monsoon seasonality on seagrass-associated fish communities, using a field survey in two MPAs (no-take zones and two unprotected (open-access sites around Zanzibar (Tanzania. We assessed the temporal stability of fish density and community structure within and outside MPAs during three monsoon seasons in 2014-2015, and investigated several possible mechanisms that could regulate temporal stability. Our results show that MPAs did not affect fish density and diversity, but that juvenile fish densities were temporally more stable within MPAs. Second, fish community structure was more stable within MPAs for juvenile and adult fish, but not for subadult fish or the total fish community. Third, the observed effects may be due to a combination of direct and indirect (seagrass-mediated effects of seasonality and, potentially, fluctuating fishing pressure outside MPAs. In summary, these MPAs may not have the ability to enhance fish density and diversity and to buffer effects of monsoon seasonality on the whole fish community. However, they may increase the temporal stability of certain groups, such as juvenile fish. Consequently, our results question whether MPAs play a general role in the maintenance of biodiversity and ecosystem functioning under changing environmental conditions in tropical seagrass fish communities.

  20. Robustness of movement models: can models bridge the gap between temporal scales of data sets and behavioural processes?

    Science.gov (United States)

    Schlägel, Ulrike E; Lewis, Mark A

    2016-12-01

    Discrete-time random walks and their extensions are common tools for analyzing animal movement data. In these analyses, resolution of temporal discretization is a critical feature. Ideally, a model both mirrors the relevant temporal scale of the biological process of interest and matches the data sampling rate. Challenges arise when resolution of data is too coarse due to technological constraints, or when we wish to extrapolate results or compare results obtained from data with different resolutions. Drawing loosely on the concept of robustness in statistics, we propose a rigorous mathematical framework for studying movement models' robustness against changes in temporal resolution. In this framework, we define varying levels of robustness as formal model properties, focusing on random walk models with spatially-explicit component. With the new framework, we can investigate whether models can validly be applied to data across varying temporal resolutions and how we can account for these different resolutions in statistical inference results. We apply the new framework to movement-based resource selection models, demonstrating both analytical and numerical calculations, as well as a Monte Carlo simulation approach. While exact robustness is rare, the concept of approximate robustness provides a promising new direction for analyzing movement models.

  1. Sleep enforces the temporal order in memory.

    Directory of Open Access Journals (Sweden)

    Spyridon Drosopoulos

    Full Text Available BACKGROUND: Temporal sequence represents the main principle underlying episodic memory. The storage of temporal sequence information is thought to involve hippocampus-dependent memory systems, preserving temporal structure possibly via chaining of sequence elements in heteroassociative networks. Converging evidence indicates that sleep enhances the consolidation of recently acquired representations in the hippocampus-dependent declarative memory system. Yet, it is unknown if this consolidation process comprises strengthening of the temporal sequence structure of the representation as well, or is restricted to sequence elements independent of their temporal order. To address this issue we tested the influence of sleep on the strength of forward and backward associations in word-triplets. METHODOLOGY/PRINCIPAL FINDINGS: Subjects learned a list of 32 triplets of unrelated words, presented successively (A-B-C in the center of a screen, and either slept normally or stayed awake in the subsequent night. After two days, retrieval was assessed for the triplets sequentially either in a forward direction (cueing with A and B and asking for B and C, respectively or in a backward direction (cueing with C and B and asking for B and A, respectively. Memory was better for forward than backward associations (p<0.01. Sleep did not affect backward associations, but enhanced forward associations, specifically for the first (AB transitions (p<0.01, which were generally more difficult to retrieve than the second transitions. CONCLUSIONS/SIGNIFICANCE: Our data demonstrate that consolidation during sleep strengthens the original temporal sequence structure in memory, presumably as a result of a replay of new representations during sleep in forward direction. Our finding suggests that the temporally directed replay of memory during sleep, apart from strengthening those traces, could be the key mechanism that explains how temporal order is integrated and maintained in

  2. Peridynamics as a rigorous coarse-graining of atomistics for multiscale materials design

    International Nuclear Information System (INIS)

    Lehoucq, Richard B.; Aidun, John Bahram; Silling, Stewart Andrew; Sears, Mark P.; Kamm, James R.; Parks, Michael L.

    2010-01-01

    This report summarizes activities undertaken during FY08-FY10 for the LDRD Peridynamics as a Rigorous Coarse-Graining of Atomistics for Multiscale Materials Design. The goal of our project was to develop a coarse-graining of finite temperature molecular dynamics (MD) that successfully transitions from statistical mechanics to continuum mechanics. The goal of our project is to develop a coarse-graining of finite temperature molecular dynamics (MD) that successfully transitions from statistical mechanics to continuum mechanics. Our coarse-graining overcomes the intrinsic limitation of coupling atomistics with classical continuum mechanics via the FEM (finite element method), SPH (smoothed particle hydrodynamics), or MPM (material point method); namely, that classical continuum mechanics assumes a local force interaction that is incompatible with the nonlocal force model of atomistic methods. Therefore FEM, SPH, and MPM inherit this limitation. This seemingly innocuous dichotomy has far reaching consequences; for example, classical continuum mechanics cannot resolve the short wavelength behavior associated with atomistics. Other consequences include spurious forces, invalid phonon dispersion relationships, and irreconcilable descriptions/treatments of temperature. We propose a statistically based coarse-graining of atomistics via peridynamics and so develop a first of a kind mesoscopic capability to enable consistent, thermodynamically sound, atomistic-to-continuum (AtC) multiscale material simulation. Peridynamics (PD) is a microcontinuum theory that assumes nonlocal forces for describing long-range material interaction. The force interactions occurring at finite distances are naturally accounted for in PD. Moreover, PDs nonlocal force model is entirely consistent with those used by atomistics methods, in stark contrast to classical continuum mechanics. Hence, PD can be employed for mesoscopic phenomena that are beyond the realms of classical continuum mechanics and

  3. Disease and community structure: white-nose syndrome alters spatial and temporal niche partitioning in sympatric bat species

    Science.gov (United States)

    Jachowski, David S.; Dobony, Christopher A.; Coleman, Laci S.; Ford, W. Mark; Britzke, Eric R.; Rodrigue, Jane L.

    2014-01-01

    AimEmerging infectious diseases present a major perturbation with apparent direct effects such as reduced population density, extirpation and/or extinction. Comparatively less is known about the potential indirect effects of disease that likely alter community structure and larger ecosystem function. Since 2006, white-nose syndrome (WNS) has resulted in the loss of over 6 million hibernating bats in eastern North America. Considerable evidence exists concerning niche partitioning in sympatric bat species in this region, and the unprecedented, rapid decline in multiple species following WNS may provide an opportunity to observe a dramatic restructuring of the bat community.LocationWe conducted our study at Fort Drum Army Installation in Jefferson and Lewis counties, New York, USA, where WNS first impacted extant bat species in winter 2007–2008.MethodsAcoustical monitoring during 2003–2011 allowed us to test the hypothesis that spatial and temporal niche partitioning by bats was relaxed post-WNS.ResultsWe detected nine bat species pre- and post-WNS. Activity for most bat species declined post-WNS. Dramatic post-WNS declines in activity of little brown bat (Myotis lucifugus, MYLU), formerly the most abundant bat species in the region, were associated with complex, often species-specific responses by other species that generally favoured increased spatial and temporal overlap with MYLU.Main conclusionsIn addition to the obvious direct effects of disease on bat populations and activity levels, our results provide evidence that disease can have cascading indirect effects on community structure. Recent occurrence of WNS in North America, combined with multiple existing stressors, is resulting in dramatic shifts in temporal and spatial niche partitioning within bat communities. These changes might influence long-term population viability of some bat species as well as broader scale ecosystem structure and function.

  4. Disentangling the drivers of coarse woody debris behavior and carbon gas emissions during fire

    Science.gov (United States)

    Zhao, Weiwei; van der Werf, Guido R.; van Logtestijn, Richard S. P.; van Hal, Jurgen R.; Cornelissen, Johannes H. C.

    2016-04-01

    The turnover of coarse woody debris, a key terrestrial carbon pool, plays fundamental roles in global carbon cycling. Biological decomposition and fire are two main fates for dead wood turnover. Compared to slow decomposition, fire rapidly transfers organic carbon from the earth surface to the atmosphere. Both a-biotic environmental factors and biotic wood properties determine coarse wood combustion and thereby its carbon gas emissions during fire. Moisture is a key inhibitory environmental factor for fire. The properties of dead wood strongly affect how it burns either directly or indirectly through interacting with moisture. Coarse wood properties vary between plant species and between various decay stages. Moreover, if we put a piece of dead wood in the context of a forest fuel bed, the soil and wood contact might also greatly affect their fire behavior. Using controlled laboratory burns, we disentangled the effects of all these driving factors: tree species (one gymnosperms needle-leaf species, three angiosperms broad-leaf species), wood decay stages (freshly dead, middle decayed, very strongly decayed), moisture content (air-dried, 30% moisture content in mass), and soil-wood contact (on versus 3cm above the ground surface) on dead wood flammability and carbon gas efflux (CO2 and CO released in grams) during fire. Wood density was measured for all coarse wood samples used in our experiment. We found that compared to other drivers, wood decay stages have predominant positive effects on coarse wood combustion (for wood mass burned, R2=0.72 when air-dried and R2=0.52 at 30% moisture content) and associated carbon gas emissions (for CO2andCO (g) released, R2=0.55 when air-dried and R2=0.42 at 30% moisture content) during fire. Thus, wood decay accelerates wood combustion and its CO2 and CO emissions during fire, which can be mainly attributed to the decreasing wood density (for wood mass burned, R2=0.91 when air-dried and R2=0.63 at 30% moisture content) as wood

  5. Root-cause analysis of the better performance of the coarse-mesh finite-difference method for CANDU-type reactors

    International Nuclear Information System (INIS)

    Shen, W.

    2012-01-01

    Recent assessment results indicate that the coarse-mesh finite-difference method (FDM) gives consistently smaller percent differences in channel powers than the fine-mesh FDM when compared to the reference MCNP solution for CANDU-type reactors. However, there is an impression that the fine-mesh FDM should always give more accurate results than the coarse-mesh FDM in theory. To answer the question if the better performance of the coarse-mesh FDM for CANDU-type reactors was just a coincidence (cancellation of errors) or caused by the use of heavy water or the use of lattice-homogenized cross sections for the cluster fuel geometry in the diffusion calculation, three benchmark problems were set up with three different fuel lattices: CANDU, HWR and PWR. These benchmark problems were then used to analyze the root cause of the better performance of the coarse-mesh FDM for CANDU-type reactors. The analyses confirm that the better performance of the coarse-mesh FDM for CANDU-type reactors is mainly caused by the use of lattice-homogenized cross sections for the sub-meshes of the cluster fuel geometry in the diffusion calculation. Based on the analyses, it is recommended to use 2 x 2 coarse-mesh FDM to analyze CANDU-type reactors when lattice-homogenized cross sections are used in the core analysis. (authors)

  6. Root-cause analysis of the better performance of the coarse-mesh finite-difference method for CANDU-type reactors

    Energy Technology Data Exchange (ETDEWEB)

    Shen, W. [Candu Energy Inc., 2285 Speakman Dr., Mississauga, ON L5B 1K (Canada)

    2012-07-01

    Recent assessment results indicate that the coarse-mesh finite-difference method (FDM) gives consistently smaller percent differences in channel powers than the fine-mesh FDM when compared to the reference MCNP solution for CANDU-type reactors. However, there is an impression that the fine-mesh FDM should always give more accurate results than the coarse-mesh FDM in theory. To answer the question if the better performance of the coarse-mesh FDM for CANDU-type reactors was just a coincidence (cancellation of errors) or caused by the use of heavy water or the use of lattice-homogenized cross sections for the cluster fuel geometry in the diffusion calculation, three benchmark problems were set up with three different fuel lattices: CANDU, HWR and PWR. These benchmark problems were then used to analyze the root cause of the better performance of the coarse-mesh FDM for CANDU-type reactors. The analyses confirm that the better performance of the coarse-mesh FDM for CANDU-type reactors is mainly caused by the use of lattice-homogenized cross sections for the sub-meshes of the cluster fuel geometry in the diffusion calculation. Based on the analyses, it is recommended to use 2 x 2 coarse-mesh FDM to analyze CANDU-type reactors when lattice-homogenized cross sections are used in the core analysis. (authors)

  7. Multi-scale coarse-graining for the study of assembly pathways in DNA-brick self-assembly

    Science.gov (United States)

    Fonseca, Pedro; Romano, Flavio; Schreck, John S.; Ouldridge, Thomas E.; Doye, Jonathan P. K.; Louis, Ard A.

    2018-04-01

    Inspired by recent successes using single-stranded DNA tiles to produce complex structures, we develop a two-step coarse-graining approach that uses detailed thermodynamic calculations with oxDNA, a nucleotide-based model of DNA, to parametrize a coarser kinetic model that can reach the time and length scales needed to study the assembly mechanisms of these structures. We test the model by performing a detailed study of the assembly pathways for a two-dimensional target structure made up of 334 unique strands each of which are 42 nucleotides long. Without adjustable parameters, the model reproduces a critical temperature for the formation of the assembly that is close to the temperature at which assembly first occurs in experiments. Furthermore, the model allows us to investigate in detail the nucleation barriers and the distribution of critical nucleus shapes for the assembly of a single target structure. The assembly intermediates are compact and highly connected (although not maximally so), and classical nucleation theory provides a good fit to the height and shape of the nucleation barrier at temperatures close to where assembly first occurs.

  8. Coarse-grained/molecular mechanics of the TAS2R38 bitter taste receptor: experimentally-validated detailed structural prediction of agonist binding.

    Directory of Open Access Journals (Sweden)

    Alessandro Marchiori

    Full Text Available Bitter molecules in humans are detected by ∼25 G protein-coupled receptors (GPCRs. The lack of atomic resolution structure for any of them is complicating an in depth understanding of the molecular mechanisms underlying bitter taste perception. Here, we investigate the molecular determinants of the interaction of the TAS2R38 bitter taste receptor with its agonists phenylthiocarbamide (PTC and propylthiouracil (PROP. We use the recently developed hybrid Molecular Mechanics/Coarse Grained (MM/CG method tailored specifically for GPCRs. The method, through an extensive exploration of the conformational space in the binding pocket, allows the identification of several residues important for agonist binding that would have been very difficult to capture from the standard bioinformatics/docking approach. Our calculations suggest that both agonists bind to Asn103, Phe197, Phe264 and Trp201, whilst they do not interact with the so-called extra cellular loop 2, involved in cis-retinal binding in the GPCR rhodopsin. These predictions are consistent with data sets based on more than 20 site-directed mutagenesis and functional calcium imaging experiments of TAS2R38. The method could be readily used for other GPCRs for which experimental information is currently lacking.

  9. Network topology exploration of mesh-based coarse-grain reconfigurable architectures

    NARCIS (Netherlands)

    Bansal, N.; Gupta, S.; Dutt, N.D.; Nicolau, A.; Gupta, R.

    2004-01-01

    Several coarse-grain reconfigurable architectures proposed recently consist of a large number of processing elements (PEs) connected in a mesh-like network topology. We study the effects of three aspects of network topology exploration on the performance of applications on these architectures: (a)

  10. DECK: Distance and environment-dependent, coarse-grained, knowledge-based potentials for protein-protein docking

    Directory of Open Access Journals (Sweden)

    Vakser Ilya A

    2011-07-01

    Full Text Available Abstract Background Computational approaches to protein-protein docking typically include scoring aimed at improving the rank of the near-native structure relative to the false-positive matches. Knowledge-based potentials improve modeling of protein complexes by taking advantage of the rapidly increasing amount of experimentally derived information on protein-protein association. An essential element of knowledge-based potentials is defining the reference state for an optimal description of the residue-residue (or atom-atom pairs in the non-interaction state. Results The study presents a new Distance- and Environment-dependent, Coarse-grained, Knowledge-based (DECK potential for scoring of protein-protein docking predictions. Training sets of protein-protein matches were generated based on bound and unbound forms of proteins taken from the DOCKGROUND resource. Each residue was represented by a pseudo-atom in the geometric center of the side chain. To capture the long-range and the multi-body interactions, residues in different secondary structure elements at protein-protein interfaces were considered as different residue types. Five reference states for the potentials were defined and tested. The optimal reference state was selected and the cutoff effect on the distance-dependent potentials investigated. The potentials were validated on the docking decoys sets, showing better performance than the existing potentials used in scoring of protein-protein docking results. Conclusions A novel residue-based statistical potential for protein-protein docking was developed and validated on docking decoy sets. The results show that the scoring function DECK can successfully identify near-native protein-protein matches and thus is useful in protein docking. In addition to the practical application of the potentials, the study provides insights into the relative utility of the reference states, the scope of the distance dependence, and the coarse-graining of

  11. Augmenting Bag-of-Words: Data-Driven Discovery of Temporal and Structural Information for Activity Recognition

    OpenAIRE

    Bettadapura, Vinay; Schindler, Grant; Plotz, Thomaz; Essa, Irfan

    2015-01-01

    We present data-driven techniques to augment Bag of Words (BoW) models, which allow for more robust modeling and recognition of complex long-term activities, especially when the structure and topology of the activities are not known a priori. Our approach specifically addresses the limitations of standard BoW approaches, which fail to represent the underlying temporal and causal information that is inherent in activity streams. In addition, we also propose the use of randomly sampled regular ...

  12. Multilevel Methods for Elliptic Problems with Highly Varying Coefficients on Nonaligned Coarse Grids

    Energy Technology Data Exchange (ETDEWEB)

    Scheichl, Robert [Univ. of Bath (United Kingdom). Dept. of Mathematical Sciences; Vassilevski, Panayot S. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Zikatanov, Ludmil T. [Pennsylvania State Univ., University Park, PA (United States). Dept. of Mathematics

    2012-06-21

    We generalize the analysis of classical multigrid and two-level overlapping Schwarz methods for 2nd order elliptic boundary value problems to problems with large discontinuities in the coefficients that are not resolved by the coarse grids or the subdomain partition. The theoretical results provide a recipe for designing hierarchies of standard piecewise linear coarse spaces such that the multigrid convergence rate and the condition number of the Schwarz preconditioned system do not depend on the coefficient variation or on any mesh parameters. One assumption we have to make is that the coarse grids are sufficiently fine in the vicinity of cross points or where regions with large diffusion coefficients are separated by a narrow region where the coefficient is small. We do not need to align them with possible discontinuities in the coefficients. The proofs make use of novel stable splittings based on weighted quasi-interpolants and weighted Poincaré-type inequalities. Finally, numerical experiments are included that illustrate the sharpness of the theoretical bounds and the necessity of the technical assumptions.

  13. Coarse Grained Transport Model for Neutrals in Turbulent SOL Plasmas

    Energy Technology Data Exchange (ETDEWEB)

    Marandet, Y.; Mekkaoui, A.; Genesio, P.; Rosato, J.; Capes, H.; Godbert-Mouret, L.; Koubiti, M.; Stamm, R., E-mail: yannick.marandet@univ-amu.fr [PIIM, CNRS/Aix-Marseille University, Marseille (France); Reiter, D.; Boerner, P. [IEK4, FZJ, Juelich (Germany)

    2012-09-15

    Full text: Edge plasmas of magnetic fusion devices exhibit strong intermittent turbulence, which governs perpendicular transport of particles and heat. Turbulent fluxes result from the coarse graining procedure used to derive the transport equation, which entails time averaging of the underlying equations governing the turbulent evolution of the electron and ion fluids. In previous works, we have pointed out that this averaging is not carried out on the Boltzmann equation that describes the transport of neutral particles (atoms, molecules) in current edge code suites (such as SOLPS). Since fluctuations in the far SOL are of order unity, calculating the transport of neutral particles, hence the source terms in plasma fluid equations, in the average plasma background might lead to misleading results. In particular, retaining the effects of fluctuations could affect the estimation of the importance of main chamber recycling, hence first wall sputtering by charge exchange atoms, as well as main chamber impurity contamination and transport. In this contribution, we obtain an exact coarse-grained equation for the average neutral density, assuming that density fluctuations are described by multivariate Gamma statistics. This equation is a scattering free Boltzmann equation, where the ionization rate has been renormalized to account for fluctuations. The coarse grained transport model for neutrals has been implemented in the EIRENE code, and applications in 2D geometry with ITER relevant plasma parameters are presented. Our results open the way for the implementation of the effects of turbulent fluctuations on the transport of neutral particles in coupled plasma/neutral edge codes like B2-EIRENE. (author)

  14. Comparison of non-parametric methods for ungrouping coarsely aggregated data

    DEFF Research Database (Denmark)

    Rizzi, Silvia; Thinggaard, Mikael; Engholm, Gerda

    2016-01-01

    group at the highest ages. When histogram intervals are too coarse, information is lost and comparison between histograms with different boundaries is arduous. In these cases it is useful to estimate detailed distributions from grouped data. Methods From an extensive literature search we identify five...

  15. Improved Parameters for the Martini Coarse-Grained Protein Force Field

    NARCIS (Netherlands)

    de Jong, Djurre H.; Singh, Gurpreet; Bennett, W. F. Drew; Arnarez, Clement; Wassenaar, Tsjerk A.; Schafer, Lars V.; Periole, Xavier; Tieleman, D. Peter; Marrink, Siewert J.

    The Martini coarse-grained force field has been successfully used for simulating a wide range of (bio)molecular systems. Recent progress in our ability to test the model against fully atomistic force fields, however, has revealed some shortcomings. Most notable, phenylalanine and proline were too

  16. Can Morphing Methods Predict Intermediate Structures?

    Science.gov (United States)

    Weiss, Dahlia R.; Levitt, Michael

    2009-01-01

    Movement is crucial to the biological function of many proteins, yet crystallographic structures of proteins can give us only a static snapshot. The protein dynamics that are important to biological function often happen on a timescale that is unattainable through detailed simulation methods such as molecular dynamics as they often involve crossing high-energy barriers. To address this coarse-grained motion, several methods have been implemented as web servers in which a set of coordinates is usually linearly interpolated from an initial crystallographic structure to a final crystallographic structure. We present a new morphing method that does not extrapolate linearly and can therefore go around high-energy barriers and which can produce different trajectories between the same two starting points. In this work, we evaluate our method and other established coarse-grained methods according to an objective measure: how close a coarse-grained dynamics method comes to a crystallographically determined intermediate structure when calculating a trajectory between the initial and final crystal protein structure. We test this with a set of five proteins with at least three crystallographically determined on-pathway high-resolution intermediate structures from the Protein Data Bank. For simple hinging motions involving a small conformational change, segmentation of the protein into two rigid sections outperforms other more computationally involved methods. However, large-scale conformational change is best addressed using a nonlinear approach and we suggest that there is merit in further developing such methods. PMID:18996395

  17. Modeling respiration from snags and coarse woody debris before and after an invasive gypsy moth disturbance

    Science.gov (United States)

    Heidi J. Renninger; Nicholas Carlo; Kenneth L. Clark; Karina V.R. Schäfer

    2014-01-01

    Although snags and coarse woody debris are a small component of ecosystem respiration, disturbances can significantly increase the mass and respiration from these carbon (C) pools. The objectives of this study were to (1) measure respiration rates of snags and coarse woody debris throughout the year in a forest previously defoliated by gypsy moths, (2) develop models...

  18. Evaluation of coarse scale land surface remote sensing albedo product over rugged terrain

    Science.gov (United States)

    Wen, J.; Xinwen, L.; You, D.; Dou, B.

    2017-12-01

    Satellite derived Land surface albedo is an essential climate variable which controls the earth energy budget and it can be used in applications such as climate change, hydrology, and numerical weather prediction. The accuracy and uncertainty of surface albedo products should be evaluated with a reliable reference truth data prior to applications. And more literatures investigated the validation methods about the albedo validation in a flat or homogenous surface. However, the albedo performance over rugged terrain is still unknow due to the validation method limited. A multi-validation strategy is implemented to give a comprehensive albedo validation, which will involve the high resolution albedo processing, high resolution albedo validation based on in situ albedo, and the method to upscale the high resolution albedo to a coarse scale albedo. Among them, the high resolution albedo generation and the upscale method is the core step for the coarse scale albedo validation. In this paper, the high resolution albedo is generated by Angular Bin algorithm. And a albedo upscale method over rugged terrain is developed to obtain the coarse scale albedo truth. The in situ albedo located 40 sites in mountain area are selected globally to validate the high resolution albedo, and then upscaled to the coarse scale albedo by the upscale method. This paper takes MODIS and GLASS albedo product as a example, and the prelimarily results show the RMSE of MODIS and GLASS albedo product over rugged terrain are 0.047 and 0.057, respectively under the RMSE with 0.036 of high resolution albedo.

  19. Effect of acicular ferrite formation on grain refinement in the coarse-grained region of heat-affected zone

    International Nuclear Information System (INIS)

    Wan, X.L.; Wei, R.; Wu, K.M.

    2010-01-01

    The microstructure of acicular ferrite and its formation for the grain refinement of coarse-grained region of heat-affected zone of high strength low-alloy bainite steels were studied using three-dimensional reconstruction technique. Crystallographic grain size was analyzed by means of electron backscatter diffraction. It was revealed that the microstructure in the coarse-grained region of the heat-affected zone consisted of predominantly bainite packets and a small proportion of acicular ferrite. Acicular ferrite was of lath or plate-like rather than needle or rod-like morphology. Tempering of the coarse-grained region of heat-affected zone showed that the acicular ferrite was more stable than the bainite, indicating that the acicular ferrite was formed prior to bainite. The acicular ferrite laths or plates divided the prior austenite grains into smaller and separate regions, and confining the bainite transformed at lower temperatures in the smaller regions and hence leading to the grain refinement in the coarse-grained region of the heat-affected zone.

  20. Effect of acicular ferrite formation on grain refinement in the coarse-grained region of heat-affected zone

    Energy Technology Data Exchange (ETDEWEB)

    Wan, X.L.; Wei, R. [Institute of Advanced Steels and Welding Technology, Hubei Provincial Key Laboratory for Systems Science on Metallurgical Processing, Key Laboratory for Ferrous Metallurgy and Resources Utilization of Ministry of Education, Wuhan University of Science and Technology, Wuhan 430081 (China); Wu, K.M., E-mail: wukaiming@wust.edu.cn [Institute of Advanced Steels and Welding Technology, Hubei Provincial Key Laboratory for Systems Science on Metallurgical Processing, Key Laboratory for Ferrous Metallurgy and Resources Utilization of Ministry of Education, Wuhan University of Science and Technology, Wuhan 430081 (China)

    2010-07-15

    The microstructure of acicular ferrite and its formation for the grain refinement of coarse-grained region of heat-affected zone of high strength low-alloy bainite steels were studied using three-dimensional reconstruction technique. Crystallographic grain size was analyzed by means of electron backscatter diffraction. It was revealed that the microstructure in the coarse-grained region of the heat-affected zone consisted of predominantly bainite packets and a small proportion of acicular ferrite. Acicular ferrite was of lath or plate-like rather than needle or rod-like morphology. Tempering of the coarse-grained region of heat-affected zone showed that the acicular ferrite was more stable than the bainite, indicating that the acicular ferrite was formed prior to bainite. The acicular ferrite laths or plates divided the prior austenite grains into smaller and separate regions, and confining the bainite transformed at lower temperatures in the smaller regions and hence leading to the grain refinement in the coarse-grained region of the heat-affected zone.

  1. Cortical Correlates of Binaural Temporal Processing Deficits in Older Adults.

    Science.gov (United States)

    Eddins, Ann Clock; Eddins, David A

    This study was designed to evaluate binaural temporal processing in young and older adults using a binaural masking level difference (BMLD) paradigm. Using behavioral and electrophysiological measures within the same listeners, a series of stimulus manipulations was used to evaluate the relative contribution of binaural temporal fine-structure and temporal envelope cues. We evaluated the hypotheses that age-related declines in the BMLD task would be more strongly associated with temporal fine-structure than envelope cues and that age-related declines in behavioral measures would be correlated with cortical auditory evoked potential (CAEP) measures. Thirty adults participated in the study, including 10 young normal-hearing, 10 older normal-hearing, and 10 older hearing-impaired adults with bilaterally symmetric, mild-to-moderate sensorineural hearing loss. Behavioral and CAEP thresholds were measured for diotic (So) and dichotic (Sπ) tonal signals presented in continuous diotic (No) narrowband noise (50-Hz wide) maskers. Temporal envelope cues were manipulated by using two different narrowband maskers; Gaussian noise (GN) with robust envelope fluctuations and low-noise noise (LNN) with minimal envelope fluctuations. The potential to use temporal fine-structure cues was controlled by varying the signal frequency (500 or 4000 Hz), thereby relying on the natural decline in phase-locking with increasing frequency. Behavioral and CAEP thresholds were similar across groups for diotic conditions, while the masking release in dichotic conditions was larger for younger than for older participants. Across all participants, BMLDs were larger for GN than LNN and for 500-Hz than for 4000-Hz conditions, where envelope and fine-structure cues were most salient, respectively. Specific age-related differences were demonstrated for 500-Hz dichotic conditions in GN and LNN, reflecting reduced binaural temporal fine-structure coding. No significant age effects were observed for 4000

  2. Effect of Temporal Neocortical Pathology on Seizure Freeness in Adult Patients with Temporal Lobe Epilepsy.

    Science.gov (United States)

    Kemerdere, Rahsan; Ahmedov, Merdin Lyutviev; Alizada, Orkhan; Yeni, Seher Naz; Oz, Buge; Tanriverdi, Taner

    2018-05-23

    Temporal lobe epilepsy (TLE) is the most common form of focal epilepsy. Focal cortical dysplasia is the most common dual pathology found in association with the hippocampal sclerosis. In this study, the effect of dual pathology on freedom from seizure was sought in patients with TLE. This study performed a retrospective analysis of patients with TLE who underwent surgery between 2010 and 2017. Histopathologic analysis was performed on patients with and without dual pathology in the temporal neocortex. Seizure outcomes were compared. A total of 54 patients with TLE were included. The rate of overall favorable seizure outcome was found to be 96.3%. In 53.7%, dual pathology was present in the temporal cortices in addition to the hippocampal sclerosis. Patients without dual pathology showed significantly greater freedom from seizure (P = 0.02). Patients without dual pathology had a significantly higher seizure-free rate after anterior temporal resection than patients with dual pathology. Resection of the temporal cortex in addition to mesial temporal structures seems to be reasonable for better seizure outcome. Copyright © 2018 Elsevier Inc. All rights reserved.

  3. A multi-temporal analysis approach for land cover mapping in support of nuclear incident response

    Science.gov (United States)

    Sah, Shagan; van Aardt, Jan A. N.; McKeown, Donald M.; Messinger, David W.

    2012-06-01

    Remote sensing can be used to rapidly generate land use maps for assisting emergency response personnel with resource deployment decisions and impact assessments. In this study we focus on constructing accurate land cover maps to map the impacted area in the case of a nuclear material release. The proposed methodology involves integration of results from two different approaches to increase classification accuracy. The data used included RapidEye scenes over Nine Mile Point Nuclear Power Station (Oswego, NY). The first step was building a coarse-scale land cover map from freely available, high temporal resolution, MODIS data using a time-series approach. In the case of a nuclear accident, high spatial resolution commercial satellites such as RapidEye or IKONOS can acquire images of the affected area. Land use maps from the two image sources were integrated using a probability-based approach. Classification results were obtained for four land classes - forest, urban, water and vegetation - using Euclidean and Mahalanobis distances as metrics. Despite the coarse resolution of MODIS pixels, acceptable accuracies were obtained using time series features. The overall accuracies using the fusion based approach were in the neighborhood of 80%, when compared with GIS data sets from New York State. The classifications were augmented using this fused approach, with few supplementary advantages such as correction for cloud cover and independence from time of year. We concluded that this method would generate highly accurate land maps, using coarse spatial resolution time series satellite imagery and a single date, high spatial resolution, multi-spectral image.

  4. Pathways of seizure propagation from the temporal to the occipital lobe.

    Science.gov (United States)

    Jacobs, Julia; Dubeau, François; Olivier, André; Andermann, Frederick

    2008-12-01

    Propagation of ictal epileptic discharges influences the clinical appearance of seizures. Fast propagation from the occipital to temporal lobe has been well described, but until now the reverse direction of spread has not been emphasized. We describe two patients who experienced ictal propagation from temporal to occipital regions. One case presented with amaurosis during a seizure with temporal onset and temporal-occipital spread. In the second, temporal-occipital spread was documented during a seizure, which continued in the occipital lobe for six minutes. Depth electrode studies suggested the temporal ictal onset of seizures in both patients. Propagation from temporal to occipital lobe structures must be considered in the assessment of patients who have seizures with both temporal and occipital features. The propagation may have predictive value for their surgical outcome. The underlying anatomical structure might be the inferior longitudinal fasciculus.

  5. Temporal Feature Integration for Music Organisation

    DEFF Research Database (Denmark)

    Meng, Anders

    2006-01-01

    This Ph.D. thesis focuses on temporal feature integration for music organisation. Temporal feature integration is the process of combining all the feature vectors of a given time-frame into a single new feature vector in order to capture relevant information in the frame. Several existing methods...... for handling sequences of features are formulated in the temporal feature integration framework. Two datasets for music genre classification have been considered as valid test-beds for music organisation. Human evaluations of these, have been obtained to access the subjectivity on the datasets. Temporal...... ranking' approach is proposed for ranking the short-time features at larger time-scales according to their discriminative power in a music genre classification task. The multivariate AR (MAR) model has been proposed for temporal feature integration. It effectively models local dynamical structure...

  6. Intra-temporal facial nerve centerline segmentation for navigated temporal bone surgery

    NARCIS (Netherlands)

    Voormolen, E.H.J.; Stralen, van M.; Woerdeman, P.A.; Pluim, J.P.W.; Noordmans, H.J.; Regli, L.; Berkelbach van der Sprenkel, J.W.; Viergever, M.A.; Wong, K.H.; Holmes III, D.R.

    2011-01-01

    Approaches through the temporal bone require surgeons to drill away bone to expose a target skull base lesion while evading vital structures contained within it, such as the sigmoid sinus, jugular bulb, and facial nerve. We hypothesize that an augmented neuronavigation system that continuously

  7. Managing coarse woody debris in forests of the Rocky Mountains

    Science.gov (United States)

    Russell T. Graham; Alan E. Harvey; Martin F. Jurgensen; Theresa B. Jain; Jonalea R. Tonn; Deborah S. Page-Dumroese

    1994-01-01

    Recommendations for managing coarse woody debris after timber harvest were developed for 14 habitat types, ranging from ponderosa pine (Pinus ponderosa) habitat types of Arizona to subalpine fir (Abies lasiocarpa) habitat types of western Montana. Ectomycorrhizae were used as a bioindicator of healthy, productive forest soils....

  8. Mineral Elements Content of some Coarse Grains used as staple ...

    African Journals Online (AJOL)

    Analysis of mineral elements were carried out on some coarse grains used as staple food in Kano metropolis. The levels of Magnesium, Calcium, Manganese, Iron, Copper and Zinc were determined using atomic absorption spectrophotometer (AAS), and that of Sodium and Potassium were obtained using flame photometer ...

  9. Temporal Evolution of Ion Spectral Structures During a Geomagnetic Storm: Observations and Modeling

    Science.gov (United States)

    Ferradas, C. P.; Zhang, J.-C.; Spence, H. E.; Kistler, L. M.; Larsen, B. A.; Reeves, G. D.; Skoug, R. M.; Funsten, H. O.

    2018-01-01

    Using the Van Allen Probes/Helium, Oxygen, Proton, and Electron mass spectrometer, we perform a case study of the temporal evolution of ion spectral structures observed in the energy range of 1 to 50 keV throughout the geomagnetic storm of 2 October 2013. The ion spectral features are observed near the inner edge of the plasma sheet and are signatures of fresh transport from the plasma sheet into the inner magnetosphere. We find that the characteristics of the ion structures are determined by the intensity of the convection electric field. Prior to the beginning of the storm, the plasma sheet inner edge exhibits narrow nose spectral structures that vary little in energy across L values. Ion access to the inner magnetosphere during these times is limited to the nose energy bands. As convection is enhanced and large amounts of plasma are injected from the plasma sheet during the main phase of the storm, ion access occurs at a wide energy range, as no nose structures are observed. As the magnetosphere recovers from the storm, single noses and then multiple noses are observed once again. We use a model of ion drift and losses due to charge exchange to simulate the ion spectra and gain insight into the main observed features.

  10. Using phase information to enhance speckle noise reduction in the ultrasonic NDE of coarse grain materials

    Energy Technology Data Exchange (ETDEWEB)

    Lardner, Timothy; Gachagan, Anthony [Centre for Ultrasonic Engineering, University of Strathclyde, Glasgow, G1 1XW (United Kingdom); Li, Minghui [School of Engineering, University of Glasgow, Glasgow, G12 8QQ (United Kingdom)

    2014-02-18

    Materials with a coarse grain structure are becoming increasingly prevalent in industry due to their resilience to stress and corrosion. These materials are difficult to inspect with ultrasound because reflections from the grains lead to high noise levels which hinder the echoes of interest. Spatially Averaged Sub-Aperture Correlation Imaging (SASACI) is an advanced array beamforming technique that uses the cross-correlation between images from array sub-apertures to generate an image weighting matrix, in order to reduce noise levels. This paper presents a method inspired by SASACI to further improve imaging using phase information to refine focusing and reduce noise. A-scans from adjacent array elements are cross-correlated using both signal amplitude and phase to refine delay laws and minimize phase aberration. The phase-based and amplitude-based corrected images are used as inputs to a two-dimensional cross-correlation algorithm that will output a weighting matrix that can be applied to any conventional image. This approach was validated experimentally using a 5MHz array a coarse grained Inconel 625 step wedge, and compared to the Total Focusing Method (TFM). Initial results have seen SNR improvements of over 20dB compared to TFM, and a resolution that is much higher.

  11. Using phase information to enhance speckle noise reduction in the ultrasonic NDE of coarse grain materials

    Science.gov (United States)

    Lardner, Timothy; Li, Minghui; Gachagan, Anthony

    2014-02-01

    Materials with a coarse grain structure are becoming increasingly prevalent in industry due to their resilience to stress and corrosion. These materials are difficult to inspect with ultrasound because reflections from the grains lead to high noise levels which hinder the echoes of interest. Spatially Averaged Sub-Aperture Correlation Imaging (SASACI) is an advanced array beamforming technique that uses the cross-correlation between images from array sub-apertures to generate an image weighting matrix, in order to reduce noise levels. This paper presents a method inspired by SASACI to further improve imaging using phase information to refine focusing and reduce noise. A-scans from adjacent array elements are cross-correlated using both signal amplitude and phase to refine delay laws and minimize phase aberration. The phase-based and amplitude-based corrected images are used as inputs to a two-dimensional cross-correlation algorithm that will output a weighting matrix that can be applied to any conventional image. This approach was validated experimentally using a 5MHz array a coarse grained Inconel 625 step wedge, and compared to the Total Focusing Method (TFM). Initial results have seen SNR improvements of over 20dB compared to TFM, and a resolution that is much higher.

  12. Shape tracking with occlusions via coarse-to-fine region-based sobolev descent

    KAUST Repository

    Yang, Yanchao

    2015-05-01

    We present a method to track the shape of an object from video. The method uses a joint shape and appearance model of the object, which is propagated to match shape and radiance in subsequent frames, determining object shape. Self-occlusions and dis-occlusions of the object from camera and object motion pose difficulties to joint shape and appearance models in tracking. They are unable to adapt to new shape and appearance information, leading to inaccurate shape detection. In this work, we model self-occlusions and dis-occlusions in a joint shape and appearance tracking framework. Self-occlusions and the warp to propagate the model are coupled, thus we formulate a joint optimization problem. We derive a coarse-to-fine optimization method, advantageous in tracking, that initially perturbs the model by coarse perturbations before transitioning to finer-scale perturbations seamlessly. This coarse-to-fine behavior is automatically induced by gradient descent on a novel infinite-dimensional Riemannian manifold that we introduce. The manifold consists of planar parameterized regions, and the metric that we introduce is a novel Sobolev metric. Experiments on video exhibiting occlusions/dis-occlusions, complex radiance and background show that occlusion/dis-occlusion modeling leads to superior shape accuracy. © 2014 IEEE.

  13. The basis of orientation decoding in human primary visual cortex: fine- or coarse-scale biases?

    Science.gov (United States)

    Maloney, Ryan T

    2015-01-01

    Orientation signals in human primary visual cortex (V1) can be reliably decoded from the multivariate pattern of activity as measured with functional magnetic resonance imaging (fMRI). The precise underlying source of these decoded signals (whether by orientation biases at a fine or coarse scale in cortex) remains a matter of some controversy, however. Freeman and colleagues (J Neurosci 33: 19695-19703, 2013) recently showed that the accuracy of decoding of spiral patterns in V1 can be predicted by a voxel's preferred spatial position (the population receptive field) and its coarse orientation preference, suggesting that coarse-scale biases are sufficient for orientation decoding. Whether they are also necessary for decoding remains an open question, and one with implications for the broader interpretation of multivariate decoding results in fMRI studies. Copyright © 2015 the American Physiological Society.

  14. A Nonlinear Transmission Line Model of the Cochlea With Temporal Integration Accounts for Duration Effects in Threshold Fine Structure

    DEFF Research Database (Denmark)

    Verhey, Jesko L.; Mauermann, Manfred; Epp, Bastian

    2017-01-01

    For normal-hearing listeners, auditory pure-tone thresholds in quiet often show quasi periodic fluctuations when measured with a high frequency resolution, referred to as threshold fine structure. Threshold fine structure is dependent on the stimulus duration, with smaller fluctuations for short...... than for long signals. The present study demonstrates how this effect can be captured by a nonlinear and active model of the cochlear in combination with a temporal integration stage. Since this cochlear model also accounts for fine structure and connected level dependent effects, it is superior...

  15. UTP and Temporal Logic Model Checking

    Science.gov (United States)

    Anderson, Hugh; Ciobanu, Gabriel; Freitas, Leo

    In this paper we give an additional perspective to the formal verification of programs through temporal logic model checking, which uses Hoare and He Unifying Theories of Programming (UTP). Our perspective emphasizes the use of UTP designs, an alphabetised relational calculus expressed as a pre/post condition pair of relations, to verify state or temporal assertions about programs. The temporal model checking relation is derived from a satisfaction relation between the model and its properties. The contribution of this paper is that it shows a UTP perspective to temporal logic model checking. The approach includes the notion of efficiency found in traditional model checkers, which reduced a state explosion problem through the use of efficient data structures

  16. The MARTINI force field : Coarse grained model for biomolecular simulations

    NARCIS (Netherlands)

    Marrink, Siewert J.; Risselada, H. Jelger; Yefimov, Serge; Tieleman, D. Peter; de Vries, Alex H.

    2007-01-01

    We present an improved and extended version of our coarse grained lipid model. The new version, coined the MARTINI force field, is parametrized in a systematic way, based on the reproduction of partitioning free energies between polar and apolar phases of a large number of chemical compounds. To

  17. Coarse woody debris metrics in a California oak woodland

    Science.gov (United States)

    William D. Tietje; Michael A. Hardy; Christopher C. Yim

    2015-01-01

    Little information is available on the metrics of coarse woody debris (CWD) in California oak woodland, most notably at the scale of the stand and woodland type. In a remote part of the National Guard Post, Camp Roberts, that has not burned in over a half century, we tallied 314 pieces of CWD in a blue oak (Quercus douglasii)-coast live oak (

  18. Generalized Coarse-Mesh Rebalance Method for Acceleration of Neutron Transport Calculations

    International Nuclear Information System (INIS)

    Yamamoto, Akio

    2005-01-01

    This paper proposes a new acceleration method for neutron transport calculations: the generalized coarse-mesh rebalance (GCMR) method. The GCMR method is a unified scheme of the traditional coarse-mesh rebalance (CMR) and the coarse-mesh finite difference (CMFD) acceleration methods. Namely, by using an appropriate acceleration factor, formulation of the GCMR method becomes identical to that of the CMR or CMFD method. This also indicates that the convergence property of the GCMR method can be controlled by the acceleration factor since the convergence properties of the CMR and CMFD methods are generally different. In order to evaluate the convergence property of the GCMR method, a linearized Fourier analysis was carried out for a one-group homogeneous medium, and the results clarified the relationship between the acceleration factor and the spectral radius. It was also shown that the spectral radius of the GCMR method is smaller than those of the CMR and CMFD methods. Furthermore, the Fourier analysis showed that when an appropriate acceleration factor was used, the spectral radius of the GCMR method did not exceed unity in this study, which was in contrast to the results of the CMR or the CMFD method. Application of the GCMR method to practical calculations will be easy when the CMFD acceleration is already adopted in a transport code. By multiplying a suitable acceleration factor to a coefficient (D FD ) of a finite difference formulation, one can improve the numerical instability of the CMFD acceleration method

  19. Integrating what and when across the primate medial temporal lobe.

    Science.gov (United States)

    Naya, Yuji; Suzuki, Wendy A

    2011-08-05

    Episodic memory or memory for the detailed events in our lives is critically dependent on structures of the medial temporal lobe (MTL). A fundamental component of episodic memory is memory for the temporal order of items within an episode. To understand the contribution of individual MTL structures to temporal-order memory, we recorded single-unit activity and local field potential from three MTL areas (hippocampus and entorhinal and perirhinal cortex) and visual area TE as monkeys performed a temporal-order memory task. Hippocampus provided incremental timing signals from one item presentation to the next, whereas perirhinal cortex signaled the conjunction of items and their relative temporal order. Thus, perirhinal cortex appeared to integrate timing information from hippocampus with item information from visual sensory area TE.

  20. Preferred Compression Speed for Speech and Music and Its Relationship to Sensitivity to Temporal Fine Structure

    OpenAIRE

    Moore, Brian C. J.; S?k, Aleksander

    2016-01-01

    Multichannel amplitude compression is widely used in hearing aids. The preferred compression speed varies across individuals. Moore (2008) suggested that reduced sensitivity to temporal fine structure (TFS) may be associated with preference for slow compression. This idea was tested using a simulated hearing aid. It was also assessed whether preferences for compression speed depend on the type of stimulus: speech or music. Twenty-two hearing-impaired subjects were tested, and the stimulated h...

  1. Properties of Concrete with Tire Derived Aggregate Partially Replacing Coarse Aggregates.

    Science.gov (United States)

    Siringi, Gideon; Abolmaali, Ali; Aswath, Pranesh B

    2015-01-01

    Tire derived aggregate (TDA) has been proposed as a possible lightweight replacement for mineral aggregate in concrete. The role played by the amount of TDA replacing coarse aggregate as well as different treatment and additives in concrete on its properties is examined. Conventional concrete (without TDA) and concrete containing TDA are compared by examining their compressive strength based on ASTM C39, workability based on ASTM C143, splitting tensile strength based on ASTM C496, modulus of rupture (flexural strength) based on ASTM C78, and bond stress based on ASTM C234. Results indicate that while replacement of coarse aggregates with TDA results in reduction in strength, it may be mitigated with addition of silica fume to obtain the desired strength. The greatest benefit of using TDA is in the development of a higher ductile product while utilizing recycled TDA.

  2. Stability of modularity and structural keystone species in temporal cumulative plant- flower-visitor networks

    DEFF Research Database (Denmark)

    Dupont, Yoko; Olesen, Jens Mogens

    2012-01-01

    Modularity is a structural property of ecological networks, which has received much interest, but has been poorly explored. Modules are distinct subsets of species interacting strongly with each other, but sparsely with species outside the subset. Using a series of temporal cumulative networks, we...... all flowering plants and flower-visiting insect species throughout the flowering season at three dry heathland sites in Denmark. For each site, we constructed cumulative networks every 0.5 months, resulting in series of 10–12 networks per site. Numbers of interactions, and plant and insect species...... around one or two hubs. These hub species encompassed a small number of plant species, many of which acted as hubs at several study sites and throughout most of their flowering season. Thus, these plants become of key importance in maintaining the structure of their pollination network. We conclude...

  3. Global-Scale Associations of Vegetation Phenology with Rainfall and Temperature at a High Spatio-Temporal Resolution

    Directory of Open Access Journals (Sweden)

    Nicholas Clinton

    2014-08-01

    Full Text Available Phenology response to climatic variables is a vital indicator for understanding changes in biosphere processes as related to possible climate change. We investigated global phenology relationships to precipitation and land surface temperature (LST at high spatial and temporal resolution for calendar years 2008–2011. We used cross-correlation between MODIS Enhanced Vegetation Index (EVI, MODIS LST and Precipitation Estimation from Remotely Sensed Information using Artificial Neural Networks (PERSIANN gridded rainfall to map phenology relationships at 1-km spatial resolution and weekly temporal resolution. We show these data to be rich in spatiotemporal information, illustrating distinct phenology patterns as a result of complex overlapping gradients of climate, ecosystem and land use/land cover. The data are consistent with broad-scale, coarse-resolution modeled ecosystem limitations to moisture, temperature and irradiance. We suggest that high-resolution phenology data are useful as both an input and complement to land use/land cover classifiers and for understanding climate change vulnerability in natural and anthropogenic landscapes.

  4. The post-birthday world: consequences of temporal landmarks for temporal self-appraisal and motivation.

    Science.gov (United States)

    Peetz, Johanna; Wilson, Anne E

    2013-02-01

    Much as physical landmarks help structure our representation of space, temporal landmarks such as birthdays and significant calendar dates structure our perception of time, such that people may organize or categorize their lives into "chunks" separated by these markers. Categories on the temporal landscape may vary depending on what landmarks are salient at a given time. We suggest these landmarks have implications for identity and motivation. The present research examined consequences of salient temporal landmarks for perceptions of the self across time and motivation to pursue successful future selves. Studies 1 and 2 show that temporally extended selves are perceived as less connected to, and more dissimilar from, the current self when an intervening landmark event has been made salient. Study 3 addresses the proposed mechanism, demonstrating that intervening landmarks lead people to categorize pre- and postlandmark selves into separate categories more often than when the same time period contains no salient landmarks. Finally, we examined whether landmark-induced mental contrasting of present state and future desired state could increase goal-pursuit motivation (in an effort to bridge the gap between inferior present and better future states). Studies 4-6 demonstrate that landmark-induced discrepancies between current health and hoped-for future health increased participants' motivation to exercise and increased the likelihood that they acted in line with their future-oriented goals. (c) 2013 APA, all rights reserved.

  5. Markup of temporal information in electronic health records.

    Science.gov (United States)

    Hyun, Sookyung; Bakken, Suzanne; Johnson, Stephen B

    2006-01-01

    Temporal information plays a critical role in the understanding of clinical narrative (i.e., free text). We developed a representation for marking up temporal information in a narrative, consisting of five elements: 1) reference point, 2) direction, 3) number, 4) time unit, and 5) pattern. We identified 254 temporal expressions from 50 discharge summaries and represented them using our scheme. The overall inter-rater reliability among raters applying the representation model was 75 percent agreement. The model can contribute to temporal reasoning in computer systems for decision support, data mining, and process and outcomes analyses by providing structured temporal information.

  6. Dynamics of Coarse-grained Model of Filled Rubber Composite under Deformation

    Science.gov (United States)

    Hagita, Katsumi; Ueno, Shinichi; Bito, Yasumasa; Takano, Hiroshi; Doi, Masao; Morita, Hiroshi

    2010-03-01

    We presented a result of coarse-grained Molecular Dynamics simulation of filled polymer melts with Sulfur-crosslink under deformation based on the Kremer-Grest Model. Because all polymer chains are connected to one network gel, the size of simulation box under periodic boundary conditions (PBC) is set to about 33nm. We put 4 fillers, 80 polymer chains of 1024 particles, and many crosslink into the PBC box. One filler consists of 1280 particles of the C1280 fullerene structure. A repulsive force from the center of the filler is applied to the particles of C1280 in order to make a sphere whose diameter is about 15nm. Some patterns of distribution of the fillers are examined. The stress-strain curves estimated by applying a deformation to the system in simulations qualitatively agree with those in experiments. It is successful to show hysteresis on the S-S curve between elongation / release of the filled rubber.

  7. Temporal Concurrent Constraint Programming

    DEFF Research Database (Denmark)

    Valencia, Frank Dan

    Concurrent constraint programming (ccp) is a formalism for concurrency in which agents interact with one another by telling (adding) and asking (reading) information in a shared medium. Temporal ccp extends ccp by allowing agents to be constrained by time conditions. This dissertation studies...... temporal ccp by developing a process calculus called ntcc. The ntcc calculus generalizes the tcc model, the latter being a temporal ccp model for deterministic and synchronouss timed reactive systems. The calculus is built upon few basic ideas but it captures several aspects of timed systems. As tcc, ntcc...... structures, robotic devises, multi-agent systems and music applications. The calculus is provided with a denotational semantics that captures the reactive computations of processes in the presence of arbitrary environments. The denotation is proven to be fully-abstract for a substantial fragment...

  8. Fine and coarse elemental components in the urban aerosol of Sao Paulo, Brazil

    International Nuclear Information System (INIS)

    Boueres, L.C.S.; Orsini, C.M.Q.

    1981-01-01

    Using cascade impactor sampling and PIXE analysis we have measured particle size distributions for approximately 15 elements in the Sao Paulo urban atmosphere. These elements, in our case, may be classified, according to their occurrence in fine or coarse aerosol log-normal modes, into three groups: (a) soil dust reference elements (coarse particle mode): Ti, Si and Ca; (b) anthropogenic fine particle mode: Zn, Br and Pb; and (c) mixed bimodal elements: S, K, V, Cr, Mn, Ni, Cu and Fe. All of the soil dust reference elements show consistently the log-normal parameters MMAD approx. 5.5 μm and sigmasub(g) approx. 3.2 (mass median aerodynamic diameter and geometric standard deviation, respectively). Enrichment factor calculations for Ti, Si, Ca and K in the coarse particle fraction (> 2 μmad), relative to Fe and the standard crustal aerosol values of Lawson and Winchester, show that Ti and Si are mainly soil derived while Ca and K may have significant industrial components in this particle fraction (i.e. coarse mode). The fine mode parameters for the other elements show variations with element suggesting different air pollution sources (such as motor vehicles, resuspended dust, refuse burning, industrial activities, etc.) and/or different chemical pathways, which presumably could be identifiable. For example, the modal parameters for group (b) are: Zn, MMAD = 0.9 μm, sigmasub(g) = 2.2; Br, MMAD = 0.5 μm, sigmasub(g) = 4.0; Pb, MMAD = 0.6 μm, sigmasub(g) = 3.0; thus suggesting a common source (automotive) for Br and Pb, unrelated to the source of Zn (possibly refuse burning). (orig.)

  9. The Importance of Temporal and Spatial Vegetation Structure Information in Biotope Mapping Schemes: A Case Study in Helsingborg, Sweden

    Science.gov (United States)

    Gao, Tian; Qiu, Ling; Hammer, Mårten; Gunnarsson, Allan

    2012-02-01

    Temporal and spatial vegetation structure has impact on biodiversity qualities. Yet, current schemes of biotope mapping do only to a limited extend incorporate these factors in the mapping. The purpose of this study is to evaluate the application of a modified biotope mapping scheme that includes temporal and spatial vegetation structure. A refined scheme was developed based on a biotope classification, and applied to a green structure system in Helsingborg city in southern Sweden. It includes four parameters of vegetation structure: continuity of forest cover, age of dominant trees, horizontal structure, and vertical structure. The major green structure sites were determined by interpretation of panchromatic aerial photographs assisted with a field survey. A set of biotope maps was constructed on the basis of each level of modified classification. An evaluation of the scheme included two aspects in particular: comparison of species richness between long-continuity and short-continuity forests based on identification of woodland continuity using ancient woodland indicators (AWI) species and related historical documents, and spatial distribution of animals in the green space in relation to vegetation structure. The results indicate that (1) the relationship between forest continuity: according to verification of historical documents, the richness of AWI species was higher in long-continuity forests; Simpson's diversity was significantly different between long- and short-continuity forests; the total species richness and Shannon's diversity were much higher in long-continuity forests shown a very significant difference. (2) The spatial vegetation structure and age of stands influence the richness and abundance of the avian fauna and rabbits, and distance to the nearest tree and shrub was a strong determinant of presence for these animal groups. It is concluded that continuity of forest cover, age of dominant trees, horizontal and vertical structures of vegetation

  10. Microsurgical techniques in temporal lobe epilepsy.

    Science.gov (United States)

    Alonso Vanegas, Mario A; Lew, Sean M; Morino, Michiharu; Sarmento, Stenio A

    2017-04-01

    Temporal lobe resection is the most prevalent epilepsy surgery procedure. However, there is no consensus on the best surgical approach to treat temporal lobe epilepsy. Complication rates are low and efficacy is very high regarding seizures after such procedures. However, there is still ample controversy regarding the best surgical approach to warrant maximum seizure control with minimal functional deficits. We describe the most frequently used microsurgical techniques for removal of both the lateral and mesial temporal lobe structures in the treatment of medically intractable temporal lobe epilepsy (TLE) due to mesial temporal sclerosis (corticoamygdalohippocampectomy and selective amygdalohippocampectomy). The choice of surgical technique appears to remain a surgeon's preference for the near future. Meticulous surgical technique and thorough three-dimensional microsurgical knowledge are essentials for obtaining the best results. Wiley Periodicals, Inc. © 2017 International League Against Epilepsy.

  11. Histology of sheep temporal bone A histologia do osso temporal do ovino

    Directory of Open Access Journals (Sweden)

    Hormy Biavatti Soares

    2011-06-01

    Full Text Available Previous studies suggest that there is an excellent correlation between the morphology and dimensions of ear structures in sheep and human beings. AIM: To analyze and describe the histology of structures inside the temporal bone in sheep. MATERIAL AND METHODS: A total of 307 slides obtained from vertical and horizontal sections of the temporal bone of eight sheep were analyzed. Structures were classified as similar or not similar to human structures, based on cellularity and histological architecture parameters. STUDY DESIGN: Experimental. RESULTS: The study revealed similarities between sheep and humans in terms of type of epithelium, bone component, spaces in the auditory meatus, in addition to a marked histological resemblance of cellularity and that of the structures surrounding the ear. The main differences observed were the presence of an anatomic bulla, the absence of aeration in the mastoid and the inferior opening of the hypotympanum into the bulla in sheep. CONCLUSION: Based on these observations, it is possible to conclude that sheep represent an adequate option for training and research in otologic surgery.Resultados prévios apontam para uma ótima correlação entre a morfologia e as dimensões das estruturas anatômicas de ovelhas e seres humanos. OBJETIVO: Analisar e descrever a histologia das estruturas que compõem o osso temporal do ovino. MATERIAL E MÉTODO: Um total de 307 lâminas obtidas a partir de secções verticais e horizontais do osso temporal de oito ovelhas foi analisado. As estruturas foram caracterizadas como semelhantes ou não semelhantes às do ser humano, com base na celularidade e na arquitetura histológica das estruturas. DESENHO CIENTÍFICO: Experimental. RESULTADOS: Constatou-se semelhança quanto ao tipo de epitélio, componente ósseo, espaços da fenda auditiva e arquitetura, além da semelhança, em nível histológico, tanto dos componentes celulares como das estruturas contíguas ao ouvido. As

  12. Effects of oil palm shell coarse aggregate species on high strength lightweight concrete.

    Science.gov (United States)

    Yew, Ming Kun; Bin Mahmud, Hilmi; Ang, Bee Chin; Yew, Ming Chian

    2014-01-01

    The objective of this study was to investigate the effects of different species of oil palm shell (OPS) coarse aggregates on the properties of high strength lightweight concrete (HSLWC). Original and crushed OPS coarse aggregates of different species and age categories were investigated in this study. The research focused on two OPS species (dura and tenera), in which the coarse aggregates were taken from oil palm trees of the following age categories (3-5, 6-9, and 10-15 years old). The results showed that the workability and dry density of the oil palm shell concrete (OPSC) increase with an increase in age category of OPS species. The compressive strength of specimen CD3 increases significantly compared to specimen CT3 by 21.8%. The maximum achievable 28-day and 90-day compressive strength is 54 and 56 MPa, respectively, which is within the range for 10-15-year-old crushed dura OPS. The water absorption was determined to be within the range for good concrete for the different species of OPSC. In addition, the ultrasonic pulse velocity (UPV) results showed that the OPS HSLWC attain good condition at the age of 3 days.

  13. Importance of the temporal structure of movement sequences on the ability of monkeys to use serial order information.

    Science.gov (United States)

    Deffains, Marc; Legallet, Eric; Apicella, Paul

    2011-10-01

    The capacity to acquire motor skills through repeated practice of a sequence of movements underlies many everyday activities. Extensive research in humans has dealt with the importance of spatial and temporal factors on motor sequence learning, standing in contrast to the few studies available in animals, particularly in nonhuman primates. In the present experiments, we studied the effect of the serial order of stimuli and associated movements in macaque monkeys overtrained to make arm-reaching movements in response to spatially distinct visual targets. Under different conditions, the temporal structure of the motor sequence was varied by changing the duration of the interval between successive target stimuli or by adding a cue that reliably signaled the onset time of the forthcoming target stimulus. In each condition, the extent to which the monkeys are sensitive to the spatial regularities was assessed by comparing performance when stimulus locations follow a repeating sequence, as opposed to a random sequence. We observed no improvement in task performance on repeated sequence blocks, compared to random sequence blocks, when target stimuli are relatively distant from each other in time. On the other hand, the shortening of the time interval between successive target stimuli or, more efficiently, the addition of a temporal cue before the target stimulus yielded a performance advantage under repeated sequence, reflected in a decrease in the latency of arm and saccadic eye movements accompanied by an increased tendency for eye movements to occur in an anticipatory manner. Contrary to the effects on movement initiation, the serial order of stimuli and movements did not markedly affect the execution of movement. Moreover, the location of a given target in the random sequence influenced task performance based on the location of the preceding target, monkeys being faster in responding as a result of familiarity caused by extensive practice with some target transitions

  14. Modelling ventricular fibrillation coarseness during cardiopulmonary resuscitation by mixed effects stochastic differential equations.

    Science.gov (United States)

    Gundersen, Kenneth; Kvaløy, Jan Terje; Eftestøl, Trygve; Kramer-Johansen, Jo

    2015-10-15

    For patients undergoing cardiopulmonary resuscitation (CPR) and being in a shockable rhythm, the coarseness of the electrocardiogram (ECG) signal is an indicator of the state of the patient. In the current work, we show how mixed effects stochastic differential equations (SDE) models, commonly used in pharmacokinetic and pharmacodynamic modelling, can be used to model the relationship between CPR quality measurements and ECG coarseness. This is a novel application of mixed effects SDE models to a setting quite different from previous applications of such models and where using such models nicely solves many of the challenges involved in analysing the available data. Copyright © 2015 John Wiley & Sons, Ltd.

  15. An exactly solvable coarse-grained model for species diversity

    Science.gov (United States)

    Suweis, Samir; Rinaldo, Andrea; Maritan, Amos

    2012-07-01

    We present novel analytical results concerning ecosystem species diversity that stem from a proposed coarse-grained neutral model based on birth-death processes. The relevance of the problem lies in the urgency for understanding and synthesizing both theoretical results from ecological neutral theory and empirical evidence on species diversity preservation. The neutral model of biodiversity deals with ecosystems at the same trophic level, where per capita vital rates are assumed to be species independent. Closed-form analytical solutions for the neutral theory are obtained within a coarse-grained model, where the only input is the species persistence time distribution. Our results pertain to: the probability distribution function of the number of species in the ecosystem, both in transient and in stationary states; the n-point connected time correlation function; and the survival probability, defined as the distribution of time spans to local extinction for a species randomly sampled from the community. Analytical predictions are also tested on empirical data from an estuarine fish ecosystem. We find that emerging properties of the ecosystem are very robust and do not depend on specific details of the model, with implications for biodiversity and conservation biology.

  16. An exactly solvable coarse-grained model for species diversity

    International Nuclear Information System (INIS)

    Suweis, Samir; Maritan, Amos; Rinaldo, Andrea

    2012-01-01

    We present novel analytical results concerning ecosystem species diversity that stem from a proposed coarse-grained neutral model based on birth–death processes. The relevance of the problem lies in the urgency for understanding and synthesizing both theoretical results from ecological neutral theory and empirical evidence on species diversity preservation. The neutral model of biodiversity deals with ecosystems at the same trophic level, where per capita vital rates are assumed to be species independent. Closed-form analytical solutions for the neutral theory are obtained within a coarse-grained model, where the only input is the species persistence time distribution. Our results pertain to: the probability distribution function of the number of species in the ecosystem, both in transient and in stationary states; the n-point connected time correlation function; and the survival probability, defined as the distribution of time spans to local extinction for a species randomly sampled from the community. Analytical predictions are also tested on empirical data from an estuarine fish ecosystem. We find that emerging properties of the ecosystem are very robust and do not depend on specific details of the model, with implications for biodiversity and conservation biology. (paper)

  17. Relationship Between Bake Hardening, Snoek-Köster and Dislocation-Enhanced Snoek Peaks in Coarse Grained Low Carbon Steel

    Directory of Open Access Journals (Sweden)

    Li Weijuan

    2016-09-01

    Full Text Available In the present work, specimens prepared from coarse grained low carbon steel with different prestrains were baked and then, their bake hardening (BH property and internal friction were determined. TEM was used to characterize the dislocation structure in BH treated samples. The measurements of internal friction in prestrained samples and baked samples were carried out using a multifunctional internal friction apparatus. The results indicate that, in coarse grained low carbon steel, the bake hardening properties (BH values were negative, which were increased by increasing the prestrain from 2 to 5%, and then were decreased by increasing the prestrain from 5 to 10%. In the specimen with prestrain 5%, the BH value reached the maximum value and the height of Snoek-Köster peak was observed to be the maximum alike. With increasing the prestrain, both of the BH value and Snoek-Köster peak heights are similarly varied. It is concluded that Snoek-Köster and dislocation-enhanced Snoek peaks, caused by the interactions between interstitial solute carbon atoms and dislocations, can be used in further development of the bake hardening steels.

  18. Importance of the ion-pair interactions in the OPEP coarse-grained force field: parametrization and validation.

    Science.gov (United States)

    Sterpone, Fabio; Nguyen, Phuong H; Kalimeri, Maria; Derreumaux, Philippe

    2013-10-08

    We have derived new effective interactions that improve the description of ion-pairs in the OPEP coarse-grained force field without introducing explicit electrostatic terms. The iterative Boltzmann inversion method was used to extract these potentials from all atom simulations by targeting the radial distribution function of the distance between the center of mass of the side-chains. The new potentials have been tested on several systems that differ in structural properties, thermodynamic stabilities and number of ion-pairs. Our modeling, by refining the packing of the charged amino-acids, impacts the stability of secondary structure motifs and the population of intermediate states during temperature folding/unfolding; it also improves the aggregation propensity of peptides. The new version of the OPEP force field has the potentiality to describe more realistically a large spectrum of situations where salt-bridges are key interactions.

  19. Temporal Organization of Sound Information in Auditory Memory

    OpenAIRE

    Song, Kun; Luo, Huan

    2017-01-01

    Memory is a constructive and organizational process. Instead of being stored with all the fine details, external information is reorganized and structured at certain spatiotemporal scales. It is well acknowledged that time plays a central role in audition by segmenting sound inputs into temporal chunks of appropriate length. However, it remains largely unknown whether critical temporal structures exist to mediate sound representation in auditory memory. To address the issue, here we designed ...

  20. Innovations in the flotation of fine and coarse particles

    Science.gov (United States)

    Fornasiero, D.; Filippov, L. O.

    2017-07-01

    Research on the mechanisms of particle-bubble interaction has provided valuable information on how to improve the flotation of fine (100 µm) with novel flotation machines which provide higher collision and attachment efficiencies of fine particles with bubbles and lower detachment of the coarse particles. Also, new grinding methods and technologies have reduced energy consumption in mining and produced better mineral liberation and therefore flotation performance.

  1. The Effect of Morphological Characteristic of Coarse Aggregates Measured with Fractal Dimension on Asphalt Mixture’s High-Temperature Performance

    Directory of Open Access Journals (Sweden)

    Hainian Wang

    2016-01-01

    Full Text Available The morphological properties of coarse aggregates, such as shape, angularity, and surface texture, have a great influence on the mechanical performance of asphalt mixtures. This study aims to investigate the effect of coarse aggregate morphological properties on the high-temperature performance of asphalt mixtures. A modified Los Angeles (LA abrasion test was employed to produce aggregates with various morphological properties by applying abrasion cycles of 0, 200, 400, 600, 800, 1000, and 1200 on crushed angular aggregates. Based on a laboratory-developed Morphology Analysis System for Coarse Aggregates (MASCA, the morphological properties of the coarse aggregate particles were quantified using the index of fractal dimension. The high-temperature performances of the dense-graded asphalt mixture (AC-16, gap-graded stone asphalt mixture (SAC-16, and stone mastic asphalt (SMA-16 mixtures containing aggregates with different fractal dimensions were evaluated through the dynamic stability (DS test and the penetration shear test in laboratory. Good linear correlations between the fractal dimension and high-temperature indexes were obtained for all three types of mixtures. Moreover, the results also indicated that higher coarse aggregate angularity leads to stronger high-temperature shear resistance of asphalt mixtures.

  2. A probabilistic fragment-based protein structure prediction algorithm.

    Directory of Open Access Journals (Sweden)

    David Simoncini

    Full Text Available Conformational sampling is one of the bottlenecks in fragment-based protein structure prediction approaches. They generally start with a coarse-grained optimization where mainchain atoms and centroids of side chains are considered, followed by a fine-grained optimization with an all-atom representation of proteins. It is during this coarse-grained phase that fragment-based methods sample intensely the conformational space. If the native-like region is sampled more, the accuracy of the final all-atom predictions may be improved accordingly. In this work we present EdaFold, a new method for fragment-based protein structure prediction based on an Estimation of Distribution Algorithm. Fragment-based approaches build protein models by assembling short fragments from known protein structures. Whereas the probability mass functions over the fragment libraries are uniform in the usual case, we propose an algorithm that learns from previously generated decoys and steers the search toward native-like regions. A comparison with Rosetta AbInitio protocol shows that EdaFold is able to generate models with lower energies and to enhance the percentage of near-native coarse-grained decoys on a benchmark of [Formula: see text] proteins. The best coarse-grained models produced by both methods were refined into all-atom models and used in molecular replacement. All atom decoys produced out of EdaFold's decoy set reach high enough accuracy to solve the crystallographic phase problem by molecular replacement for some test proteins. EdaFold showed a higher success rate in molecular replacement when compared to Rosetta. Our study suggests that improving low resolution coarse-grained decoys allows computational methods to avoid subsequent sampling issues during all-atom refinement and to produce better all-atom models. EdaFold can be downloaded from http://www.riken.jp/zhangiru/software.html [corrected].

  3. Properties of Concrete with Tire Derived Aggregate Partially Replacing Coarse Aggregates

    Science.gov (United States)

    Siringi, Gideon; Abolmaali, Ali; Aswath, Pranesh B.

    2015-01-01

    Tire derived aggregate (TDA) has been proposed as a possible lightweight replacement for mineral aggregate in concrete. The role played by the amount of TDA replacing coarse aggregate as well as different treatment and additives in concrete on its properties is examined. Conventional concrete (without TDA) and concrete containing TDA are compared by examining their compressive strength based on ASTM C39, workability based on ASTM C143, splitting tensile strength based on ASTM C496, modulus of rupture (flexural strength) based on ASTM C78, and bond stress based on ASTM C234. Results indicate that while replacement of coarse aggregates with TDA results in reduction in strength, it may be mitigated with addition of silica fume to obtain the desired strength. The greatest benefit of using TDA is in the development of a higher ductile product while utilizing recycled TDA. PMID:26161440

  4. Making coarse grained polymer simulations quantitatively predictive for statics and dynamics

    Science.gov (United States)

    Kremer, Kurt

    2010-03-01

    By combining input from short simulation runs of rather small systems with all atomistic details together with properly adapted coarse grained models we are able quantitatively predict static and especially dynamical properties of both pure polymer melts of long fully entangled but also of systems with low molecular weight additives. Comparisons to rather different experiments such as diffusion constant measurements or NMR relaxation experiments show a remarkable quantitative agreement without any adjustable parameter. Reintroduction of chemical details into the coarse grained trajectories allows the study of long time trajectories in all atomistic detail providing the opportunity for rather different means of data analysis. References: V. Harmandaris, K. Kremer, Macromolecules, in press (2009) V. Harmandaris et al, Macromolecules, 40, 7026 (2007) B. Hess, S. Leon, N. van der Vegt, K. Kremer, Soft Matter 2, 409 (2006) D. Fritz et al, Soft Matter 5, 4556 (2009)

  5. Properties of Concrete with Tire Derived Aggregate Partially Replacing Coarse Aggregates

    Directory of Open Access Journals (Sweden)

    Gideon Siringi

    2015-01-01

    Full Text Available Tire derived aggregate (TDA has been proposed as a possible lightweight replacement for mineral aggregate in concrete. The role played by the amount of TDA replacing coarse aggregate as well as different treatment and additives in concrete on its properties is examined. Conventional concrete (without TDA and concrete containing TDA are compared by examining their compressive strength based on ASTM C39, workability based on ASTM C143, splitting tensile strength based on ASTM C496, modulus of rupture (flexural strength based on ASTM C78, and bond stress based on ASTM C234. Results indicate that while replacement of coarse aggregates with TDA results in reduction in strength, it may be mitigated with addition of silica fume to obtain the desired strength. The greatest benefit of using TDA is in the development of a higher ductile product while utilizing recycled TDA.

  6. Time series analysis of temporal networks

    Science.gov (United States)

    Sikdar, Sandipan; Ganguly, Niloy; Mukherjee, Animesh

    2016-01-01

    A common but an important feature of all real-world networks is that they are temporal in nature, i.e., the network structure changes over time. Due to this dynamic nature, it becomes difficult to propose suitable growth models that can explain the various important characteristic properties of these networks. In fact, in many application oriented studies only knowing these properties is sufficient. For instance, if one wishes to launch a targeted attack on a network, this can be done even without the knowledge of the full network structure; rather an estimate of some of the properties is sufficient enough to launch the attack. We, in this paper show that even if the network structure at a future time point is not available one can still manage to estimate its properties. We propose a novel method to map a temporal network to a set of time series instances, analyze them and using a standard forecast model of time series, try to predict the properties of a temporal network at a later time instance. To our aim, we consider eight properties such as number of active nodes, average degree, clustering coefficient etc. and apply our prediction framework on them. We mainly focus on the temporal network of human face-to-face contacts and observe that it represents a stochastic process with memory that can be modeled as Auto-Regressive-Integrated-Moving-Average (ARIMA). We use cross validation techniques to find the percentage accuracy of our predictions. An important observation is that the frequency domain properties of the time series obtained from spectrogram analysis could be used to refine the prediction framework by identifying beforehand the cases where the error in prediction is likely to be high. This leads to an improvement of 7.96% (for error level ≤20%) in prediction accuracy on an average across all datasets. As an application we show how such prediction scheme can be used to launch targeted attacks on temporal networks. Contribution to the Topical Issue

  7. A general coarse and fine mesh solution scheme for fluid flow modeling in VHTRS

    International Nuclear Information System (INIS)

    Clifford, I; Ivanov, K; Avramova, M.

    2011-01-01

    Coarse mesh Computational Fluid Dynamics (CFD) methods offer several advantages over traditional coarse mesh methods for the safety analysis of helium-cooled graphite-moderated Very High Temperature Reactors (VHTRs). This relatively new approach opens up the possibility for system-wide calculations to be carried out using a consistent set of field equations throughout the calculation, and subsequently the possibility for hybrid coarse/fine mesh or hierarchical multi scale CFD simulations. To date, a consistent methodology for hierarchical multi-scale CFD has not been developed. This paper describes work carried out in the initial development of a multi scale CFD solver intended to be used for the safety analysis of VHTRs. The VHTR is considered on any scale to consist of a homogenized two-phase mixture of fluid and stationary solid material of varying void fraction. A consistent set of conservation equations was selected such that they reduce to the single-phase conservation equations for the case where void fraction is unity. The discretization of the conservation equations uses a new pressure interpolation scheme capable of capturing the discontinuity in pressure across relatively large changes in void fraction. Based on this, a test solver was developed which supports fully unstructured meshes for three-dimensional time-dependent compressible flow problems, including buoyancy effects. For typical VHTR flow phenomena the new solver shows promise as an effective candidate for predicting the flow behavior on multiple scales, as it is capable of modeling both fine mesh single phase flows as well as coarse mesh flows in homogenized regions containing both fluid and solid materials. (author)

  8. Geostatistical investigation into the temporal evolution of spatial structure in a shallow water table

    Directory of Open Access Journals (Sweden)

    S. W. Lyon

    2006-01-01

    Full Text Available Shallow water tables near-streams often lead to saturated, overland flow generating areas in catchments in humid climates. While these saturated areas are assumed to be principal biogeochemical hot-spots and important for issues such as non-point pollution sources, the spatial and temporal behavior of shallow water tables, and associated saturated areas, is not completely understood. This study demonstrates how geostatistical methods can be used to characterize the spatial and temporal variation of the shallow water table for the near-stream region. Event-based and seasonal changes in the spatial structure of the shallow water table, which influences the spatial pattern of surface saturation and related runoff generation, can be identified and used in conjunction to characterize the hydrology of an area. This is accomplished through semivariogram analysis and indicator kriging to produce maps combining soft data (i.e., proxy information to the variable of interest representing general shallow water table patterns with hard data (i.e., actual measurements that represent variation in the spatial structure of the shallow water table per rainfall event. The area used was a hillslope in the Catskill Mountains region of New York State. The shallow water table was monitored for a 120 m×180 m near-stream region at 44 sampling locations on 15-min intervals. Outflow of the area was measured at the same time interval. These data were analyzed at a short time interval (15 min and at a long time interval (months to characterize the changes in the hydrologic behavior of the hillslope. Indicator semivariograms based on binary-transformed ground water table data (i.e., 1 if exceeding the time-variable median depth to water table and 0 if not were created for both short and long time intervals. For the short time interval, the indicator semivariograms showed a high degree of spatial structure in the shallow water table for the spring, with increased range

  9. A distance limited method for sampling downed coarse woody debris

    Science.gov (United States)

    Jeffrey H. Gove; Mark J. Ducey; Harry T. Valentine; Michael S. Williams

    2012-01-01

    A new sampling method for down coarse woody debris is proposed based on limiting the perpendicular distance from individual pieces to a randomly chosen sample point. Two approaches are presented that allow different protocols to be used to determine field measurements; estimators for each protocol are also developed. Both protocols are compared via simulation against...

  10. A multi-state coarse grained modeling approach for an intrinsically disordered peptide

    Science.gov (United States)

    Ramezanghorbani, Farhad; Dalgicdir, Cahit; Sayar, Mehmet

    2017-09-01

    Many proteins display a marginally stable tertiary structure, which can be altered via external stimuli. Since a majority of coarse grained (CG) models are aimed at structure prediction, their success for an intrinsically disordered peptide's conformational space with marginal stability and sensitivity to external stimuli cannot be taken for granted. In this study, by using the LKα 14 peptide as a test system, we demonstrate a bottom-up approach for constructing a multi-state CG model, which can capture the conformational behavior of this peptide in three distinct environments with a unique set of interaction parameters. LKα 14 is disordered in dilute solutions; however, it strictly adopts the α -helix conformation upon aggregation or when in contact with a hydrophobic/hydrophilic interface. Our bottom-up approach combines a generic base model, that is unbiased for any particular secondary structure, with nonbonded interactions which represent hydrogen bonds, electrostatics, and hydrophobic forces. We demonstrate that by using carefully designed all atom potential of mean force calculations from all three states of interest, one can get a balanced representation of the nonbonded interactions. Our CG model behaves intrinsically disordered in bulk water, folds into an α -helix in the presence of an interface or a neighboring peptide, and is stable as a tetrameric unit, successfully reproducing the all atom molecular dynamics simulations and experimental results.

  11. Comparison of coarse coal dust sampling techniques in a laboratory-simulated longwall section.

    Science.gov (United States)

    Patts, Justin R; Barone, Teresa L

    2017-05-01

    Airborne coal dust generated during mining can deposit and accumulate on mine surfaces, presenting a dust explosion hazard. When assessing dust hazard mitigation strategies for airborne dust reduction, sampling is done in high-velocity ventilation air, which is used to purge the mining face and gallery tunnel. In this environment, the sampler inlet velocity should be matched to the air stream velocity (isokinetic sampling) to prevent oversampling of coarse dust at low sampler-to-air velocity ratios. Low velocity ratios are often encountered when using low flow rate, personal sampling pumps commonly used in underground mines. In this study, with a goal of employing mine-ready equipment, a personal sampler was adapted for area sampling of coarse coal dust in high-velocity ventilation air. This was done by adapting an isokinetic nozzle to the inlet of an Institute of Occupational Medicine (Edinburgh, Scotland) sampling cassette (IOM). Collected dust masses were compared for the modified IOM isokinetic sampler (IOM-MOD), the IOM without the isokinetic nozzle, and a conventional dust sampling cassette without the cyclone on the inlet. All samplers were operated at a flow rate typical of personal sampling pumps: 2 L/min. To ensure differences between collected masses that could be attributed to sampler design and were not influenced by artifacts from dust concentration gradients, relatively uniform and repeatable dust concentrations were demonstrated in the sampling zone of the National Institute for Occupational Safety and Health experimental mine gallery. Consistent with isokinetic theory, greater differences between isokinetic and non-isokinetic sampled masses were found for larger dust volume-size distributions and higher ventilation air velocities. Since isokinetic sampling is conventionally used to determine total dust concentration, and isokinetic sampling made a difference in collected masses, the results suggest when sampling for coarse coal dust the IOM-MOD may

  12. High-field magnetic resonance imaging of the human temporal lobe

    Directory of Open Access Journals (Sweden)

    Luis M. Colon-Perez

    2015-01-01

    Conclusions: Fresh ex vivo MR imaging, along with tractography, revealed complex intra-temporal structural variation corresponding to neuronal cell body layers, dendritic fields, and axonal projection systems evident histologically. This is the first study to describe in detail the human temporal lobe structural organization using high-field MR imaging and tractography. By preserving the 3-dimensional structures of the hippocampus and surrounding structures, specific changes in anatomy may inform us about the changes that occur in TLE in relation to the disease process and structural underpinnings in epilepsy-related memory dysfunction.

  13. Spatio-temporal patterns of chlorophyll fluorescence and physiological and structural indices acquired from hyperspectral imagery as compared with carbon fluxes measured with eddy covariance

    NARCIS (Netherlands)

    Zarco-Tejada, P.J.; Morales Sierra, A.; Testi, L.; Villalobos, F.

    2013-01-01

    This study provides insight into the assessment of the spatio-temporal trends of chlorophyll fluorescence, narrow-band physiological indices, and structural indices acquired with a hyperspectral imager flown over a flux tower in a canopy characterized by small seasonal structural changes and a

  14. Homogenization-based topology optimization for high-resolution manufacturable micro-structures

    DEFF Research Database (Denmark)

    Groen, Jeroen Peter; Sigmund, Ole

    2018-01-01

    This paper presents a projection method to obtain high-resolution, manufacturable structures from efficient and coarse-scale, homogenization-based topology optimization results. The presented approach bridges coarse and fine scale, such that the complex periodic micro-structures can be represented...... by a smooth and continuous lattice on the fine mesh. A heuristic methodology allows control of the projected topology, such that a minimum length-scale on both solid and void features is ensured in the final result. Numerical examples show excellent behavior of the method, where performances of the projected...

  15. Linear mixing model applied to coarse spatial resolution data from multispectral satellite sensors

    Science.gov (United States)

    Holben, Brent N.; Shimabukuro, Yosio E.

    1993-01-01

    A linear mixing model was applied to coarse spatial resolution data from the NOAA Advanced Very High Resolution Radiometer. The reflective component of the 3.55-3.95 micron channel was used with the two reflective channels 0.58-0.68 micron and 0.725-1.1 micron to run a constrained least squares model to generate fraction images for an area in the west central region of Brazil. The fraction images were compared with an unsupervised classification derived from Landsat TM data acquired on the same day. The relationship between the fraction images and normalized difference vegetation index images show the potential of the unmixing techniques when using coarse spatial resolution data for global studies.

  16. Correlation between memory, proton magnetic resonance spectroscopy, and interictal epileptiform discharges in temporal lobe epilepsy related to mesial temporal sclerosis.

    Science.gov (United States)

    Mantoan, Marcele Araújo Silva; Caboclo, Luís Otávio Sales Ferreira; de Figueiredo Ferreira Guilhoto, Laura Maria; Lin, Katia; da Silva Noffs, Maria Helena; de Souza Silva Tudesco, Ivanda; Belzunces, Erich; Carrete, Henrique; Bussoletti, Renato Tavares; Centeno, Ricardo Silva; Sakamoto, Américo Ceiki; Yacubian, Elza Márcia Targas

    2009-11-01

    The aim of the study described here was to examine the relationship between memory function, proton magnetic resonance spectroscopy ((1)H-MRS) abnormalities, and interictal epileptiform discharge (IED) lateralization in patients with temporal lobe epilepsy (TLE) related to unilateral mesial temporal sclerosis. We assessed performance on tests of memory function and intelligence quotient (IQ) in 29 right-handed outpatients and 24 controls. IEDs were assessed on 30-minute-awake and 30-minute-sleep EEG samples. Patients had (1)H-MRS at 1.5 T. There was a negative correlation between IQ (P=0.031) and Rey Auditory Verbal Learning Test results (P=0.022) and epilepsy duration; between(1)H-MRS findings and epilepsy duration (P=0.027); and between N-acetylaspartate (NAA) levels and IEDs (P=0.006) in contralateral mesial temporal structures in the left MTS group. (1)H-MRS findings, IEDs, and verbal function were correlated. These findings suggest that IEDs and NAA/(Cho+Cr) ratios reflecting neural metabolism are closely related to verbal memory function in mesial temporal sclerosis. Higher interictal activity on the EEG was associated with a decline in total NAA in contralateral mesial temporal structures.

  17. A new technique for online measurement of total and water-soluble copper (Cu) in coarse particulate matter (PM)

    International Nuclear Information System (INIS)

    Wang, Dongbin; Shafer, Martin M.; Schauer, James J.; Sioutas, Constantinos

    2015-01-01

    This study presents a novel system for online, field measurement of copper (Cu) in ambient coarse (2.5–10 μm) particulate matter (PM). This new system utilizes two virtual impactors combined with a modified liquid impinger (BioSampler) to collect coarse PM directly as concentrated slurry samples. The total and water-soluble Cu concentrations are subsequently measured by a copper Ion Selective Electrode (ISE). Laboratory evaluation results indicated excellent collection efficiency (over 85%) for particles in the coarse PM size ranges. In the field evaluations, very good agreements for both total and water-soluble Cu concentrations were obtained between online ISE-based monitor measurements and those analyzed by means of inductively coupled plasma mass spectrometry (ICP-MS). Moreover, the field tests indicated that the Cu monitor could achieve near-continuous operation for at least 6 consecutive days (a time resolution of 2–4 h) without obvious shortcomings. - Highlights: • A novel only PM sampling and Cu measuring technology is developed. • Very good particle collection efficiency for coarse PM is observed. • Excellent agreement is obtained between Cu ISE and offline ICP-MS measurements. • The new system can be continuously operated for at least 6 consecutive days. - A new technique for online measurements of Cu in coarse PM is described

  18. Bottom-up derivation of conservative and dissipative interactions for coarse-grained molecular liquids with the conditional reversible work method

    Energy Technology Data Exchange (ETDEWEB)

    Deichmann, Gregor; Marcon, Valentina; Vegt, Nico F. A. van der, E-mail: vandervegt@csi.tu-darmstadt.de [Center of Smart Interfaces, Technische Universität Darmstadt, Alarich-Weiss-Straße 10, 64287 Darmstadt (Germany)

    2014-12-14

    Molecular simulations of soft matter systems have been performed in recent years using a variety of systematically coarse-grained models. With these models, structural or thermodynamic properties can be quite accurately represented while the prediction of dynamic properties remains difficult, especially for multi-component systems. In this work, we use constraint molecular dynamics simulations for calculating dissipative pair forces which are used together with conditional reversible work (CRW) conservative forces in dissipative particle dynamics (DPD) simulations. The combined CRW-DPD approach aims to extend the representability of CRW models to dynamic properties and uses a bottom-up approach. Dissipative pair forces are derived from fluctuations of the direct atomistic forces between mapped groups. The conservative CRW potential is obtained from a similar series of constraint dynamics simulations and represents the reversible work performed to couple the direct atomistic interactions between the mapped atom groups. Neopentane, tetrachloromethane, cyclohexane, and n-hexane have been considered as model systems. These molecular liquids are simulated with atomistic molecular dynamics, coarse-grained molecular dynamics, and DPD. We find that the CRW-DPD models reproduce the liquid structure and diffusive dynamics of the liquid systems in reasonable agreement with the atomistic models when using single-site mapping schemes with beads containing five or six heavy atoms. For a two-site representation of n-hexane (3 carbons per bead), time scale separation can no longer be assumed and the DPD approach consequently fails to reproduce the atomistic dynamics.

  19. Bottom-up derivation of conservative and dissipative interactions for coarse-grained molecular liquids with the conditional reversible work method

    International Nuclear Information System (INIS)

    Deichmann, Gregor; Marcon, Valentina; Vegt, Nico F. A. van der

    2014-01-01

    Molecular simulations of soft matter systems have been performed in recent years using a variety of systematically coarse-grained models. With these models, structural or thermodynamic properties can be quite accurately represented while the prediction of dynamic properties remains difficult, especially for multi-component systems. In this work, we use constraint molecular dynamics simulations for calculating dissipative pair forces which are used together with conditional reversible work (CRW) conservative forces in dissipative particle dynamics (DPD) simulations. The combined CRW-DPD approach aims to extend the representability of CRW models to dynamic properties and uses a bottom-up approach. Dissipative pair forces are derived from fluctuations of the direct atomistic forces between mapped groups. The conservative CRW potential is obtained from a similar series of constraint dynamics simulations and represents the reversible work performed to couple the direct atomistic interactions between the mapped atom groups. Neopentane, tetrachloromethane, cyclohexane, and n-hexane have been considered as model systems. These molecular liquids are simulated with atomistic molecular dynamics, coarse-grained molecular dynamics, and DPD. We find that the CRW-DPD models reproduce the liquid structure and diffusive dynamics of the liquid systems in reasonable agreement with the atomistic models when using single-site mapping schemes with beads containing five or six heavy atoms. For a two-site representation of n-hexane (3 carbons per bead), time scale separation can no longer be assumed and the DPD approach consequently fails to reproduce the atomistic dynamics

  20. Effects of Oil Palm Shell Coarse Aggregate Species on High Strength Lightweight Concrete

    Directory of Open Access Journals (Sweden)

    Ming Kun Yew

    2014-01-01

    Full Text Available The objective of this study was to investigate the effects of different species of oil palm shell (OPS coarse aggregates on the properties of high strength lightweight concrete (HSLWC. Original and crushed OPS coarse aggregates of different species and age categories were investigated in this study. The research focused on two OPS species (dura and tenera, in which the coarse aggregates were taken from oil palm trees of the following age categories (3–5, 6–9, and 10–15 years old. The results showed that the workability and dry density of the oil palm shell concrete (OPSC increase with an increase in age category of OPS species. The compressive strength of specimen CD3 increases significantly compared to specimen CT3 by 21.8%. The maximum achievable 28-day and 90-day compressive strength is 54 and 56 MPa, respectively, which is within the range for 10–15-year-old crushed dura OPS. The water absorption was determined to be within the range for good concrete for the different species of OPSC. In addition, the ultrasonic pulse velocity (UPV results showed that the OPS HSLWC attain good condition at the age of 3 days.

  1. An experimental study on the hazard assessment and mechanical properties of porous concrete utilizing coal bottom ash coarse aggregate in Korea.

    Science.gov (United States)

    Park, Seung Bum; Jang, Young Il; Lee, Jun; Lee, Byung Jae

    2009-07-15

    This study evaluates quality properties and toxicity of coal bottom ash coarse aggregate and analyzes mechanical properties of porous concrete depending on mixing rates of coal bottom ash. As a result, soundness and resistance to abrasion of coal bottom ash coarse aggregate were satisfied according to the standard of coarse aggregate for concrete. To satisfy the standard pertaining to chloride content, the coarse aggregates have to be washed more than twice. In regards to the result of leaching test for coal bottom ash coarse aggregate and porous concrete produced with these coarse aggregates, it was satisfied with the environment criteria. As the mixing rate of coal bottom ash increased, influence of void ratio and permeability coefficient was very little, but compressive and flexural strength decreased. When coal bottom ash was mixed over 40%, strength decreased sharply (compressive strength: by 11.7-27.1%, flexural strength: by maximum 26.4%). Also, as the mixing rate of coal bottom ash increased, it was confirmed that test specimens were destroyed by aggregate fracture more than binder fracture and interface fracture. To utilize coal bottom ash in large quantities, it is thought that an improvement method in regards to strength has to be discussed such as incorporation of reinforcing materials and improvement of aggregate hardness.

  2. Comparing non-parametric methods for ungrouping coarsely aggregated age-specific distributions

    DEFF Research Database (Denmark)

    Rizzi, Silvia; Thinggaard, Mikael; Vaupel, James W.

    2016-01-01

    Demographers have often access to vital statistics that are less than ideal for the purpose of their research. In many instances demographic data are reported in coarse histograms, where the values given are only the summation of true latent values, thereby making detailed analysis troublesome. O...

  3. Topology optimization of adaptive fluid-actuated cellular structures with arbitrary polygonal motor cells

    International Nuclear Information System (INIS)

    Lv, Jun; Tang, Liang; Li, Wenbo; Liu, Lei; Zhang, Hongwu

    2016-01-01

    This paper mainly focuses on the fast and efficient design method for plant bioinspired fluidic cellular materials and structures composed of polygonal motor cells. Here we developed a novel structural optimization method with arbitrary polygonal coarse-grid elements based on multiscale finite element frameworks. The fluidic cellular structures are meshed with irregular polygonal coarse-grid elements according to their natural size and the shape of the imbedded motor cells. The multiscale base functions of solid displacement and hydraulic pressure are then constructed to bring the small-scale information of the irregular motor cells to the large-scale simulations on the polygonal coarse-grid elements. On this basis, a new topology optimization method based on the resulting polygonal coarse-grid elements is proposed to determine the optimal distributions or number of motor cells in the smart cellular structures. Three types of optimization problems are solved according to the usages of the fluidic cellular structures. Firstly, the proposed optimization method is utilized to minimize the system compliance of the load-bearing fluidic cellular structures. Second, the method is further extended to design biomimetic compliant actuators of the fluidic cellular materials due to the fact that non-uniform volume expansions of fluid in the cells can induce elastic action. Third, the optimization problem focuses on the weight minimization of the cellular structure under the constraints for the compliance of the whole system. Several representative examples are investigated to validate the effectiveness of the proposed polygon-based topology optimization method of the smart materials. (paper)

  4. Multi-Temporal Land Cover Classification with Sequential Recurrent Encoders

    Science.gov (United States)

    Rußwurm, Marc; Körner, Marco

    2018-03-01

    Earth observation (EO) sensors deliver data with daily or weekly temporal resolution. Most land use and land cover (LULC) approaches, however, expect cloud-free and mono-temporal observations. The increasing temporal capabilities of today's sensors enables the use of temporal, along with spectral and spatial features. Domains, such as speech recognition or neural machine translation, work with inherently temporal data and, today, achieve impressive results using sequential encoder-decoder structures. Inspired by these sequence-to-sequence models, we adapt an encoder structure with convolutional recurrent layers in order to approximate a phenological model for vegetation classes based on a temporal sequence of Sentinel 2 (S2) images. In our experiments, we visualize internal activations over a sequence of cloudy and non-cloudy images and find several recurrent cells, which reduce the input activity for cloudy observations. Hence, we assume that our network has learned cloud-filtering schemes solely from input data, which could alleviate the need for tedious cloud-filtering as a preprocessing step for many EO approaches. Moreover, using unfiltered temporal series of top-of-atmosphere (TOA) reflectance data, we achieved in our experiments state-of-the-art classification accuracies on a large number of crop classes with minimal preprocessing compared to other classification approaches.

  5. Multiblob coarse-graining for mixtures of long polymers and soft colloids

    Science.gov (United States)

    Locatelli, Emanuele; Capone, Barbara; Likos, Christos N.

    2016-11-01

    Soft nanocomposites represent both a theoretical and an experimental challenge due to the high number of the microscopic constituents that strongly influence the behaviour of the systems. An effective theoretical description of such systems invokes a reduction of the degrees of freedom to be analysed, hence requiring the introduction of an efficient, quantitative, coarse-grained description. We here report on a novel coarse graining approach based on a set of transferable potentials that quantitatively reproduces properties of mixtures of linear and star-shaped homopolymeric nanocomposites. By renormalizing groups of monomers into a single effective potential between a f-functional star polymer and an homopolymer of length N0, and through a scaling argument, it will be shown how a substantial reduction of the to degrees of freedom allows for a full quantitative description of the system. Our methodology is tested upon full monomer simulations for systems of different molecular weight, proving its full predictive potential.

  6. The role of the medial temporal limbic system in processing emotions in voice and music.

    Science.gov (United States)

    Frühholz, Sascha; Trost, Wiebke; Grandjean, Didier

    2014-12-01

    Subcortical brain structures of the limbic system, such as the amygdala, are thought to decode the emotional value of sensory information. Recent neuroimaging studies, as well as lesion studies in patients, have shown that the amygdala is sensitive to emotions in voice and music. Similarly, the hippocampus, another part of the temporal limbic system (TLS), is responsive to vocal and musical emotions, but its specific roles in emotional processing from music and especially from voices have been largely neglected. Here we review recent research on vocal and musical emotions, and outline commonalities and differences in the neural processing of emotions in the TLS in terms of emotional valence, emotional intensity and arousal, as well as in terms of acoustic and structural features of voices and music. We summarize the findings in a neural framework including several subcortical and cortical functional pathways between the auditory system and the TLS. This framework proposes that some vocal expressions might already receive a fast emotional evaluation via a subcortical pathway to the amygdala, whereas cortical pathways to the TLS are thought to be equally used for vocal and musical emotions. While the amygdala might be specifically involved in a coarse decoding of the emotional value of voices and music, the hippocampus might process more complex vocal and musical emotions, and might have an important role especially for the decoding of musical emotions by providing memory-based and contextual associations. Copyright © 2014 Elsevier Ltd. All rights reserved.

  7. Experimentally induced thyrotoxicosis leads to increased connectivity in temporal lobe structures: a resting state fMRI study.

    Science.gov (United States)

    Göttlich, Martin; Heldmann, Marcus; Göbel, Anna; Dirk, Anna-Luise; Brabant, Georg; Münte, Thomas F

    2015-06-01

    Adult onset hyperthyroidism may impact on different cognitive domains, including attention and concentration, memory, perceptual function, language and executive function. Previous PET studies implicated changed functionality of limbic regions, the temporal and frontal lobes in hyperthyroidism, whereas it is unknown whether cognitive effects of hyperthyroidism may be due to changed brain connectivity. This study aimed to investigate the effect of experimentally induced short-term hyperthyroidism thyrotoxicosis on resting-state functional connectivity using functional magnetic resonance imaging. Twenty-nine healthy male right-handed subjects were examined twice, once prior and once after 8 weeks of oral administration of 250 μg levothyroxine per day. Resting-state fMRI was subjected to graph-theory based analysis methods to investigate whole-brain intrinsic functional connectivity. Despite a lack of subjective changes noticed by the subjects significant thyrotoxicosis was confirmed in all subjects. This induced a significant increase in resting-state functional connectivity specifically in the rostral temporal lobes (0.05 FDR corrected at the cluster level), which is caused by an increased connectivity to the cognitive control network. The increased connectivity between temporal poles and the cognitive control network shown here under experimental conditions supports an important function of thyroid hormones in the regulation of paralimbic structures. Copyright © 2015 Elsevier Ltd. All rights reserved.

  8. Chemical composition of free tropospheric aerosol for PM1 and coarse mode at the high alpine site Jungfraujoch

    Directory of Open Access Journals (Sweden)

    J. Cozic

    2008-01-01

    Full Text Available The chemical composition of submicron (fine mode and supermicron (coarse mode aerosol particles has been investigated at the Jungfraujoch high alpine research station (3580 m a.s.l., Switzerland as part of the GAW aerosol monitoring program since 1999. A clear seasonality was observed for all major components throughout the period with low concentrations in winter (predominantly free tropospheric aerosol and higher concentrations in summer (enhanced vertical transport of boundary layer pollutants. In addition, mass closure was attempted during intensive campaigns in March 2004, February–March 2005 and August 2005. Ionic, carbonaceous and non-refractory components of the aerosol were quantified as well as the PM1 and coarse mode total aerosol mass concentrations. A relatively low conversion factor of 1.8 for organic carbon (OC to particulate organic matter (OM was found in winter (February–March 2005. Organics, sulfate, ammonium, and nitrate were the major components of the fine aerosol fraction that were identified, while calcium and nitrate were the only two measured components contributing to the coarse mode. The aerosol mass concentrations for fine and coarse mode aerosol measured during the intensive campaigns were not typical of the long-term seasonality due largely to dynamical differences. Average fine and coarse mode concentrations during the intensive field campaigns were 1.7 μg m−3 and 2.4 μg m−3 in winter and 2.5 μg m−3 and 2.0 μg m−3 in summer, respectively. The mass balance of aerosols showed higher contributions of calcium and nitrate in the coarse mode during Saharan dust events (SDE than without SDE.

  9. Structural Optimization of Wind Turbine Rotor Blades by Multi-Level Sectional/Multibody/3DFEM Analysis

    DEFF Research Database (Denmark)

    Bottasso, C. L.; Campagnolo, F.; Croce, A.

    fully-populated cross sectional stiffness matrices. Next, a “fine”-level 3D FEM model is used for the refinement of the coarse-level solution. Improved results obtained at the level of the 3D model are utilized at the following coarse-level iteration through a heuristic modification of the design...... constraints. In addition, a buckling analysis is performed at the fine description level, which in turn affects the non-structural blade mass. The updated constraint bounds and mass make their effects felt at the next coarse-level constrained design optimization, thereby closing the loop between the coarse...

  10. Influence of canopy closure and shrub coverage on travel along coarse woody debris by Eastern chipmunks (Tamias striatus)

    Science.gov (United States)

    Patrick A. Zollner; Kevin J. Crane

    2003-01-01

    We investigated relationships between canopy closure, shrub cover and the use of coarse woody debris as a travel path by eastern chipmunks (Tamias striatus) in the north central United States. Fine scale movements of chipmunks were followed with tracking spools and the percentage of each movement path directly along coarse woody debris was recorded...

  11. Middle Temporal Gyrus Versus Inferior Temporal Gyrus Transcortical Approaches to High-Grade Astrocytomas in the Mediobasal Temporal Lobe: A Comparison of Outcomes, Functional Restoration, and Surgical Considerations.

    Science.gov (United States)

    Quinones-Hinojosa, Alfredo; Raza, Shaan M; Ahmed, Ishrat; Rincon-Torroella, Jordina; Chaichana, Kaisorn; Olivi, Alessandro

    2017-01-01

    High-grade astrocytomas of the mesial temporal lobe may pose surgical challenges. Several approaches (trans-sylvian, subtemporal, and transcortical) have been designed to circumnavigate the critical neurovascular structures and white fiber tracts that surround this area. Considering the paucity of literature on the transcortical approach for these lesions, we describe our institutional experience with transcortical approaches to Grade III/IV astrocytomas in the mesial temporal lobe. Between 1999 and 2009, 23 patients underwent surgery at the Johns Hopkins Medical Institutions for Grade III/IV astrocytomas involving the mesial temporal lobe (without involvement of the temporal neocortex). Clinical notes, operative records, and imaging were reviewed. Thirteen patients had tumors in the dominant hemisphere. All patients underwent surgery via a transcortical approach (14 via the inferior temporal gyrus and 9 via the middle temporal gyrus). Gross total resection was obtained in 92 % of the cohort. Neurological outcomes were: clinically significant stroke (2 patients), new visual deficits (2 patients), new speech deficit (1 patient); seizure control (53 %). In comparison to reported results in the literature for the transylvian and subtemporal approaches, the transcortical approach may provide the access necessary for a gross total resection with minimal neurological consequences. In our series of patients, there was no statistically significant difference in outcomes between the middle temporal gyrus versus the inferior temporal gyrus trajectories.

  12. Statistical properties of the coarse-grained velocity gradient tensor in turbulence: Monte-Carlo simulations of the tetrad model

    International Nuclear Information System (INIS)

    Pumir, Alain; Naso, Aurore

    2010-01-01

    A proper description of the velocity gradient tensor is crucial for understanding the dynamics of turbulent flows, in particular the energy transfer from large to small scales. Insight into the statistical properties of the velocity gradient tensor and into its coarse-grained generalization can be obtained with the help of a stochastic 'tetrad model' that describes the coarse-grained velocity gradient tensor based on the evolution of four points. Although the solution of the stochastic model can be formally expressed in terms of path integrals, its numerical determination in terms of the Monte-Carlo method is very challenging, as very few configurations contribute effectively to the statistical weight. Here, we discuss a strategy that allows us to solve the tetrad model numerically. The algorithm is based on the importance sampling method, which consists here of identifying and sampling preferentially the configurations that are likely to correspond to a large statistical weight, and selectively rejecting configurations with a small statistical weight. The algorithm leads to an efficient numerical determination of the solutions of the model and allows us to determine their qualitative behavior as a function of scale. We find that the moments of order n≤4 of the solutions of the model scale with the coarse-graining scale and that the scaling exponents are very close to the predictions of the Kolmogorov theory. The model qualitatively reproduces quite well the statistics concerning the local structure of the flow. However, we find that the model generally tends to predict an excess of strain compared to vorticity. Thus, our results show that while some physical aspects are not fully captured by the model, our approach leads to a very good description of several important qualitative properties of real turbulent flows.

  13. MISTICA: Minimum Spanning Tree-Based Coarse Image Alignment for Microscopy Image Sequences.

    Science.gov (United States)

    Ray, Nilanjan; McArdle, Sara; Ley, Klaus; Acton, Scott T

    2016-11-01

    Registration of an in vivo microscopy image sequence is necessary in many significant studies, including studies of atherosclerosis in large arteries and the heart. Significant cardiac and respiratory motion of the living subject, occasional spells of focal plane changes, drift in the field of view, and long image sequences are the principal roadblocks. The first step in such a registration process is the removal of translational and rotational motion. Next, a deformable registration can be performed. The focus of our study here is to remove the translation and/or rigid body motion that we refer to here as coarse alignment. The existing techniques for coarse alignment are unable to accommodate long sequences often consisting of periods of poor quality images (as quantified by a suitable perceptual measure). Many existing methods require the user to select an anchor image to which other images are registered. We propose a novel method for coarse image sequence alignment based on minimum weighted spanning trees (MISTICA) that overcomes these difficulties. The principal idea behind MISTICA is to reorder the images in shorter sequences, to demote nonconforming or poor quality images in the registration process, and to mitigate the error propagation. The anchor image is selected automatically making MISTICA completely automated. MISTICA is computationally efficient. It has a single tuning parameter that determines graph width, which can also be eliminated by the way of additional computation. MISTICA outperforms existing alignment methods when applied to microscopy image sequences of mouse arteries.

  14. Impacts into Coarse-Grained Spheres at Moderate Impact Velocities: Implications for Cratering on Asteroids and Planets

    Science.gov (United States)

    Barnouin, Olivier S.; Daly, R. Terik; Cintala, Mark J.; Crawford, David A.

    2018-01-01

    The surfaces of many planets and asteroids contain coarsely fragmental material generated by impacts or other geologic processes. The presence of such pre-existing structures may affect subsequent impacts, particularly when the width of the shock is comparable to or smaller than the size of pre-existing structures. Reasonable theoretical predictions and low speed (<300m/s) impact experiments suggest that in such targets the cratering process should be highly dissipative, which would reduce cratering efficiencies and cause a rapid decay in ejection velocity as a function of distance from the impact point. In this study, we assess whether these results apply at higher impact speeds between 0.5 and 2.5 km s-1. This study shows little change in cratering efficiency when 3.18 mm diameter glass beads are launched into targets composed of these same beads. These impacts are very efficient, and ejection velocity decays slowly as function of distance from the impact point. This slow decay in ejection velocity probably indicates a correspondingly slow decay of the shock stresses. However, these experiments reveal that initial interactions between projectile and target strongly influence the cratering process and lead to asymmetries in crater shape and ejection angles, as well as significant variations in ejection velocity at a given launch position. Such effects of asymmetric coupling could be further enhanced by heterogeneity in the initial distribution of grains in the target and by mechanical collisions between grains. These experiments help to explain why so few craters are seen on the rubble-pile asteroid Itokawa: impacts into its coarsely fragmental surface by projectiles comparable to or smaller than the size of these fragments likely yield craters that are not easily recognizable.

  15. Automated Coarse Registration of Point Clouds in 3d Urban Scenes Using Voxel Based Plane Constraint

    Science.gov (United States)

    Xu, Y.; Boerner, R.; Yao, W.; Hoegner, L.; Stilla, U.

    2017-09-01

    For obtaining a full coverage of 3D scans in a large-scale urban area, the registration between point clouds acquired via terrestrial laser scanning (TLS) is normally mandatory. However, due to the complex urban environment, the automatic registration of different scans is still a challenging problem. In this work, we propose an automatic marker free method for fast and coarse registration between point clouds using the geometric constrains of planar patches under a voxel structure. Our proposed method consists of four major steps: the voxelization of the point cloud, the approximation of planar patches, the matching of corresponding patches, and the estimation of transformation parameters. In the voxelization step, the point cloud of each scan is organized with a 3D voxel structure, by which the entire point cloud is partitioned into small individual patches. In the following step, we represent points of each voxel with the approximated plane function, and select those patches resembling planar surfaces. Afterwards, for matching the corresponding patches, a RANSAC-based strategy is applied. Among all the planar patches of a scan, we randomly select a planar patches set of three planar surfaces, in order to build a coordinate frame via their normal vectors and their intersection points. The transformation parameters between scans are calculated from these two coordinate frames. The planar patches set with its transformation parameters owning the largest number of coplanar patches are identified as the optimal candidate set for estimating the correct transformation parameters. The experimental results using TLS datasets of different scenes reveal that our proposed method can be both effective and efficient for the coarse registration task. Especially, for the fast orientation between scans, our proposed method can achieve a registration error of less than around 2 degrees using the testing datasets, and much more efficient than the classical baseline methods.

  16. Cyclic Behavior of Low Rise Concrete Shear Walls Containing Recycled Coarse and Fine Aggregates.

    Science.gov (United States)

    Qiao, Qiyun; Cao, Wanlin; Qian, Zhiwei; Li, Xiangyu; Zhang, Wenwen; Liu, Wenchao

    2017-12-07

    In this study, the cyclic behaviors of low rise concrete shear walls using recycled coarse or fine aggregates were investigated. Eight low rise Recycled Aggregates Concrete (RAC) shear wall specimens were designed and tested under a cyclic loading. The following parameters were varied: replacement percentages of recycled coarse or fine aggregates, reinforcement ratio, axial force ratio and X-shaped rebars brace. The failure characteristics, hysteretic behavior, strength and deformation capacity, strain characteristics and stiffness were studied. Test results showed that the using of the Recycled Coarse Aggregates (RCA) and its replacement ratio had almost no influence on the mechanical behavior of the shear wall; however, the using of Recycled Fine Aggregates (RFA) had a certain influence on the ductility of the shear wall. When the reinforcement ratio increased, the strength and ductility also increased. By increasing the axial force ratio, the stren