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Sample records for generalized folding model

  1. Folding-type coupling potentials in the context of the generalized rotation-vibration model

    Science.gov (United States)

    Chamon, L. C.; Morales Botero, D. F.

    2018-03-01

    The generalized rotation-vibration model was proposed in previous works to describe the structure of heavy nuclei. The model was successfully tested in the description of experimental results related to the electron-nucleus elastic and inelastic scattering. In the present work, we consider heavy-ion collisions and assume this model to calculate folding-type coupling potentials for inelastic states, through the corresponding transition densities. As an example, the method is applied to coupled-channel data analyses for the α + 70,72,74,76Ge systems.

  2. MODELS OF PROTEIN FOLDING

    Directory of Open Access Journals (Sweden)

    Unnati Ahluwalia

    2012-12-01

    Full Text Available In an attempt to explore the understanding of protein folding mechanism, various models have been proposed in the literature. Advances in recent experimental and computational techniques rationalized our understanding on some of the fundamental features of the protein folding pathways. The goal of this review is to revisit the various models and outline the essential aspects of the folding reaction.

  3. Vocal Fold Collision Modeling

    DEFF Research Database (Denmark)

    Granados, Alba; Brunskog, Jonas; Misztal, M. K.

    2015-01-01

    When vocal folds vibrate at normal speaking frequencies, collisions occurs. The numerics and formulations behind a position-based continuum model of contact is an active field of research in the contact mechanics community. In this paper, a frictionless three-dimensional finite element model...... of the vocal fold collision is proposed, which incorporates different procedures used in contact mechanics and mathematical optimization theories. The penalty approach and the Lagrange multiplier method are investigated. The contact force solution obtained by the penalty formulation is highly dependent...

  4. Soliton behavior for a generalized mixed nonlinear Schrödinger model with N-fold Darboux transformation

    Science.gov (United States)

    Lü, Xing

    2013-09-01

    A spectral problem, the x-derivative part of which is a simple generalization of the standard Ablowitz-Kaup-Newell-Segur and Kaup-Newell spectral problems, is presented with its associated generalized mixed nonlinear Schrödinger (GMNLS) model. The N-fold Darboux transformation with multi-parameters for the spectral problem is constructed with the help of gauge transformation. According to the Darboux transformation, the solution of the GMNLS model is reduced to solving a linear algebraic system and two first-order ordinary differential equations. As an example of application, we list the modulus formulae of the envelope one- and two-soliton solutions. Note that our model is a generalized one with the inclusion of four coefficients (a, b, c, and d), which involves abundant NLS-type models such as the standard cubic NLS equation, the Gerdjikov-Ivanov equation, the Chen-Lee-Liu equation, the Kaup-Newell equation, and the mixed NLS of Wadati and/or Kundu, among others.

  5. Folded resonant non-Gaussianity in general single field inflation

    International Nuclear Information System (INIS)

    Chen, Xingang

    2010-01-01

    We compute a novel type of large non-Gaussianity due to small periodic features in general single field inflationary models. We show that the non-Bunch-Davies vacuum component generated by features, although has a very small amplitude, can have significant impact on the non-Gaussianity. Three mechanisms are turned on simultaneously in such models, namely the resonant effect, non-Bunch-Davies vacuum and higher derivative kinetic terms, resulting in a bispectrum with distinctive shapes and running. The size can be equal to or larger than that previously found in each single mechanism. Our full results, including the resonant and folded resonant non-Gaussianities, give the leading order bispectra due to general periodic features in general single field inflation

  6. Mechanical Models of Fault-Related Folding

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, A. M.

    2003-01-09

    The subject of the proposed research is fault-related folding and ground deformation. The results are relevant to oil-producing structures throughout the world, to understanding of damage that has been observed along and near earthquake ruptures, and to earthquake-producing structures in California and other tectonically-active areas. The objectives of the proposed research were to provide both a unified, mechanical infrastructure for studies of fault-related foldings and to present the results in computer programs that have graphical users interfaces (GUIs) so that structural geologists and geophysicists can model a wide variety of fault-related folds (FaRFs).

  7. Numerical modeling of fold-and-thrust belts: Applications to Kuqa foreland fold belt, China

    Science.gov (United States)

    Yin, H.; Morgan, J. K.; Zhang, J.; Wang, Z.

    2009-12-01

    We constructed discrete element models to simulate the evolution of fold-and-thrust belts. The impact of rock competence and decollement strength on the geometric pattern and deformation mechanics of fold-and-thrust belts has been investigated. The models reproduced some characteristic features of fold-and-thrust belts, such as faulted detachment folds, pop-ups, far-traveled thrust sheets, passive-roof duplexes, and back thrusts. In general, deformation propagates farther above a weak decollement than above a strong decollement. Our model results confirm that fold-and-thrust belts with strong frictional decollements develop relatively steep and narrow wedges formed by closely spaced imbricate thrust slices, whereas fold belts with weak decollements form wide low-taper wedges composed of faulted detachment folds, pop-ups, and back thrusts. Far-traveled thrust sheets and passive-roof duplexes are observed in the model with a strong lower decollement and a weak upper detachment. Model results also indicate that the thickness of the weak layer is critical. If it is thick enough, it acts as a ductile layer that is able to flow under differential stress, which helps to partition deformation above and below it. The discrete element modeling results were used to interpret the evolution of Kuqa Cenozoic fold-and-thrust belt along northern Tarim basin, China. Seismic and well data show that the widely distributed Paleogene rock salt has a significant impact on the deformation in this area. Structures beneath salt are closely spaced imbricate thrust and passive-roof duplex systems. Deformation above salt propagates much farther than below the salt. Faults above salt are relatively wide spaced. A huge controversy over the Kuqa fold-and-thrust belt is whether it is thin-skinned or thick-skinned. With the insights from DEM results, we suggest that Kuqa structures are mostly thin-skinned with Paleogene salt as decollement, except for the rear part near the backstop, where the

  8. SDEM modelling of fault-propagation folding

    DEFF Research Database (Denmark)

    Clausen, O.R.; Egholm, D.L.; Poulsen, Jane Bang

    2009-01-01

    Understanding the dynamics and kinematics of fault-propagation-folding is important for evaluating the associated hydrocarbon play, for accomplishing reliable section balancing (structural reconstruction), and for assessing seismic hazards. Accordingly, the deformation style of fault-propagation-......Understanding the dynamics and kinematics of fault-propagation-folding is important for evaluating the associated hydrocarbon play, for accomplishing reliable section balancing (structural reconstruction), and for assessing seismic hazards. Accordingly, the deformation style of fault......-propagation-folding has already been the topic of a large number of empirical studies as well as physical and computational model experiments. However, with the newly developed Stress-based Discrete Element Method (SDEM), we have, for the first time, explored computationally the link between self-emerging fault patterns...

  9. Protein Folding: Search for Basic Physical Models

    Directory of Open Access Journals (Sweden)

    Ivan Y. Torshin

    2003-01-01

    Full Text Available How a unique three-dimensional structure is rapidly formed from the linear sequence of a polypeptide is one of the important questions in contemporary science. Apart from biological context of in vivo protein folding (which has been studied only for a few proteins, the roles of the fundamental physical forces in the in vitro folding remain largely unstudied. Despite a degree of success in using descriptions based on statistical and/or thermodynamic approaches, few of the current models explicitly include more basic physical forces (such as electrostatics and Van Der Waals forces. Moreover, the present-day models rarely take into account that the protein folding is, essentially, a rapid process that produces a highly specific architecture. This review considers several physical models that may provide more direct links between sequence and tertiary structure in terms of the physical forces. In particular, elaboration of such simple models is likely to produce extremely effective computational techniques with value for modern genomics.

  10. Protein folding simulations by generalized-ensemble algorithms.

    Science.gov (United States)

    Yoda, Takao; Sugita, Yuji; Okamoto, Yuko

    2014-01-01

    In the protein folding problem, conventional simulations in physical statistical mechanical ensembles, such as the canonical ensemble with fixed temperature, face a great difficulty. This is because there exist a huge number of local-minimum-energy states in the system and the conventional simulations tend to get trapped in these states, giving wrong results. Generalized-ensemble algorithms are based on artificial unphysical ensembles and overcome the above difficulty by performing random walks in potential energy, volume, and other physical quantities or their corresponding conjugate parameters such as temperature, pressure, etc. The advantage of generalized-ensemble simulations lies in the fact that they not only avoid getting trapped in states of energy local minima but also allows the calculations of physical quantities as functions of temperature or other parameters from a single simulation run. In this article we review the generalized-ensemble algorithms. Four examples, multicanonical algorithm, replica-exchange method, replica-exchange multicanonical algorithm, and multicanonical replica-exchange method, are described in detail. Examples of their applications to the protein folding problem are presented.

  11. Generalized Dependence of Semi-Microscopic Folding-Model Parameters for Alpha-Particles in the Field of Low and Medium Energy

    CERN Document Server

    Kuterbekov, K A; Penionzhkevich, Yu E; Zholdybaev, T K

    2003-01-01

    Energy and mass dependences of the semi-microscopic alpha-particle potential parameters have been investigated for the first time. In general, a good description of elastic and inelastic differential and total reaction cross sections for different nuclei using the revealed global parameters has been obtained within the framework of semi-microscopic approaches.

  12. Nuclear interaction potential in a folded-Yukawa model with diffuse densities

    International Nuclear Information System (INIS)

    Randrup, J.

    1975-09-01

    The folded-Yukawa model for the nuclear interaction potential is generalized to diffuse density distributions which are generated by folding a Yukawa function into sharp generating distributions. The effect of a finite density diffuseness or of a finite interaction range is studied. The Proximity Formula corresponding to the generalized model is derived and numerical comparison is made with the exact results. (8 figures)

  13. Double folding model analysis of elastic scattering of halo nucleus ...

    Indian Academy of Sciences (India)

    barrier energy have been performed using a potential obtained from the double folding model and are compared with the ... In double folding (DF) model, the real nucleus–nucleus optical potential is given by the expression [9]. V DF(r) = ∫ dr1. ∫ ... expressed as a sum of three Yukawa terms. It is obtained from the fitting of ...

  14. Learning generative models for protein fold families.

    Science.gov (United States)

    Balakrishnan, Sivaraman; Kamisetty, Hetunandan; Carbonell, Jaime G; Lee, Su-In; Langmead, Christopher James

    2011-04-01

    We introduce a new approach to learning statistical models from multiple sequence alignments (MSA) of proteins. Our method, called GREMLIN (Generative REgularized ModeLs of proteINs), learns an undirected probabilistic graphical model of the amino acid composition within the MSA. The resulting model encodes both the position-specific conservation statistics and the correlated mutation statistics between sequential and long-range pairs of residues. Existing techniques for learning graphical models from MSA either make strong, and often inappropriate assumptions about the conditional independencies within the MSA (e.g., Hidden Markov Models), or else use suboptimal algorithms to learn the parameters of the model. In contrast, GREMLIN makes no a priori assumptions about the conditional independencies within the MSA. We formulate and solve a convex optimization problem, thus guaranteeing that we find a globally optimal model at convergence. The resulting model is also generative, allowing for the design of new protein sequences that have the same statistical properties as those in the MSA. We perform a detailed analysis of covariation statistics on the extensively studied WW and PDZ domains and show that our method out-performs an existing algorithm for learning undirected probabilistic graphical models from MSA. We then apply our approach to 71 additional families from the PFAM database and demonstrate that the resulting models significantly out-perform Hidden Markov Models in terms of predictive accuracy. Copyright © 2011 Wiley-Liss, Inc.

  15. The shadow map: a general contact definition for capturing the dynamics of biomolecular folding and function.

    Science.gov (United States)

    Noel, Jeffrey K; Whitford, Paul C; Onuchic, José N

    2012-07-26

    Structure-based models (SBMs) are simplified models of the biomolecular dynamics that arise from funneled energy landscapes. We recently introduced an all-atom SBM that explicitly represents the atomic geometry of a biomolecule. While this initial study showed the robustness of the all-atom SBM Hamiltonian to changes in many of the energetic parameters, an important aspect, which has not been explored previously, is the definition of native interactions. In this study, we propose a general definition for generating atomically grained contact maps called "Shadow". The Shadow algorithm initially considers all atoms within a cutoff distance and then, controlled by a screening parameter, discards the occluded contacts. We show that this choice of contact map is not only well behaved for protein folding, since it produces consistently cooperative folding behavior in SBMs but also desirable for exploring the dynamics of macromolecular assemblies since, it distributes energy similarly between RNAs and proteins despite their disparate internal packing. All-atom structure-based models employing Shadow contact maps provide a general framework for exploring the geometrical features of biomolecules, especially the connections between folding and function.

  16. Criteria for folding in structure-based models of proteins

    Energy Technology Data Exchange (ETDEWEB)

    Wołek, Karol; Cieplak, Marek, E-mail: mc@ifpan.edu.pl [Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw (Poland)

    2016-05-14

    In structure-based models of proteins, one often assumes that folding is accomplished when all contacts are established. This assumption may frequently lead to a conceptual problem that folding takes place in a temperature region of very low thermodynamic stability, especially when the contact map used is too sparse. We consider six different structure-based models and show that allowing for a small, but model-dependent, percentage of the native contacts not being established boosts the folding temperature substantially while affecting the time scales of folding only in a minor way. We also compare other properties of the six models. We show that the choice of the description of the backbone stiffness has a substantial effect on the values of characteristic temperatures that relate both to equilibrium and kinetic properties. Models without any backbone stiffness (like the self-organized polymer) are found to perform similar to those with the stiffness, including in the studies of stretching.

  17. Matrix models of RNA folding with external interactions: A review

    Indian Academy of Sciences (India)

    Abstract. The matrix model of (simplified) RNA folding with an external linear interaction in the action of the partition function is reviewed. The important results for structure combinatorics of the model are discussed and analysed in terms of the already existing models.

  18. Mechanical Modeling and Computer Simulation of Protein Folding

    Science.gov (United States)

    Prigozhin, Maxim B.; Scott, Gregory E.; Denos, Sharlene

    2014-01-01

    In this activity, science education and modern technology are bridged to teach students at the high school and undergraduate levels about protein folding and to strengthen their model building skills. Students are guided from a textbook picture of a protein as a rigid crystal structure to a more realistic view: proteins are highly dynamic…

  19. Measurement of flow separation in a human vocal folds model

    Czech Academy of Sciences Publication Activity Database

    Šidlof, Petr; Doaré, O.; Cadot, O.; Chaigne, A.

    2011-01-01

    Roč. 51, č. 1 (2011), s. 123-136 ISSN 0723-4864 R&D Projects: GA AV ČR KJB200760801 Institutional research plan: CEZ:AV0Z20760514 Keywords : vocal folds * flow separation * physical model Subject RIV: BI - Acoustics Impact factor: 1.735, year: 2011 http://www.springerlink.com/content/t81114611760jp23/

  20. A Folding Pathway Model of Mini-Protein BBA5

    Directory of Open Access Journals (Sweden)

    In-Ho Lee

    2015-01-01

    Full Text Available We present the folding pathway model of mini-protein BBA5, a bundle of secondary structures, α-helix and β-hairpin, by using action-derived molecular dynamics (ADMD simulations. From ten independent ADMD simulations, we extracted common features of the folding pathway of BBA5, from which we found that the early stage chain compaction was followed by the formation of C-terminal α-helix. The N-terminal β-hairpin was observed to form only after α-helix was stabilized. This result is in good agreement with the experimental observation that BBA5 mutants were moderately cooperative folders, and their C-terminal helical fragments were of higher secondary structure propensity while the N-terminal hairpin fragments were of a random coil spectrum. We found that the most flexible part of BBA5 is the N-terminal four residues. Although both are made of the identical ββα motif, the secondary structure formation sequence of BBA5 is found to be different from that of FSD-1. Finally, a description of the folding pathway in terms of principal component analysis is presented to characterize the folding dynamics in reduced dimensions. With only three principal components, we were able to describe 83.4% of the pathway.

  1. On the single-mass model of the vocal folds

    International Nuclear Information System (INIS)

    Howe, M S; McGowan, R S

    2010-01-01

    An analysis is made of the fluid-structure interactions necessary to support self-sustained oscillations of a single-mass mechanical model of the vocal folds subject to a nominally steady subglottal overpressure. The single-mass model of Fant and Flanagan is re-examined and an analytical representation of vortex shedding during 'voiced speech' is proposed that promotes cooperative, periodic excitation of the folds by the glottal flow. Positive feedback that sustains glottal oscillations is shown to occur during glottal contraction, when the flow separates from the 'trailing edge' of the glottis producing a low-pressure 'suction' force that tends to pull the folds together. Details are worked out for flow that can be regarded as locally two-dimensional in the glottal region. Predictions of free-streamline theory are used to model the effects of quasi-static variations in the separation point on the glottal wall. Numerical predictions are presented to illustrate the waveform of the sound radiated towards the mouth from the glottis. The theory is easily modified to include feedback on the glottal flow of standing acoustic waves, both in the vocal tract beyond the glottis and in the subglottal region. (invited paper)

  2. Glottal aerodynamics in compliant, life-sized vocal fold models

    Science.gov (United States)

    McPhail, Michael; Dowell, Grant; Krane, Michael

    2013-11-01

    This talk presents high-speed PIV measurements in compliant, life-sized models of the vocal folds. A clearer understanding of the fluid-structure interaction of voiced speech, how it produces sound, and how it varies with pathology is required to improve clinical diagnosis and treatment of vocal disorders. Physical models of the vocal folds can answer questions regarding the fundamental physics of speech, as well as the ability of clinical measures to detect the presence and extent of disorder. Flow fields were recorded in the supraglottal region of the models to estimate terms in the equations of fluid motion, and their relative importance. Experiments were conducted over a range of driving pressures with flow rates, given by a ball flowmeter, and subglottal pressures, given by a micro-manometer, reported for each case. Imaging of vocal fold motion, vector fields showing glottal jet behavior, and terms estimated by control volume analysis will be presented. The use of these results for a comparison with clinical measures, and for the estimation of aeroacoustic source strengths will be discussed. Acknowledge support from NIH R01 DC005642.

  3. Parasupersymmetry and N-fold supersymmetry in quantum many-body systems. I: General formalism and second order

    International Nuclear Information System (INIS)

    Tanaka, Toshiaki

    2007-01-01

    We propose an elegant formulation of parafermionic algebra and parasupersymmetry of arbitrary order in quantum many-body systems without recourse to any specific matrix representation of parafermionic operators and any kind of deformed algebra. Within our formulation, we show generically that every parasupersymmetric quantum system of order p consists of N-fold supersymmetric pairs with N≤p and thus has weak quasi-solvability and isospectral property. We also propose a new type of non-linear supersymmetries, called quasi-parasupersymmetry, which is less restrictive than parasupersymmetry and is different from N-fold supersymmetry even in one-body systems though the conserved charges are represented by higher-order linear differential operators. To illustrate how our formulation works, we construct second-order parafermionic algebra and three simple examples of parasupersymmetric quantum systems of order 2, one is essentially equivalent to the one-body Rubakov-Spiridonov type and the others are two-body systems in which two supersymmetries are folded. In particular, we show that the first model admits a generalized 2-fold superalgebra

  4. Folded Sheet Versus Transparent Sheet Models for Human Symmetry Judgments

    Directory of Open Access Journals (Sweden)

    Jacques Ninio

    2011-07-01

    Full Text Available As a contribution to the mysteries of human symmetry perception, reaction time data were collected on the detection of symmetry or repetition violations, in the context of short term visual memory studies. The histograms for reaction time distributions are rather narrow in the case of symmetry judgments. Their analysis was performed in terms of a simple kinetic model of a mental process in two steps, a slow one for the construction of the representation of the images to be compared, and a fast one, in the 50 ms range, for the decision. There was no need for an additional ‘mental rotation’ step. Symmetry seems to facilitate the construction step. I also present here original stimuli showing a color equalization effect across a symmetry axis, and its counterpart in periodic patterns. According to a “folded sheet model”, when a shape is perceived, the brain automatically constructs a mirror-image representation of the shape. Based in part on the reaction time analysis, I present here an alternative “transparent sheet” model in which the brain constructs a single representation, which can be accessed from two sides, thus generating simultaneously a pattern and its mirror-symmetric partner. Filtering processes, implied by current models of symmetry perception could intervene at an early stage, by nucleating the propagation of similar perceptual groupings in the two symmetric images.

  5. Flow separation in a computational oscillating vocal fold model

    Science.gov (United States)

    Alipour, Fariborz; Scherer, Ronald C.

    2004-09-01

    A finite-volume computational model that solves the time-dependent glottal airflow within a forced-oscillation model of the glottis was employed to study glottal flow separation. Tracheal input velocity was independently controlled with a sinusoidally varying parabolic velocity profile. Control parameters included flow rate (Reynolds number), oscillation frequency and amplitude of the vocal folds, and the phase difference between the superior and inferior glottal margins. Results for static divergent glottal shapes suggest that velocity increase caused glottal separation to move downstream, but reduction in velocity increase and velocity decrease moved the separation upstream. At the fixed frequency, an increase of amplitude of the glottal walls moved the separation further downstream during glottal closing. Increase of Reynolds number caused the flow separation to move upstream in the glottis. The flow separation cross-sectional ratio ranged from approximately 1.1 to 1.9 (average of 1.47) for the divergent shapes. Results suggest that there may be a strong interaction of rate of change of airflow, inertia, and wall movement. Flow separation appeared to be ``delayed'' during the vibratory cycle, leading to movement of the separation point upstream of the glottal end only after a significant divergent angle was reached, and to persist upstream into the convergent phase of the cycle.

  6. Characteristics of phonation onset in a two-layer vocal fold model.

    Science.gov (United States)

    Zhang, Zhaoyan

    2009-02-01

    Characteristics of phonation onset were investigated in a two-layer body-cover continuum model of the vocal folds as a function of the biomechanical and geometric properties of the vocal folds. The analysis showed that an increase in either the body or cover stiffness generally increased the phonation threshold pressure and phonation onset frequency, although the effectiveness of varying body or cover stiffness as a pitch control mechanism varied depending on the body-cover stiffness ratio. Increasing body-cover stiffness ratio reduced the vibration amplitude of the body layer, and the vocal fold motion was gradually restricted to the medial surface, resulting in more effective flow modulation and higher sound production efficiency. The fluid-structure interaction induced synchronization of more than one group of eigenmodes so that two or more eigenmodes may be simultaneously destabilized toward phonation onset. At certain conditions, a slight change in vocal fold stiffness or geometry may cause phonation onset to occur as eigenmode synchronization due to a different pair of eigenmodes, leading to sudden changes in phonation onset frequency, vocal fold vibration pattern, and sound production efficiency. Although observed in a linear stability analysis, a similar mechanism may also play a role in register changes at finite-amplitude oscillations.

  7. How to fold a spin chain: Integrable boundaries of the Heisenberg XXX and Inozemtsev hyperbolic models

    Science.gov (United States)

    De La Rosa Gomez, Alejandro; MacKay, Niall; Regelskis, Vidas

    2017-04-01

    We present a general method of folding an integrable spin chain, defined on a line, to obtain an integrable open spin chain, defined on a half-line. We illustrate our method through two fundamental models with sl2 Lie algebra symmetry: the Heisenberg XXX and the Inozemtsev hyperbolic spin chains. We obtain new long-range boundary Hamiltonians and demonstrate that they exhibit Yangian symmetries, thus ensuring integrability of the models we obtain. The method presented provides a ;bottom-up; approach for constructing integrable boundaries and can be applied to any spin chain model.

  8. Modeling Vocal Fold Intravascular Flow using Synthetic Replicas

    Science.gov (United States)

    Terry, Aaron D.; Ricks, Matthew T.; Thomson, Scott L.

    2017-11-01

    Vocal fold vibration that is induced by air flowing from the lungs is believed to decrease blood flow through the vocal folds. This is important due to the critical role of blood flow in maintaining tissue health. However, the precise mechanical relationships between vocal fold vibration and blood perfusion remain understudied. A platform for studying liquid perfusion in a synthetic, life-size, self-oscillating vocal fold replica has recently been developed. The replicas are fabricated using molded silicone with material properties comparable to those of human vocal fold tissues and that include embedded microchannels through which liquid is perfused. The replicas are mounted on an air flow supply tube to initiate flow-induced vibration. A liquid reservoir is attached to the microchannel to cause liquid to perfuse through replica in the anterior-posterior direction. As replica vibration is initiated and amplitude increases, perfusion flow rate decreases. In this presentation, the replica design will be presented, along with data quantifying the relationships between parameters such as replica vibration amplitude, stiffness, microchannel diameter, and perfusion flow rate. This work was supported by Grant NIDCD R01DC005788 from the National Institutes of Health.

  9. Self-organized critical model for protein folding

    Science.gov (United States)

    Moret, M. A.

    2011-09-01

    The major factor that drives a protein toward collapse and folding is the hydrophobic effect. At the folding process a hydrophobic core is shielded by the solvent-accessible surface area of the protein. We study the fractal behavior of 5526 protein structures present in the Brookhaven Protein Data Bank. Power laws of protein mass, volume and solvent-accessible surface area are measured independently. The present findings indicate that self-organized criticality is an alternative explanation for the protein folding. Also we note that the protein packing is an independent and constant value because the self-similar behavior of the volumes and protein masses have the same fractal dimension. This power law guarantees that a protein is a complex system. From the analyzed data, q-Gaussian distributions seem to fit well this class of systems.

  10. Aeroelastic-aeroacoustic measurements in a self-oscillating physical model of the human vocal folds

    Science.gov (United States)

    Krane, Michael; Cates, Zachary

    2009-11-01

    Measurements are presented characterizing the relationship between the structure of physical models of the human vocal folds and the sound produced by their vibration by airflow from the lungs. The model vocal folds are fabricated by molding two layers of silicone rubber of specified stiffness, approximating the body/cover structure. These are mounted in a model vocal tract, where the prephonatory gap adjusted using micropositioners. Measurements conducted in an anechoic chamber include radiated sound pressure, and high-speed video of the vibrating model vocal folds, using prephonatory separation, body stiffness, and subglottal pressure as input parameters.. Essential behavior of the vocal fold models is presented. Vibration fundamental frequency and radiated sound pressure level outside the model vocal tract as a function of subglottal pressure and prephonatory gap are presented for the cases of two identical vocal folds and one vocal fold with lower stiffness, approximating vocal fold paralysis.

  11. Matrix models of RNA folding with external interactions: A review

    Indian Academy of Sciences (India)

    The improved understanding of the role of RNA in biological activities with discoveries and developments in the field of biophysics has highlighted the importance of studying their tertiary (folded 3D) conformations [1]. At the very base of understanding the different lev- els of structures of these biomolecules, lies the quest for ...

  12. Extreme Folding

    Science.gov (United States)

    Demaine, Erik

    2012-02-01

    Our understanding of the mathematics and algorithms behind paper folding, and geometric folding in general, has increased dramatically over the past several years. These developments have found a surprisingly broad range of applications. In the art of origami, it has helped spur the technical origami revolution. In engineering and science, it has helped solve problems in areas such as manufacturing, robotics, graphics, and protein folding. On the recreational side, it has led to new kinds of folding puzzles and magic. I will give an overview of the mathematics and algorithms of folding, with a focus on new mathematics and sculpture.

  13. The generalized circular model

    NARCIS (Netherlands)

    Webers, H.M.

    1995-01-01

    In this paper we present a generalization of the circular model. In this model there are two concentric circular markets, which enables us to study two types of markets simultaneously. There are switching costs involved for moving from one circle to the other circle, which can also be thought of as

  14. Double folding model including the Pauli exclusion principle

    International Nuclear Information System (INIS)

    Gridnev, K.A.; Soubbotin, V.B.; Oertzen, W. von; Bohlen, H.G.; Vinas, X.

    2002-01-01

    A new method to incorporate the Pauli principle into the double folding approach to the heavy ion potential is proposed. It is shown that in order to take into account the Pauli blocking a redefinition of the density matrices of the free isolated nuclei must be one. A solution to the self-consistent incorporation of the Pauli-blocking effects in the mean-field nucleus-nucleus potential is obtained in the Thomas-Fermi approximation [ru

  15. Studying the Vocal Fold Vibration Using a Nonlinear Finite-Element Model

    Science.gov (United States)

    Tao, Chao; Jiang, Jack. J.; Zhang, Yu

    2006-05-01

    The vocal fold vibration and voice production are highly complex nonlinear processes. Nonlinear relationship of glottal pressure to airflow and the nonlinearities of vocal fold collision are two important nonlinear factors of vocal fold vibration. In this paper, we will study the vocal fold vibration using a nonlinear finite-element model. In this model, the nonlinear relationship of glottal pressure to airflow, the nonlinearities of vocal fold collision, and the interaction between the airflow and vocal folds are taken into account. The impact pressure, vocal fold vibration, and glottal pressure under various lung pressures are studies. The results show that the nonlinear finite-element model is a useful tool for studying the voice production and predicting mechanical trauma leading to injurious abuse, misuse of the voice and vocal nodule.

  16. Double-folding model including the Pauli exclusion principle

    International Nuclear Information System (INIS)

    Gridnev, K.A.; Soubbotin, V.B.; Oertzen, W. von; Bohlen, H.G.; Vinas, X.

    2002-01-01

    A new method for incorporating the Pauli exclusion principle into the double-folding approach to the heavy-ion potential is proposed. The description of the exchange terms at the level of the semiclassical one-body density matrix is used. It is shown that, in order to take into account Pauli blocking properly, the density matrices of free isolated nuclei must be redefined. A solution to the self-consistent incorporation of Pauli blocking effects in the mean-field nucleus-nucleus potential is obtained in the Thomas-Fermi approximation

  17. A 9-state hidden Markov model using protein secondary structure information for protein fold recognition.

    Science.gov (United States)

    Lee, Sun Young; Lee, Jong Yun; Jung, Kwang Su; Ryu, Keun Ho

    2009-06-01

    In protein fold recognition, the main disadvantage of hidden Markov models (HMMs) is the employment of large-scale model architectures which require large data sets and high computational resources for training. Also, HMMs must consider sequential information about secondary structures of proteins, to improve prediction performance and reduce model parameters. Therefore, we propose a novel method for protein fold recognition based on a hidden Markov model, called a 9-state HMM. The method can (i) reduce the number of states using secondary structure information about proteins for each fold and (ii) recognize protein folds more accurately than other HMMs.

  18. The Shadow Map: A General Contact Definition for Capturing the Dynamics of Biomolecular Folding and Function

    OpenAIRE

    Noel, Jeffrey K.; Whitford, Paul C.; Onuchic, José N

    2012-01-01

    Structure-based models (SBMs) are simplified models of the biomolecular dynamics that arise from funneled energy landscapes. We recently introduced an all-atom SBM that explicitly represents the atomic geometry of a biomolecule. While this initial study showed the robustness of the all-atom SBM Hamiltonian to changes in many of the energetic parameters, an important aspect, which has not been explored previously, is the definition of native interactions. In this study, we propose a general de...

  19. Modeling and imaging of the vocal fold vibration for voice health

    DEFF Research Database (Denmark)

    Granados, Alba

    of vibration, showing dierent characteristics in normal and abnormal phonation. In the last part of this thesis research, the optical ow algorithm for data acquisition as well as the biomechanical model of the vocal fold are used to formulate a nonstationary statistical inverse problem for vocal fold features......, analysis and inference. This thesis deals with biomechanical models of the vocal fold, specially of the collision, and laryngeal videoendoscopic analysis procedures suitable for the inference of the underlying vocal fold characteristics. The rst part of this research is devoted to frictionless contact...... modeling during asymmetric vocal fold vibration. The prediction problem is numerically addressed with a self-sustained three-dimensional nite element model of the vocal fold with position-based contact constraints. A novel contact detection mechanism is shown to successfully detect collision in asymmetric...

  20. Self-organization and mismatch tolerance in protein folding: General theory and an application

    Science.gov (United States)

    Fernández, Ariel; Berry, R. Stephen

    2000-03-01

    The folding of a protein is a process both expeditious and robust. The analysis of this process presented here uses a coarse, discretized representation of the evolving form of the backbone chain, based on its torsional states. This coarse description consists of discretizing the torsional coordinates modulo the Ramachandran basins in the local softmode dynamics. Whenever the representation exhibits "contact patterns" that correspond to topological compatibilities with particular structural forms, secondary and then tertiary, the elements constituting the pattern are effectively entrained by a reduction of their rates of exploration of their discretized configuration space. The properties "expeditious and robust" imply that the folding protein must have some tolerance to both torsional "frustrated" and side-chain contact mismatches which may occur during the folding process. The energy-entropy consequences of the staircase or funnel topography of the potential surface should allow the folding protein to correct these mismatches, eventually. This tolerance lends itself to an iterative pattern-recognition-and-feedback description of the folding process that reflects mismatched local torsional states and hydrophobic/polar contacts. The predictive potential of our algorithm is tested by application to the folding of bovine pancreatic trypsin inhibitor (BPTI), a protein whose ability to form its active structure is contingent upon its frustration tolerance.

  1. Folding energetics of ligand binding proteins. I. Theoretical model.

    Science.gov (United States)

    Rösgen, J; Hinz, H J

    2001-03-02

    Heat capacity curves as obtained from differential scanning calorimetry are an outstanding source for molecular information on protein folding and ligand-binding energetics. However, deconvolution of C(p) data of proteins in the presence of ligands can be compromised by indeterminacies concerning the correct choice of the statistical thermodynamic ensemble. By convent, the assumption of constant free ligand concentration has been used to derive formulae for the enthalpy. Unless the ligand occurs at large excess, this assumption is incorrect. Still the relevant ensemble is the grand canonical ensemble. We derive formulae for both constraints, constancy of total or free ligand concentration and illustrate the equations by application to the typical equilibrium Nx N + x D + x. It is demonstrated that as long as the thermodynamic properties of the ligand can be completely corrected for by performing a reference measurement, the grand canonical approach provides the proper and mathematically significantly simpler choice. We demonstrate on the two cases of sequential or independent ligand-binding the fact, that similar binding mechanisms result in different and distinguishable heat capacity equations. Finally, we propose adequate strategies for DSC experiments as well as for obtaining first estimates of the characteristic thermodynamic parameters, which can be used as starting values in a global fit of DSC data. Copyright 2001 Academic Press.

  2. An optical flow-based state-space model of the vocal folds

    DEFF Research Database (Denmark)

    Granados, Alba; Brunskog, Jonas

    2017-01-01

    High-speed movies of the vocal fold vibration are valuable data to reveal vocal fold features for voice pathology diagnosis. This work presents a suitable Bayesian model and a purely theoretical discussion for further development of a framework for continuum biomechanical features estimation....... A linear and Gaussian nonstationary state-space model is proposed and thoroughly discussed. The evolution model is based on a self-sustained three-dimensional finite element model of the vocal folds, and the observation model involves a dense optical flow algorithm. The results show that the method is able...

  3. Ocean General Circulation Models

    Energy Technology Data Exchange (ETDEWEB)

    Yoon, Jin-Ho; Ma, Po-Lun

    2012-09-30

    1. Definition of Subject The purpose of this text is to provide an introduction to aspects of oceanic general circulation models (OGCMs), an important component of Climate System or Earth System Model (ESM). The role of the ocean in ESMs is described in Chapter XX (EDITOR: PLEASE FIND THE COUPLED CLIMATE or EARTH SYSTEM MODELING CHAPTERS). The emerging need for understanding the Earth’s climate system and especially projecting its future evolution has encouraged scientists to explore the dynamical, physical, and biogeochemical processes in the ocean. Understanding the role of these processes in the climate system is an interesting and challenging scientific subject. For example, a research question how much extra heat or CO2 generated by anthropogenic activities can be stored in the deep ocean is not only scientifically interesting but also important in projecting future climate of the earth. Thus, OGCMs have been developed and applied to investigate the various oceanic processes and their role in the climate system.

  4. A New Heuristic Algorithm for Protein Folding in the HP Model.

    Science.gov (United States)

    Traykov, Metodi; Angelov, Slav; Yanev, Nicola

    2016-08-01

    This article presents an efficient heuristic for protein folding. The protein folding problem is to predict the compact three-dimensional structure of a protein based on its amino acid sequence. The focus is on an original integer programming model derived from a platform used for Contact Map Overlap problem.

  5. Double folding model analysis of elastic scattering of halo nucleus ...

    Indian Academy of Sciences (India)

    With the continuous advancement of radioactive ion beam facilities worldwide, acceler- ated radioactive beams including halo nuclei have become accessible for investigation. The nuclei such as ... As there is integration over two densities, this is called the DF model. The M3Y NN interaction used is the one prescribed by ...

  6. 100-fold but not 50-fold dystrophin overexpression aggravates electrocardiographic defects in the mdx model of Duchenne muscular dystrophy

    Directory of Open Access Journals (Sweden)

    Yongping Yue

    2016-01-01

    Full Text Available Dystrophin gene replacement holds the promise of treating Duchenne muscular dystrophy. Supraphysiological expression is a concern for all gene therapy studies. In the case of Duchenne muscular dystrophy, Chamberlain and colleagues found that 50-fold overexpression did not cause deleterious side effect in skeletal muscle. To determine whether excessive dystrophin expression in the heart is safe, we studied two lines of transgenic mdx mice that selectively expressed a therapeutic minidystrophin gene in the heart at 50-fold and 100-fold of the normal levels. In the line with 50-fold overexpression, minidystrophin showed sarcolemmal localization and electrocardiogram abnormalities were corrected. However, in the line with 100-fold overexpression, we not only detected sarcolemmal minidystrophin expression but also observed accumulation of minidystrophin vesicles in the sarcoplasm. Excessive minidystrophin expression did not correct tachycardia, a characteristic feature of Duchenne muscular dystrophy. Importantly, several electrocardiogram parameters (QT interval, QRS duration and the cardiomyopathy index became worse than that of mdx mice. Our data suggests that the mouse heart can tolerate 50-fold minidystrophin overexpression, but 100-fold overexpression leads to cardiac toxicity.

  7. Modeling RNA secondary structure folding ensembles using SHAPE mapping data.

    Science.gov (United States)

    Spasic, Aleksandar; Assmann, Sarah M; Bevilacqua, Philip C; Mathews, David H

    2018-01-09

    RNA secondary structure prediction is widely used for developing hypotheses about the structures of RNA sequences, and structure can provide insight about RNA function. The accuracy of structure prediction is known to be improved using experimental mapping data that provide information about the pairing status of single nucleotides, and these data can now be acquired for whole transcriptomes using high-throughput sequencing. Prior methods for using these experimental data focused on predicting structures for sequences assuming that they populate a single structure. Most RNAs populate multiple structures, however, where the ensemble of strands populates structures with different sets of canonical base pairs. The focus on modeling single structures has been a bottleneck for accurately modeling RNA structure. In this work, we introduce Rsample, an algorithm for using experimental data to predict more than one RNA structure for sequences that populate multiple structures at equilibrium. We demonstrate, using SHAPE mapping data, that we can accurately model RNA sequences that populate multiple structures, including the relative probabilities of those structures. This program is freely available as part of the RNAstructure software package. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  8. Thermodynamics of protein folding using a modified Wako-Saitô-Muñoz-Eaton model.

    Science.gov (United States)

    Tsai, Min-Yeh; Yuan, Jian-Min; Teranishi, Yoshiaki; Lin, Sheng Hsien

    2012-09-01

    Herein, we propose a modified version of the Wako-Saitô-Muñoz-Eaton (WSME) model. The proposed model introduces an empirical temperature parameter for the hypothetical structural units (i.e., foldons) in proteins to include site-dependent thermodynamic behavior. The thermodynamics for both our proposed model and the original WSME model were investigated. For a system with beta-hairpin topology, a mathematical treatment (contact-pair treatment) to facilitate the calculation of its partition function was developed. The results show that the proposed model provides better insight into the site-dependent thermodynamic behavior of the system, compared with the original WSME model. From this site-dependent point of view, the relationship between probe-dependent experimental results and model's thermodynamic predictions can be explained. The model allows for suggesting a general principle to identify foldon behavior. We also find that the backbone hydrogen bonds may play a role of structural constraints in modulating the cooperative system. Thus, our study may contribute to the understanding of the fundamental principles for the thermodynamics of protein folding.

  9. Unusual armadillo fold in the human general vesicular transport factor p115.

    Directory of Open Access Journals (Sweden)

    Harald Striegl

    Full Text Available The golgin family gives identity and structure to the Golgi apparatus and is part of a complex protein network at the Golgi membrane. The golgin p115 is targeted by the GTPase Rab1a, contains a large globular head region and a long region of coiled-coil which forms an extended rod-like structure. p115 serves as vesicle tethering factor and plays an important role at different steps of vesicular transport. Here we present the 2.2 A-resolution X-ray structure of the globular head region of p115. The structure exhibits an armadillo fold that is decorated by elongated loops and carries a C-terminal non-canonical repeat. This terminal repeat folds into the armadillo superhelical groove and allows homodimeric association with important implications for p115 mediated multiple protein interactions and tethering.

  10. Model-unrestricted scattering potentials for light ions and their interpretation in the folding model

    International Nuclear Information System (INIS)

    Ermer, M.; Clement, H.; Frank, G.; Grabmayr, P.; Heberle, N.; Wagner, G.J.

    1989-01-01

    High-quality data for elastic proton, deuteron and α-particle scattering on 40 Ca and 208 Pb at 26-30 MeV/N have been analyzed in terms of the model-unrestricted Fourier-Bessel concept. While extracted scattering potentials show substantial deviations from Woods-Saxon shapes, their real central parts are well described by folding calculations using a common effective nucleon-nucleon interaction with a weak density dependence. (orig.)

  11. General theory of the long-range interactions in protein folding

    International Nuclear Information System (INIS)

    Namiot, V.A.; Batyanovskii, A.V.; Filatov, I.V.; Tumanyan, V.G.; Esipova, N.G.

    2011-01-01

    The process of the globular structure formation from a long molecular chain is examined in a general sense. In the course of this process various regions of the chain interact with each other. The bonds formed during this process are classified as native and non-native ones. Native bonds are formed in native globular structure. All other bonds are 'incorrect' (non-native). It is demonstrated that the globule formation can occur actually without production and subsequent decay of non-native contacts. The proposed model allows to avoid a search of numerous non-native variants since long-distance interactions with a high selectivity take place between the chain regions that form native bonds. The presence of these interactions prompts the chain regions which yield native contacts start to draw together and to interact. The databank data analysis shows that the developed model can be applied not only to the abstract structures but also to real polypeptide chains which are able to form both globular structures and helical fibrils. -- Highlights: → The process of the globular structure formation from a long molecular chain is examined. → It is shown that the globule formation can occur without production of non-native contacts. → The proposed model allows to avoid a search of non-native variants since long-distance interactions with a high selectivity. → This interaction takes place between the chain regions that form native bonds. → The databank data analysis shows that the developed model can be applied to real polypeptide chains.

  12. The general dynamic model

    DEFF Research Database (Denmark)

    Borregaard, Michael K.; Matthews, Thomas J.; Whittaker, Robert James

    2016-01-01

    Aim: Island biogeography focuses on understanding the processes that underlie a set of well-described patterns on islands, but it lacks a unified theoretical framework for integrating these processes. The recently proposed general dynamic model (GDM) of oceanic island biogeography offers a step...... towards this goal. Here, we present an analysis of causality within the GDM and investigate its potential for the further development of island biogeographical theory. Further, we extend the GDM to include subduction-based island arcs and continental fragment islands. Location: A conceptual analysis...... dynamics of distinct island types are predicted to lead to markedly different evolutionary dynamics. This sets the stage for a more predictive theory incorporating the processes governing temporal dynamics of species diversity on islands....

  13. The IntFOLD server: an integrated web resource for protein fold recognition, 3D model quality assessment, intrinsic disorder prediction, domain prediction and ligand binding site prediction.

    Science.gov (United States)

    Roche, Daniel B; Buenavista, Maria T; Tetchner, Stuart J; McGuffin, Liam J

    2011-07-01

    The IntFOLD server is a novel independent server that integrates several cutting edge methods for the prediction of structure and function from sequence. Our guiding principles behind the server development were as follows: (i) to provide a simple unified resource that makes our prediction software accessible to all and (ii) to produce integrated output for predictions that can be easily interpreted. The output for predictions is presented as a simple table that summarizes all results graphically via plots and annotated 3D models. The raw machine readable data files for each set of predictions are also provided for developers, which comply with the Critical Assessment of Methods for Protein Structure Prediction (CASP) data standards. The server comprises an integrated suite of five novel methods: nFOLD4, for tertiary structure prediction; ModFOLD 3.0, for model quality assessment; DISOclust 2.0, for disorder prediction; DomFOLD 2.0 for domain prediction; and FunFOLD 1.0, for ligand binding site prediction. Predictions from the IntFOLD server were found to be competitive in several categories in the recent CASP9 experiment. The IntFOLD server is available at the following web site: http://www.reading.ac.uk/bioinf/IntFOLD/.

  14. Assessing groundwater availability in a folded carbonate aquifer through the development of a numerical model

    Science.gov (United States)

    Di Salvo, Cristina; Romano, Emanuele; Guyennon, Nicolas; Bruna Petrangeli, Anna; Preziosi, Elisabetta

    2015-04-01

    multilayer aquifer was conceptualized as five folded hydrostratigraphic units: three main carbonate aquifers are separated by two aquitards, which can be locally discontinuous, leading to a complicated flow pattern. In general the vertical leakance is upward from the basal aquifer to the unconfined uppermost aquifer. As shown by the increasing discharge from north to south, the Nera river acts as the main sink of the study area, gaining groundwater as it cuts through the folded terrain. The numerical model was implemented using the MODFLOW-2000 code and extends over an area of 235 km2 with a grid spacing of 100 meters in each of the 5 layers. Model calibration was achieved by comparing the model results with observed streamflow of the Nera river (8-10 measures per year during 1991-1993 and 1996-2012) which on the basis of the river hydrograph at gaging locations is considered to be derived entirely from groundwater. The effects of climate variation on groundwater discharge to the river in the past 60 years are analyzed. Key issues related to the elaboration of a numerical model of a folded structure are also described.

  15. FoldEco: A Model for Proteostasis in E. coli

    Directory of Open Access Journals (Sweden)

    Evan T. Powers

    2012-03-01

    Full Text Available To gain insight into the interplay of processes and species that maintain a correctly folded, functional proteome, we have developed a computational model called FoldEco. FoldEco models the cellular proteostasis network of the E. coli cytoplasm, including protein synthesis, degradation, aggregation, chaperone systems, and the folding characteristics of protein clients. We focused on E. coli because much of the needed input information—including mechanisms, rate parameters, and equilibrium coefficients—is available, largely from in vitro experiments; however, FoldEco will shed light on proteostasis in other organisms. FoldEco can generate hypotheses to guide the design of new experiments. Hypothesis generation leads to system-wide questions and shows how to convert these questions to experimentally measurable quantities, such as changes in protein concentrations with chaperone or protease levels, which can then be used to improve our current understanding of proteostasis and refine the model. A web version of FoldEco is available at http://foldeco.scripps.edu.

  16. Thermodynamics of model prions and its implications for the problem of prion protein folding.

    Science.gov (United States)

    Harrison, P M; Chan, H S; Prusiner, S B; Cohen, F E

    1999-02-19

    Prion disease is caused by the propagation of a particle containing PrPSc, a misfolded form of the normal cellular prion protein (PrPC). PrPC can re-fold to form PrPSc with loss of alpha-helical structure and formation of extensive beta-sheet structure. Here, we model this prion folding problem with a simple, low-resolution lattice model of protein folding. If model proteins are allowed to re-fold upon dimerization, a minor proportion of them (up to approximately 17%) encrypts an alternative native state as a homodimer. The structures in this homodimeric native state re-arrange so that they are very different in conformation from the monomeric native state. We find that model proteins that are relatively less stable as monomers are more susceptible to the formation of alternative native states as homodimers. These results suggest that less-stable proteins have a greater need for a well-designed energy landscape for protein folding to overcome an increased chance of encrypting substantially different native conformations stabilized by multimeric interactions. This conceptual framework for aberrant folding should be relevant in Alzheimer's disease and other disorders associated with protein aggregation. Copyright 1999 Academic Press.

  17. Simulating the folding of HP-sequences with a minimalist model in an inhomogeneous medium.

    Science.gov (United States)

    Alas, S J; González-Pérez, P P

    2016-01-01

    The phenomenon of protein folding is a fundamental issue in the field of the computational molecular biology. The protein folding inside the cells is performed in a highly inhomogeneous, tortuous, and correlated environment. Therefore, it is important to include in the theoretical studies the medium where the protein folding is developed. In this work we present the combination of three models to mimic the protein folding inside of an inhomogeneous medium. The models used here are Hydrophobic-Polar (HP) in 2D square arrangement, Evolutionary Algorithms (EA), and the Dual Site Bond Model (DSBM). The DSBM model is used to simulate the environment where the HP beads are folded; in this case the medium is correlated and is fractal-like. The analysis of five benchmark HP sequences shows that the inhomogeneous space provided with a given correlation length and fractal dimension plays an important role for correct folding of these sequences, which does not occur in a homogeneous space. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  18. How the Cortex Gets Its Folds: An Inside-Out, Connectivity-Driven Model for the Scaling of Mammalian Cortical Folding

    Science.gov (United States)

    Mota, Bruno; Herculano-Houzel, Suzana

    2012-01-01

    Larger mammalian cerebral cortices tend to have increasingly folded surfaces, often considered to result from the lateral expansion of the gray matter (GM), which, in a volume constrained by the cranium, causes mechanical compression that is relieved by inward folding of the white matter (WM), or to result from differential expansion of cortical layers. Across species, thinner cortices, presumably more pliable, would offer less resistance and hence become more folded than thicker cortices of a same size. However, such models do not acknowledge evidence in favor of a tension-based pull onto the GM from the inside, holding it in place even when the constraint imposed by the cranium is removed. Here we propose a testable, quantitative model of cortical folding driven by tension along the length of axons in the WM that assumes that connections through the WM are formed early in development, at the same time as the GM becomes folded, and considers that axonal connections through the WM generate tension that leads to inward folding of the WM surface, which pulls the GM surface inward. As an important necessary simplifying hypothesis, we assume that axons leaving or entering the WM do so approximately perpendicularly to the WM–GM interface. Cortical folding is thus driven by WM connectivity, and is a function of the fraction of cortical neurons connected through the WM, the average length, and the average cross-sectional area of the axons in the WM. Our model predicts that the different scaling of cortical folding across mammalian orders corresponds to different combinations of scaling of connectivity, axonal cross-sectional area, and tension along WM axons, instead of being a simple function of the number of GM neurons. Our model also explains variations in average cortical thickness as a result of the factors that lead to cortical folding, rather than as a determinant of folding; predicts that for a same tension, folding increases with connectivity through the WM and

  19. General Protein Data Bank-Based Collective Variables for Protein Folding.

    Science.gov (United States)

    Ardevol, Albert; Palazzesi, Ferruccio; Tribello, Gareth A; Parrinello, Michele

    2016-01-12

    New, automated forms of data analysis are required to understand the high-dimensional trajectories that are obtained from molecular dynamics simulations on proteins. Dimensionality reduction algorithms are particularly appealing in this regard as they allow one to construct unbiased, low-dimensional representations of the trajectory using only the information encoded in the trajectory. The downside of this approach is that a different set of coordinates are required for each different chemical system under study precisely because the coordinates are constructed using information from the trajectory. In this paper, we show how one can resolve this problem by using the sketch-map algorithm that we recently proposed to construct a low-dimensional representation of the structures contained in the protein data bank. We show that the resulting coordinates are as useful for analyzing trajectory data as coordinates constructed using landmark configurations taken from the trajectory and that these coordinates can thus be used for understanding protein folding across a range of systems.

  20. A Turing Reaction-Diffusion Model for Human Cortical Folding Patterns and Cortical Pattern Malformations

    Science.gov (United States)

    Hurdal, Monica K.; Striegel, Deborah A.

    2011-11-01

    Modeling and understanding cortical folding pattern formation is important for quantifying cortical development. We present a biomathematical model for cortical folding pattern formation in the human brain and apply this model to study diseases involving cortical pattern malformations associated with neural migration disorders. Polymicrogyria is a cortical malformation disease resulting in an excessive number of small gyri. Our mathematical model uses a Turing reaction-diffusion system to model cortical folding. The lateral ventricle (LV) and ventricular zone (VZ) of the brain are critical components in the formation of cortical patterning. In early cortical development the shape of the LV can be modeled with a prolate spheroid and the VZ with a prolate spheroid surface. We use our model to study how global cortex characteristics, such as size and shape of the LV, affect cortical pattern formation. We demonstrate increasing domain scale can increase the number of gyri and sulci formed. Changes in LV shape can account for sulcus directionality. By incorporating LV size and shape, our model is able to elucidate which parameters can lead to excessive cortical folding.

  1. Glauber model and its generalizations

    International Nuclear Information System (INIS)

    Bialkowski, G.

    The physical aspects of the Glauber model problems are studied: potential model, profile function and Feynman diagrams approaches. Different generalizations of the Glauber model are discussed: particularly higher and lower energy processes and large angles [fr

  2. Generalized instrumental variable models

    OpenAIRE

    Andrew Chesher; Adam Rosen

    2014-01-01

    This paper develops characterizations of identified sets of structures and structural features for complete and incomplete models involving continuous or discrete variables. Multiple values of unobserved variables can be associated with particular combinations of observed variables. This can arise when there are multiple sources of heterogeneity, censored or discrete endogenous variables, or inequality restrictions on functions of observed and unobserved variables. The models g...

  3. A bovine acellular scaffold for vocal fold reconstruction in a rat model.

    Science.gov (United States)

    Xu, Chet C; Chan, Roger W; Weinberger, Debra G; Efune, Guy; Pawlowski, Karen S

    2010-01-01

    With a rat model of vocal fold injury, this study examined the in vivo host response to an acellular xenogeneic scaffold derived from the bovine vocal fold lamina propria, and the potential of the scaffold for constructive tissue remodeling. Bilateral wounds were created in the posterior vocal folds of 20 rats, and bovine acellular scaffolds were implanted into the wounds unilaterally, with the contralateral vocal folds as control. The rats were humanely sacrificed after 3 days, 7 days, 1 month, and 3 months, and the coronal sections of their larynges were examined histologically. Expressions of key matrix proteins including collagen I, collagen III, elastin, fibronectin, hyaluronic acid, and glycosaminoglycans (GAGs) were quantified with digital image analysis. Significant infiltration of host inflammatory cells and host fibroblasts in the scaffold implant was observed in the acute stage of wound repair (3 days and 7 days postsurgery). The mean relative densities of collagen I, collagen III, and GAGs in the implanted vocal folds were significantly higher than those in the control after 3 days, followed by gradual decreases over 3 months. Histological results showed that the scaffolds were apparently degraded by 3 months, with no fibrotic tissue formation or calcification. These preliminary findings suggested that the bovine acellular scaffold could be a potential xenograft for vocal fold regeneration.

  4. Coupled channel folding model description of α scattering from 9Be

    International Nuclear Information System (INIS)

    Roy, S.; Chatterjee, J.M.; Majumdar, H.; Datta, S.K.; Banerjee, S.R.; Chintalapudi, S.N.

    1995-01-01

    Alpha scattering from 9 Be at E α = 65 MeV is described in the coupled channel framework with phenomenological as well as folded potentials. The multipole components of the deformed density of 9 Be are derived from Nilsson model wave functions. Reasonably good agreements are obtained for the angular distributions of 3/2 - (g.s.) and 5/2 - (2.43 MeV) states of the ground state band with folded potentials. The deformation predicted by the model corroborates with that derived from the phenomenological analysis with potentials of different geometries

  5. Coupled channel folding model description of {alpha} scattering from {sup 9}Be

    Energy Technology Data Exchange (ETDEWEB)

    Roy, S.; Chatterjee, J.M.; Majumdar, H. [Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Calcutta 700064 (India); Datta, S.K. [Nuclear Science Centre, P.O.10502, New Delhi 110067 (India); Banerjee, S.R. [Variable Energy Cyclotron Centre, 1/AF Bidhannagar, Calcutta 700064 (India); Chintalapudi, S.N. [Inter-University Consortium, Department of Atomic Energy Facilities, Bidhannagar, Calcutta 700064 (India)

    1995-09-01

    Alpha scattering from {sup 9}Be at {ital E}{sub {alpha}}= 65 MeV is described in the coupled channel framework with phenomenological as well as folded potentials. The multipole components of the deformed density of {sup 9}Be are derived from Nilsson model wave functions. Reasonably good agreements are obtained for the angular distributions of 3/2{sup {minus}}(g.s.) and 5/2{sup {minus}}(2.43 MeV) states of the ground state band with folded potentials. The deformation predicted by the model corroborates with that derived from the phenomenological analysis with potentials of different geometries.

  6. Modeling of folds and folding pathways for some protein families of (α + β)- and (α/β)-classes.

    Science.gov (United States)

    Gordeev, Alexey B; Efimov, Alexander V

    2013-01-01

    In this paper, updated structural trees for α/β-proteins containing five- and seven-segment (α/β)-motifs are represented. Novel structural motifs occurring in some families of (α + β)- and (α/β)-proteins are also characterized. Databases of these proteins have been compiled from the Protein Data Bank (PDB) and Structural Classification of Proteins (SCOP) and the corresponding structural trees have been constructed. The classification of these proteins has been developed and organized as an extension of the PCBOST database, which is available at http://strees.protres.ru . In total, the updated Protein Classification Based on Structural Trees database contains 11 structural trees, 106 levels, 635 folds, 4911 proteins and domains, and 14,202 PDB entries.

  7. Three-Dimensional Flow Separation Induced by a Model Vocal Fold Polyp

    Science.gov (United States)

    Stewart, Kelley C.; Erath, Byron D.; Plesniak, Michael W.

    2012-11-01

    The fluid-structure energy exchange process for normal speech has been studied extensively, but it is not well understood for pathological conditions. Polyps and nodules, which are geometric abnormalities that form on the medial surface of the vocal folds, can disrupt vocal fold dynamics and thus can have devastating consequences on a patient's ability to communicate. A recent in-vitro investigation of a model polyp in a driven vocal fold apparatus demonstrated that such a geometric abnormality considerably disrupts the glottal jet behavior and that this flow field adjustment was a likely reason for the severe degradation of the vocal quality in patients. Understanding of the formation and propagation of vortical structures from a geometric protuberance, and their subsequent impact on the aerodynamic loadings that drive vocal fold dynamic, is a critical component in advancing the treatment of this pathological condition. The present investigation concerns the three-dimensional flow separation induced by a wall-mounted prolate hemispheroid with a 2:1 aspect ratio in cross flow, i.e. a model vocal fold polyp. Unsteady three-dimensional flow separation and its impact of the wall pressure loading are examined using skin friction line visualization and wall pressure measurements. Supported by the National Science Foundation, Grant No. CBET-1236351 and GW Center for Biomimetics and Bioinspired Engineering (COBRE).

  8. Cross-tropopause Transport In Tropopause Folds: Mechanisms and Sensitivity To Model Resolution

    Science.gov (United States)

    Gray, S. L.

    The rate and processes of transfer of mass and chemical species between the strato- sphere and troposphere (stratosphere-troposphere exchange) are currently uncertain. In the midlatitudes exchange appears to be dominated by processes associated with tropopause folds and cut-off lows. The development of a tropopause fold is a reversible process and thus irreversible processes must occur for the permanent transfer of ma- terial across the tropopause boundary. Proposed processes include turbulent mixing, quasi-isentropic mixing, convectively breaking gravity waves, deep convection and radiative heating. Numerical models run at typical climate or regional-scale resolutions are unable to re- solve the fine-scale features observed in tropopause folds. It is hypothesised that both the rate of exchange and its partitioning into different processes, as derived from nu- merical model simulations, are sensitive to model resolution. This hypothesis is tested through simulations of a tropopause folding event associated with a vigorous surface cold front which tracked across the British Isles. Climate to high-mesoscale resolution simulations incorporating passive tracers are performed using the mesoscale version of the Met Office Unified Model. The mechanism by which the parametrized convec- tion leads to exchange is the subject of further examination.

  9. Folding model analysis of the nucleus–nucleus scattering based on ...

    Indian Academy of Sciences (India)

    2016-11-03

    Nov 3, 2016 ... using the hyperspherical calculations on the basis of Jacobi coordinates. The numerical results for the interaction potential and the differential scattering are in good agreement with the previous works. Keywords. Double folding model; M3Y interaction; differential equation; Yukawa potential; hyperspherical.

  10. Folding model analysis of the nucleus–nucleus scattering based on ...

    Indian Academy of Sciences (India)

    ... Lecture Workshops · Refresher Courses · Symposia · Live Streaming. Home; Journals; Pramana – Journal of Physics; Volume 87; Issue 6. Folding model analysis of the nucleus–nucleus scattering based on Jacobi coordinates. F PAKDEL A A RAJABI L NICKHAH. Regular Volume 87 Issue 6 December 2016 Article ID 90 ...

  11. Finite Element Modelling of Bends and Creases during Folding Ultra Thin Stainless Steel Foils

    NARCIS (Netherlands)

    Datta, K.; Akagi, H.; Geijselaers, Hubertus J.M.; Huetink, Han

    2003-01-01

    Finite Element Modelling of an ultra thin foil of SUS 304 stainless steel is carried out. These foils are 20 mm and below in thickness. The development of stresses and strains during folding of these foils is studied. The objective of this study is to induce qualities of paper in the foils of

  12. Structural model of the eastern Achara-Trialeti fold and thrust belt using seismic reflection profiles

    Science.gov (United States)

    Alania, Victor; Chabukiani, Alexander; Enukidze, Onise; Razmadze, Alexander; Sosson, Marc; Tsereteli, Nino; Varazanashvili, Otar

    2017-04-01

    Our study focused on the structural geometry at the eastern Achara-Trialeti fold and thrust belt (ATFTB) located at the retro-wedge of the Lesser Caucasus orogen (Alania et al., 2016a). Our interpretation has integrated seismic reflection profiles, several oil-wells, and the surface geology data to reveal structural characteristics of the eastern ATFTB. Fault-related folding theories were used to seismic interpretation (Shaw et al., 2004). Seismic reflection data reveal the presence of basement structural wedge, south-vergent backthrust, north-vergent forethrust and some structural wedges (or duplex). The rocks are involved in the deformation range from Paleozoic basement rocks to Tertiary strata. Building of thick-skinned structures of eastern Achara-Trialeti was formed by basement wedges propagated from south to north along detachment horizons within the cover generating thin-skinned structures. The kinematic evolution of the south-vergent backthrust zone with respect to the northward propagating structural wedge (or duplexes). The main style of deformation within the backthrust belt is a series of fault-propagation folds. Frontal part of eastern ATFTB are represent by triangle zone (Alania et al., 2016b; Sosson et al., 2016). A detailed study was done for Tbilisi area: seismic refection profiles, serial balanced cross-sections, and earthquakes reveal the presence of an active blind thrust fault beneath Tbilisi. 2 & 3-D structural models show that 2002 Mw 4.5 Tbilisi earthquake related to a north-vergent blind thrust. Empirical relations between blind fault rupture area and magnitude suggest that these fault segments could generate earthquakes of Mw 6.5. The growth fault-propagation fold has been observed near Tbilisi in the frontal part of eastern ATFTB. Seismic reflection profile through Ormoiani syncline shows that south-vergent growth fault-propagation fold related to out-of-the-syncline thrust. The outcrop of fault-propagation fold shown the geometry of the

  13. Folding of proteins with an all-atom Go-model.

    Science.gov (United States)

    Wu, L; Zhang, J; Qin, M; Liu, F; Wang, W

    2008-06-21

    The Go-like potential at a residual level has been successfully applied to the folding of proteins in many previous works. However, taking into consideration more detailed structural information in the atomic level, the definition of contacts used in these traditional Go-models may not be suitable for all-atom simulations. Here, in this work, we develop a rational definition of contacts considering the screening effect in the crowded intramolecular environment. In such a scheme, a large amount of screened atom pairs are excluded and the number of contacts is decreased compared to the case of the traditional definition. These contacts defined by such a new definition are compatible with the all-atom representation of protein structures. To verify the rationality of the new definition of contacts, the folding of proteins CI2 and SH3 is simulated by all-atom molecular dynamics simulations. A high folding cooperativity and good correlation of the simulated Phi-values with those obtained experimentally, especially for CI2, are found. This suggests that the all-atom Go-model is improved compared to the traditional Go-model. Based on the comparison of the Phi-values, the roles of side chains in the folding are discussed, and it is concluded that the side-chain structures are more important for local contacts in determining the transition state structures. Moreover, the relations between side chain and backbone orderings are also discussed.

  14. Identifying Conformational-Selection and Induced-Fit Aspects in the Binding-Induced Folding of PMI from Markov State Modeling of Atomistic Simulations.

    Science.gov (United States)

    Paul, Fabian; Noé, Frank; Weikl, Thomas R

    2018-03-27

    Unstructured proteins and peptides typically fold during binding to ligand proteins. A challenging problem is to identify the mechanism and kinetics of these binding-induced folding processes in experiments and atomistic simulations. In this Article, we present a detailed picture for the folding of the inhibitor peptide PMI into a helix during binding to the oncoprotein fragment 25-109 Mdm2 obtained from atomistic, explicit-water simulations and Markov state modeling. We find that binding-induced folding of PMI is highly parallel and can occur along a multitude of pathways. Some pathways are induced-fit-like with binding occurring prior to PMI helix formation, while other pathways are conformational-selection-like with binding after helix formation. On the majority of pathways, however, binding is intricately coupled to folding, without clear temporal ordering. A central feature of these pathways is PMI motion on the Mdm2 surface, along the binding groove of Mdm2 or over the rim of this groove. The native binding groove of Mdm2 thus appears as an asymmetric funnel for PMI binding. Overall, binding-induced folding of PMI does not fit into the classical picture of induced fit or conformational selection that implies a clear temporal ordering of binding and folding events. We argue that this holds in general for binding-induced folding processes because binding and folding events in these processes likely occur on similar time scales and do exhibit the time-scale separation required for temporal ordering.

  15. Generic framework for mining cellular automata models on protein-folding simulations.

    Science.gov (United States)

    Diaz, N; Tischer, I

    2016-05-13

    Cellular automata model identification is an important way of building simplified simulation models. In this study, we describe a generic architectural framework to ease the development process of new metaheuristic-based algorithms for cellular automata model identification in protein-folding trajectories. Our framework was developed by a methodology based on design patterns that allow an improved experience for new algorithms development. The usefulness of the proposed framework is demonstrated by the implementation of four algorithms, able to obtain extremely precise cellular automata models of the protein-folding process with a protein contact map representation. Dynamic rules obtained by the proposed approach are discussed, and future use for the new tool is outlined.

  16. Generalized, Linear, and Mixed Models

    CERN Document Server

    McCulloch, Charles E; Neuhaus, John M

    2011-01-01

    An accessible and self-contained introduction to statistical models-now in a modernized new editionGeneralized, Linear, and Mixed Models, Second Edition provides an up-to-date treatment of the essential techniques for developing and applying a wide variety of statistical models. The book presents thorough and unified coverage of the theory behind generalized, linear, and mixed models and highlights their similarities and differences in various construction, application, and computational aspects.A clear introduction to the basic ideas of fixed effects models, random effects models, and mixed m

  17. IntFOLD: an integrated server for modelling protein structures and functions from amino acid sequences.

    Science.gov (United States)

    McGuffin, Liam J; Atkins, Jennifer D; Salehe, Bajuna R; Shuid, Ahmad N; Roche, Daniel B

    2015-07-01

    IntFOLD is an independent web server that integrates our leading methods for structure and function prediction. The server provides a simple unified interface that aims to make complex protein modelling data more accessible to life scientists. The server web interface is designed to be intuitive and integrates a complex set of quantitative data, so that 3D modelling results can be viewed on a single page and interpreted by non-expert modellers at a glance. The only required input to the server is an amino acid sequence for the target protein. Here we describe major performance and user interface updates to the server, which comprises an integrated pipeline of methods for: tertiary structure prediction, global and local 3D model quality assessment, disorder prediction, structural domain prediction, function prediction and modelling of protein-ligand interactions. The server has been independently validated during numerous CASP (Critical Assessment of Techniques for Protein Structure Prediction) experiments, as well as being continuously evaluated by the CAMEO (Continuous Automated Model Evaluation) project. The IntFOLD server is available at: http://www.reading.ac.uk/bioinf/IntFOLD/. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  18. Influence of Embedded Fibers and an Epithelium Layer on the Glottal Closure Pattern in a Physical Vocal Fold Model

    Science.gov (United States)

    Xuan, Yue; Zhang, Zhaoyan

    2014-01-01

    Purpose: The purpose of this study was to explore the possible structural and material property features that may facilitate complete glottal closure in an otherwise isotropic physical vocal fold model. Method: Seven vocal fold models with different structural features were used in this study. An isotropic model was used as the baseline model, and…

  19. The general NFP hospital model.

    Science.gov (United States)

    Al-Amin, Mona

    2012-01-01

    Throughout the past 30 years, there has been a lot of controversy surrounding the proliferation of new forms of health care delivery organizations that challenge and compete with general NFP community hospitals. Traditionally, the health care system in the United States has been dominated by general NFP (NFP) voluntary hospitals. With the number of for-profit general hospitals, physician-owned specialty hospitals, and ambulatory surgical centers increasing, a question arises: “Why is the general NFP community hospital the dominant model?” In order to address this question, this paper reexamines the history of the hospital industry. By understanding how the “general NFP hospital” model emerged and dominated, we attempt to explain the current dominance of general NFP hospitals in the ever changing hospital industry in the United States.

  20. Introduction to generalized linear models

    CERN Document Server

    Dobson, Annette J

    2008-01-01

    Introduction Background Scope Notation Distributions Related to the Normal Distribution Quadratic Forms Estimation Model Fitting Introduction Examples Some Principles of Statistical Modeling Notation and Coding for Explanatory Variables Exponential Family and Generalized Linear Models Introduction Exponential Family of Distributions Properties of Distributions in the Exponential Family Generalized Linear Models Examples Estimation Introduction Example: Failure Times for Pressure Vessels Maximum Likelihood Estimation Poisson Regression Example Inference Introduction Sampling Distribution for Score Statistics Taylor Series Approximations Sampling Distribution for MLEs Log-Likelihood Ratio Statistic Sampling Distribution for the Deviance Hypothesis Testing Normal Linear Models Introduction Basic Results Multiple Linear Regression Analysis of Variance Analysis of Covariance General Linear Models Binary Variables and Logistic Regression Probability Distributions ...

  1. Prediction of RNA pseudoknots using heuristic modeling with mapping and sequential folding.

    Directory of Open Access Journals (Sweden)

    Wayne K Dawson

    Full Text Available Predicting RNA secondary structure is often the first step to determining the structure of RNA. Prediction approaches have historically avoided searching for pseudoknots because of the extreme combinatorial and time complexity of the problem. Yet neglecting pseudoknots limits the utility of such approaches. Here, an algorithm utilizing structure mapping and thermodynamics is introduced for RNA pseudoknot prediction that finds the minimum free energy and identifies information about the flexibility of the RNA. The heuristic approach takes advantage of the 5' to 3' folding direction of many biological RNA molecules and is consistent with the hierarchical folding hypothesis and the contact order model. Mapping methods are used to build and analyze the folded structure for pseudoknots and to add important 3D structural considerations. The program can predict some well known pseudoknot structures correctly. The results of this study suggest that many functional RNA sequences are optimized for proper folding. They also suggest directions we can proceed in the future to achieve even better results.

  2. Lost in folding space? Comparing four variants of the thermodynamic model for RNA secondary structure prediction

    Directory of Open Access Journals (Sweden)

    Janssen Stefan

    2011-11-01

    Full Text Available Abstract Background Many bioinformatics tools for RNA secondary structure analysis are based on a thermodynamic model of RNA folding. They predict a single, "optimal" structure by free energy minimization, they enumerate near-optimal structures, they compute base pair probabilities and dot plots, representative structures of different abstract shapes, or Boltzmann probabilities of structures and shapes. Although all programs refer to the same physical model, they implement it with considerable variation for different tasks, and little is known about the effects of heuristic assumptions and model simplifications used by the programs on the outcome of the analysis. Results We extract four different models of the thermodynamic folding space which underlie the programs RNAFOLD, RNASHAPES, and RNASUBOPT. Their differences lie within the details of the energy model and the granularity of the folding space. We implement probabilistic shape analysis for all models, and introduce the shape probability shift as a robust measure of model similarity. Using four data sets derived from experimentally solved structures, we provide a quantitative evaluation of the model differences. Conclusions We find that search space granularity affects the computed shape probabilities less than the over- or underapproximation of free energy by a simplified energy model. Still, the approximations perform similar enough to implementations of the full model to justify their continued use in settings where computational constraints call for simpler algorithms. On the side, we observe that the rarely used level 2 shapes, which predict the complete arrangement of helices, multiloops, internal loops and bulges, include the "true" shape in a rather small number of predicted high probability shapes. This calls for an investigation of new strategies to extract high probability members from the (very large level 2 shape space of an RNA sequence. We provide implementations of all four

  3. Short-wavelength Contractional Structures in Venusian Fold Belts: Additional Constraints From New Models

    Science.gov (United States)

    Ghent, R.; Phillips, R.; Hansen, V.; Nunes, D.

    2002-12-01

    We have previously reported on the development of very short-wavelength (30 km [1, 2]. We simulated the initiation and growth of VST using finite-element models with uniform composition and elasto-visco-plastic rheology undergoing simultaneous cooling and shortening. The models were constrained by Magellan SAR imagery and motivated by the current plume hypothesis for crustal plateau origin [3, 4]. We determined that VST developed only in models with surface temperatures near 1000 K and elevated thermal gradients derived from a halfspace cooling model with initial uniform temperatures of 1200-1400 K. Model rheological profiles indicated a truly viscoplastic character, in which both creep and plastic mechanisms were significant at shallow depths. The resulting topography showed both very short-wavelength components and slightly longer-wavelength, low amplitude folds, as is common in Venusian crustal plateau fold belts. New simulations with greater spatial extent and higher mesh resolution allow further exploration of the interplay between viscous and plastic processes during VST development. Wider models allow more detailed investigation of viscous folding on the 1-4 km scale. We also employ temperature-dependent thermal conductivity [5] to better represent the thermal behavior of the model crust. The additional insight and expanded parameter space provided by these new models allow us to place improved constraints on the early thermal and mechanical evolution of crustal plateaus. [1] Ghent, R.R., R.J. Phillips, V.L. Hansen, and D.C. Nunes, Eos Trans. AGU, 83(19), Spring Meet. Suppl., Abstract P21A-05, 2002. [2] Ghent, R.R., R.J. Phillips, and V.L. Hansen, 2001, Eos Trans. AGU, 82(47), Spring Meet. Suppl., Abstract T41B-0865, 2001. [3] Hansen, V.L. and J.J. Willis, Icarus, 132, 321-343, 1998. [4] Phillips, R.J. and V.L. Hansen, Science, 279, p1492, 1998. [5] Hofmeister, A, Science, 283, p1699, 1999.

  4. 3D Fault modeling of the active Chittagong-Myanmar fold belt, Bangladesh

    Science.gov (United States)

    Peterson, D. E.; Hubbard, J.; Akhter, S. H.; Shamim, N.

    2013-12-01

    The Chittagong-Myanmar fold belt (CMFB), located in eastern Bangladesh, eastern India and western Myanmar, accommodates east-west shortening at the India-Burma plate boundary. Oblique subduction of the Indian Plate beneath the Burma Plate since the Eocene has led to the development of a large accretionary prism complex, creating a series of north-south trending folds. A continuous sediment record from ~55 Ma to the present has been deposited in the Bengal Basin by the Ganges-Brahmaputra-Meghna rivers, providing an opportunity to learn about the history of tectonic deformation and activity in this fold-and-thrust belt. Surface mapping indicates that the fold-and-thrust belt is characterized by extensive N-S-trending anticlines and synclines in a belt ~150-200 km wide. Seismic reflection profiles from the Chittagong and Chittagong Hill Tracts, Bangladesh, indicate that the anticlines mapped at the surface narrow with depth and extend to ~3.0 seconds TWTT (two-way travel time), or ~6.0 km. The folds of Chittagong and Chittagong Hill Tracts are characterized by doubly plunging box-shaped en-echelon anticlines separated by wide synclines. The seismic data suggest that some of these anticlines are cored by thrust fault ramps that extend to a large-scale décollement that dips gently to the east. Other anticlines may be the result of detachment folding from the same décollement. The décollement likely deepens to the east and intersects with the northerly-trending, oblique-slip Kaladan fault. The CMFB region is bounded to the north by the north-dipping Dauki fault and the Shillong Plateau. The tectonic transition from a wide band of E-W shortening in the south to a narrow zone of N-S shortening along the Dauki fault is poorly understood. We integrate surface and subsurface datasets, including topography, geological maps, seismicity, and industry seismic reflection profiles, into a 3D modeling environment and construct initial 3D surfaces of the major faults in this

  5. A numerical strategy for finite element modeling of frictionless asymmetric vocal fold collision

    DEFF Research Database (Denmark)

    Granados, Alba; Misztal, Marek Krzysztof; Brunskog, Jonas

    2016-01-01

    . Theoretical background and numerical analysis of the finite-element position-based contact model are presented, along with validation. A novel contact detection mechanism capable to detect collision in asymmetric oscillations is developed. The effect of inexact contact constraint enforcement on vocal fold...... dynamics is examined by different variational methods for inequality constrained minimization problems, namely the Lagrange multiplier method and the penalty method. In contrast to the penalty solution, which is related to classical spring-like contact forces, numerical examples show that the parameter......-independent Lagrange multiplier solution is more robust and accurate in the estimation of dynamical and mechanical features at vocal fold contact. Furthermore, special attention is paid to the temporal integration schemes in relation to the contact problem, the results suggesting an advantage of highly diffusive...

  6. The limit fold change model: A practical approach for selecting differentially expressed genes from microarray data

    Directory of Open Access Journals (Sweden)

    Rytz Andreas

    2002-06-01

    Full Text Available Abstract Background The biomedical community is developing new methods of data analysis to more efficiently process the massive data sets produced by microarray experiments. Systematic and global mathematical approaches that can be readily applied to a large number of experimental designs become fundamental to correctly handle the otherwise overwhelming data sets. Results The gene selection model presented herein is based on the observation that: (1 variance of gene expression is a function of absolute expression; (2 one can model this relationship in order to set an appropriate lower fold change limit of significance; and (3 this relationship defines a function that can be used to select differentially expressed genes. The model first evaluates fold change (FC across the entire range of absolute expression levels for any number of experimental conditions. Genes are systematically binned, and those genes within the top X% of highest FCs for each bin are evaluated both with and without the use of replicates. A function is fitted through the top X% of each bin, thereby defining a limit fold change. All genes selected by the 5% FC model lie above measurement variability using a within standard deviation (SDwithin confidence level of 99.9%. Real time-PCR (RT-PCR analysis demonstrated 85.7% concordance with microarray data selected by the limit function. Conclusion The FC model can confidently select differentially expressed genes as corroborated by variance data and RT-PCR. The simplicity of the overall process permits selecting model limits that best describe experimental data by extracting information on gene expression patterns across the range of expression levels. Genes selected by this process can be consistently compared between experiments and enables the user to globally extract information with a high degree of confidence.

  7. Brane brick models, toric Calabi-Yau 4-folds and 2d (0,2) quivers

    Energy Technology Data Exchange (ETDEWEB)

    Franco, Sebastián [Physics Department, The City College of the CUNY, 160 Convent Avenue, New York, NY 10031 (United States); The Graduate School and University Center, The City University of New York,365 Fifth Avenue, New York NY 10016 (United States); Lee, Sangmin [Center for Theoretical Physics, Seoul National University,Seoul 08826 (Korea, Republic of); Department of Physics and Astronomy, Seoul National University,Seoul 08826 (Korea, Republic of); College of Liberal Studies, Seoul National University,Seoul 08826 (Korea, Republic of); School of Natural Sciences, Institute for Advanced Study,Princeton, NJ 08540 (United States); Seong, Rak-Kyeong [School of Physics, Korea Institute for Advanced Study,Seoul 02455 (Korea, Republic of)

    2016-02-08

    We introduce brane brick models, a novel type of Type IIA brane configurations consisting of D4-branes ending on an NS5-brane. Brane brick models are T-dual to D1-branes over singular toric Calabi-Yau 4-folds. They fully encode the infinite class of 2d (generically) N=(0,2) gauge theories on the worldvolume of the D1-branes and streamline their connection to the probed geometries. For this purpose, we also introduce new combinatorial procedures for deriving the Calabi-Yau associated to a given gauge theory and vice versa.

  8. ModFOLD6: an accurate web server for the global and local quality estimation of 3D protein models.

    Science.gov (United States)

    Maghrabi, Ali H A; McGuffin, Liam J

    2017-07-03

    Methods that reliably estimate the likely similarity between the predicted and native structures of proteins have become essential for driving the acceptance and adoption of three-dimensional protein models by life scientists. ModFOLD6 is the latest version of our leading resource for Estimates of Model Accuracy (EMA), which uses a pioneering hybrid quasi-single model approach. The ModFOLD6 server integrates scores from three pure-single model methods and three quasi-single model methods using a neural network to estimate local quality scores. Additionally, the server provides three options for producing global score estimates, depending on the requirements of the user: (i) ModFOLD6_rank, which is optimized for ranking/selection, (ii) ModFOLD6_cor, which is optimized for correlations of predicted and observed scores and (iii) ModFOLD6 global for balanced performance. The ModFOLD6 methods rank among the top few for EMA, according to independent blind testing by the CASP12 assessors. The ModFOLD6 server is also continuously automatically evaluated as part of the CAMEO project, where significant performance gains have been observed compared to our previous server and other publicly available servers. The ModFOLD6 server is freely available at: http://www.reading.ac.uk/bioinf/ModFOLD/. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  9. Determination of true bed thickness using folded bed model and borehole data

    Energy Technology Data Exchange (ETDEWEB)

    Xu, S.S.; Velasquillo-Martinez, L.G.; Grajales-Nishimura, J.M.; Murillo-Muneton, G. [Inst. Mexicano del Petroleo, Mexico City (Mexico); Garcia-Hernandez, J. [Petroleos Mexicanos Exploracion y Produccion, Tamaulipas (Mexico); Nieto-Samaniego, A.F. [Nacional Autonoma de Mexico Univ., Veracruz (Mexico). Centro de Geociencias

    2007-11-15

    The actual thickness of a given formation perpendicular to the bedding plane is known as the true bed thickness. Petroleum engineers rely on information regarding true bed thickness, particularly in dipping beds and in deviated holes because reservoir volume and isochore maps depend on these properties and not on the measured thickness. True bed thickness can be estimated from information gathered from well logs such as the dipmeter and borehole images. However, when deviations and dips exceed 10 degrees, corrections are needed. In this paper, a folded bed model was proposed to calculate the true bed thickness in the subsurface utilizing well log data. The value of true bed thickness (t) was shown to depend on the angle and the direction of the dip of the measured formation, as well as the drift angle and azimuth of the borehole. A case study from the Cantarell oil field in the southern Gulf of Mexico, offshore Campeche, was used to test the folded bed method. The model was shown to yield more uniform spatial change of the values of t, compared to the monoclinal bed model that often overestimates the average value of t. The maximum relative deviation of t from the monoclinal bed model reached 22.3 per cent and the maximum absolute deviation of t reached 34.5 m. The key factors that influence the values of t were found to be the bed dip, the dip difference between the top and base of the bed and the deviated angle of the well. The folded bed model yielded fewer changed values of the true bed thickness. 10 refs., 2 tabs., 9 figs.

  10. Multivariate covariance generalized linear models

    DEFF Research Database (Denmark)

    Bonat, W. H.; Jørgensen, Bent

    2016-01-01

    We propose a general framework for non-normal multivariate data analysis called multivariate covariance generalized linear models, designed to handle multivariate response variables, along with a wide range of temporal and spatial correlation structures defined in terms of a covariance link...... function combined with a matrix linear predictor involving known matrices. The method is motivated by three data examples that are not easily handled by existing methods. The first example concerns multivariate count data, the second involves response variables of mixed types, combined with repeated...... measures and longitudinal structures, and the third involves a spatiotemporal analysis of rainfall data. The models take non-normality into account in the conventional way by means of a variance function, and the mean structure is modelled by means of a link function and a linear predictor. The models...

  11. A Self-Assisting Protein Folding Model for Teaching Structural Molecular Biology.

    Science.gov (United States)

    Davenport, Jodi; Pique, Michael; Getzoff, Elizabeth; Huntoon, Jon; Gardner, Adam; Olson, Arthur

    2017-04-04

    Structural molecular biology is now becoming part of high school science curriculum thus posing a challenge for teachers who need to convey three-dimensional (3D) structures with conventional text and pictures. In many cases even interactive computer graphics does not go far enough to address these challenges. We have developed a flexible model of the polypeptide backbone using 3D printing technology. With this model we have produced a polypeptide assembly kit to create an idealized model of the Triosephosphate isomerase mutase enzyme (TIM), which forms a structure known as TIM barrel. This kit has been used in a laboratory practical where students perform a step-by-step investigation into the nature of protein folding, starting with the handedness of amino acids to the formation of secondary and tertiary structure. Based on the classroom evidence we collected, we conclude that these models are valuable and inexpensive resource for teaching structural molecular biology. Copyright © 2017 Elsevier Ltd. All rights reserved.

  12. Communication: Role of explicit water models in the helix folding/unfolding processes

    Science.gov (United States)

    Palazzesi, Ferruccio; Salvalaglio, Matteo; Barducci, Alessandro; Parrinello, Michele

    2016-09-01

    In the last years, it has become evident that computer simulations can assume a relevant role in modelling protein dynamical motions for their ability to provide a full atomistic image of the processes under investigation. The ability of the current protein force-fields in reproducing the correct thermodynamics and kinetics systems behaviour is thus an essential ingredient to improve our understanding of many relevant biological functionalities. In this work, employing the last developments of the metadynamics framework, we compare the ability of state-of-the-art all-atom empirical functions and water models to consistently reproduce the folding and unfolding of a helix turn motif in a model peptide. This theoretical study puts in evidence that the choice of the water models can influence the thermodynamic and the kinetics of the system under investigation, and for this reason cannot be considered trivial.

  13. Cosmological models in general relativity

    Indian Academy of Sciences (India)

    Cosmological models in general relativity. B B PAUL. Department of Physics, Nowgong College, Nagaon, Assam, India. MS received 4 October 2002; revised 6 March 2003; accepted 21 May 2003. Abstract. LRS Bianchi type-I space-time filled with perfect fluid is considered here with deceler- ation parameter as variable.

  14. Deuteron nuclear interaction potential with heavy nuclei in single folding model

    Directory of Open Access Journals (Sweden)

    O. V. Babak

    2013-09-01

    Full Text Available Deuteron interaction potential with heavy nuclei at sub-barrier energies has been constructed in the frame-work of single folding model using the complex dynamic polarization potential. It is shown that the account of finite deuteron size leads to significant increasing of nuclear potential in outer region of interaction. Cross sec-tions of deuteron elastic scattering on 208Pb at energy 7, 7.3 and 8 MeV were calculated and compared with ex-periment data. Calculations were performed without any variations of parameters.

  15. Use of the peritracheal fold in the dog tracheal transplantation model.

    Science.gov (United States)

    Gannon, P J; Costantino, P D; Lueg, E A; Chaplin, J M; Brandwein, M S; Passalaqua, P J; Fliegelman, L J; Laitman, J T; Marquez, S; Urken, M L

    1999-09-01

    To investigate the technical aspects of the canine model of human tracheal transplantation for potential application to reconstruction of extremely long tracheal defects (> 10 cm). In phase 1, long tracheal segments were skeletonized and pedicled with the thyroid glands, cranial thyroid arteries and veins, and internal jugular vein branches. The segments were elevated completely, attached to the vascular pedicle only, and replaced with primary tracheal anastomoses. In phase 2, long segments were elevated along with a diffuse soft tissue "blanket" that envelops the trachea and thyroid glands. Because this study was designed to primarily address, in situ, tracheal perfusion territories of a cranially located vascular pedicle, microvascular anastomoses were not conducted. Two small-bodied beagles (10-15 kg) and 5 large-bodied mixed-breed dogs (20-30 kg) were humanely killed 2 to 41 days after surgery, and anatomic and histological analyses were conducted. Unlike that of humans, the thyroid gland complex of dogs is not intimately associated with the trachea but is conjoined with a peritracheal soft tissue "fold." Within this fold, blood is transmitted to the trachea via a diffuse, segmental vascular plexus. In phase 1, pronounced tracheal necrosis occurred within 2 to 5 days. In phase 2, extremely long tracheal segments (10-12 cm), based only on a cranially located pedicle, were still viable at 2 to 6 weeks. Preservation of the "peritracheal fold" in the dog model of tracheal transplantation is critical to the onset and maintenance of vascular perfusion in a long tracheal segment. Furthermore, the use of large-bodied dogs is necessary to provide for a usable venous efflux component.

  16. Quasy-3D models of restored folded sedimentary cover of Alpine Greater Caucasus and evidences of isostasy participation in processes of folding formation and of mountain building

    Science.gov (United States)

    Yakovlev, Fedor

    2015-04-01

    structural cells were found as 49% in average for ShZ (with deviations 37÷62%), 55% for TZ (36÷67%), 57% for ChZ (46÷67%) and 35% for NWC (0÷15÷67%). Correlations of six parameters of 78 cells were analyzed [4]: 1) value of shortening, 2) initial thickness of a sedimentary cover (stage A), 3) depth of post-folded basement top (stage B, calculation on 1 and 2), 4) actual depth of the basement (stage C, calculation on 3 and 5), 5) "amplitude of a neotectonic uplift", 6) "difference of depths" of basement top (between positions for stages C and A, parameters 2 and 4). For structures of NWC, for full (42 cells) and selected (32) sampling, important correlations of parameters were found: 1/5 R=0.79 (0.59), strong association; 1/6 R = -0.40 (-0.52), moderate; 2/6 R=0.40 (0.54) moderate. The same correlations for structures of TZ, ShZ and ChZ together made values R (1/5, 1/6, 2/6) = 0.63, -0.63, 0.36, and all-78 cells together have R = 0.81, -0.44, 0.39. Genetic interpretation of these three correlations were found as following: the more initial thickness of a sedimentary cover (2) preset the more difference of depths of the basement (6), deeper syn-folding and general subsidence (3 and 6) preset the more the value of shortening (1), and uplift and erosion (5) depends on shortening (1). Average actual depths of basement top were close to initial thickness of sedimentary cover (parameters 2, 4) in the regions ShZ, TZ, ChZ, NWC [1, 3, 4]: -10 (-10) km, -13 (-12), -15 (-21) km, -13 (-13) km. Stability of this position is confirming by dependence of "uplift" from shortening (5/1) for the same regions: +9.64km/52%, +19.16/55%, +16.0/57%, +8.9km/35%. For NWC, as sequence for 8 sections, average values of "depth difference" (6) have small deviation from "0" (as maximal ±3.5), but inside sections it may be very large (+2.1/-14.6, +7.5/-11, +5.8/-12.9 km). Analyses of stratigraphic column and of geological history of GC together with data about shortening values for tectonic zones (in

  17. Spherical aberration correction with an in-lens N-fold symmetric line currents model.

    Science.gov (United States)

    Hoque, Shahedul; Ito, Hiroyuki; Nishi, Ryuji

    2018-04-01

    In our previous works, we have proposed N-SYLC (N-fold symmetric line currents) models for aberration correction. In this paper, we propose "in-lens N-SYLC" model, where N-SYLC overlaps rotationally symmetric lens. Such overlap is possible because N-SYLC is free of magnetic materials. We analytically prove that, if certain parameters of the model are optimized, an in-lens 3-SYLC (N = 3) doublet can correct 3rd order spherical aberration. By computer simulation, we show that the required excitation current for correction is less than 0.25 AT for beam energy 5 keV, and the beam size after correction is smaller than 1 nm at the corrector image plane for initial slope less than 4 mrad. Copyright © 2018 Elsevier B.V. All rights reserved.

  18. A replica exchange Monte Carlo algorithm for protein folding in the HP model

    Directory of Open Access Journals (Sweden)

    Shmygelska Alena

    2007-09-01

    Full Text Available Abstract Background The ab initio protein folding problem consists of predicting protein tertiary structure from a given amino acid sequence by minimizing an energy function; it is one of the most important and challenging problems in biochemistry, molecular biology and biophysics. The ab initio protein folding problem is computationally challenging and has been shown to be NP MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaat0uy0HwzTfgDPnwy1egaryqtHrhAL1wy0L2yHvdaiqaacqWFneVtcqqGqbauaaa@3961@-hard even when conformations are restricted to a lattice. In this work, we implement and evaluate the replica exchange Monte Carlo (REMC method, which has already been applied very successfully to more complex protein models and other optimization problems with complex energy landscapes, in combination with the highly effective pull move neighbourhood in two widely studied Hydrophobic Polar (HP lattice models. Results We demonstrate that REMC is highly effective for solving instances of the square (2D and cubic (3D HP protein folding problem. When using the pull move neighbourhood, REMC outperforms current state-of-the-art algorithms for most benchmark instances. Additionally, we show that this new algorithm provides a larger ensemble of ground-state structures than the existing state-of-the-art methods. Furthermore, it scales well with sequence length, and it finds significantly better conformations on long biological sequences and sequences with a provably unique ground-state structure, which is believed to be a characteristic of real proteins. We also present evidence that our REMC algorithm can fold sequences which exhibit significant interaction between termini in the hydrophobic core relatively easily. Conclusion We demonstrate that REMC utilizing the pull move

  19. Factors controlling the evolution of the Perdido Fold Belt, northwestern Gulf of Mexico, determined from numerical models

    Science.gov (United States)

    Gradmann, Sofie; Beaumont, Christopher; Albertz, Markus

    2009-04-01

    The Perdido Fold Belt (PFB) is a prominent salt-cored deep water structure in the northwestern Gulf of Mexico. It is characterized by symmetric, kink-banded folds of a ˜4.5 km thick prekinematic layer and its vicinity to the extensive Sigsbee Salt Canopy. We use 2-D finite element numerical models to study the evolution of the PFB as a gravity-driven fold belt both in a local context and in the context of the larger-scale passive margin, influenced by adjacent allochthonous salt structures. We show that parameters such as overburden strength, salt geometry, or salt viscosity determine timing, extent, and location of the modeled fold belt. Simplified models of the Gulf of Mexico show that toe-of-slope folding is a viable mechanism to develop diapirs in the deep salt basin and to delay folding of the distal overburden. In this scenario, the PFB likely represents the terminal folding of a much larger, diachronously formed fold belt system.

  20. Markov modeling of peptide folding in the presence of protein crowders

    Science.gov (United States)

    Nilsson, Daniel; Mohanty, Sandipan; Irbäck, Anders

    2018-02-01

    We use Markov state models (MSMs) to analyze the dynamics of a β-hairpin-forming peptide in Monte Carlo (MC) simulations with interacting protein crowders, for two different types of crowder proteins [bovine pancreatic trypsin inhibitor (BPTI) and GB1]. In these systems, at the temperature used, the peptide can be folded or unfolded and bound or unbound to crowder molecules. Four or five major free-energy minima can be identified. To estimate the dominant MC relaxation times of the peptide, we build MSMs using a range of different time resolutions or lag times. We show that stable relaxation-time estimates can be obtained from the MSM eigenfunctions through fits to autocorrelation data. The eigenfunctions remain sufficiently accurate to permit stable relaxation-time estimation down to small lag times, at which point simple estimates based on the corresponding eigenvalues have large systematic uncertainties. The presence of the crowders has a stabilizing effect on the peptide, especially with BPTI crowders, which can be attributed to a reduced unfolding rate ku, while the folding rate kf is left largely unchanged.

  1. Theoretical models for designing a 220-GHz folded waveguide backward wave oscillator

    Science.gov (United States)

    Cai, Jin-Chi; Hu, Lin-Lin; Ma, Guo-Wu; Chen, Hong-Bin; Jin, Xiao; Chen, Huai-Bi

    2015-06-01

    In this paper, the basic equations of beam-wave interaction for designing the 220 GHz folded waveguide (FW) backward wave oscillator (BWO) are described. On the whole, these equations are mainly classified into small signal model (SSM), large signal model (LSM), and simplified small signal model (SSSM). Using these linear and nonlinear one-dimensional (1D) models, the oscillation characteristics of the FW BWO of a given configuration of slow wave structure (SWS) can be calculated by numerical iteration algorithm, which is more time efficient than three-dimensional (3D) particle-in-cell (PIC) simulation. The SSSM expressed by analytical formulas is innovatively derived for determining the initial values of the FW SWS conveniently. The dispersion characteristics of the FW are obtained by equivalent circuit analysis. The space charge effect, the end reflection effect, the lossy wall effect, and the relativistic effect are all considered in our models to offer more accurate results. The design process of the FW BWO tube with output power of watt scale in a frequency range between 215 GHz and 225 GHz based on these 1D models is demonstrated. The 3D PIC method is adopted to verify the theoretical design results, which shows that they are in good agreement with each other. Project supported by the Innovative Research Foundation of China Academy of Engineering Physics (Grant No. 426050502-2).

  2. Asymptotic distribution of motifs in a stochastic context-free grammar model of RNA folding.

    Science.gov (United States)

    Poznanović, Svetlana; Heitsch, Christine E

    2014-12-01

    We analyze the distribution of RNA secondary structures given by the Knudsen-Hein stochastic context-free grammar used in the prediction program Pfold. Our main theorem gives relations between the expected number of these motifs--independent of the grammar probabilities. These relations are a consequence of proving that the distribution of base pairs, of helices, and of different types of loops is asymptotically Gaussian in this model of RNA folding. Proof techniques use singularity analysis of probability generating functions. We also demonstrate that these asymptotic results capture well the expected number of RNA base pairs in native ribosomal structures, and certain other aspects of their predicted secondary structures. In particular, we find that the predicted structures largely satisfy the expected relations, although the native structures do not.

  3. Constructing multi-resolution Markov State Models (MSMs) to elucidate RNA hairpin folding mechanisms.

    Science.gov (United States)

    Huang, Xuhui; Yao, Yuan; Bowman, Gregory R; Sun, Jian; Guibas, Leonidas J; Carlsson, Gunnar; Pande, Vijay S

    2010-01-01

    Simulating biologically relevant timescales at atomic resolution is a challenging task since typical atomistic simulations are at least two orders of magnitude shorter. Markov State Models (MSMs) provide one means of overcoming this gap without sacrificing atomic resolution by extracting long time dynamics from short simulations. MSMs coarse grain space by dividing conformational space into long-lived, or metastable, states. This is equivalent to coarse graining time by integrating out fast motions within metastable states. By varying the degree of coarse graining one can vary the resolution of an MSM; therefore, MSMs are inherently multi-resolution. Here we introduce a new algorithm Super-level-set Hierarchical Clustering (SHC), to our knowledge, the first algorithm focused on constructing MSMs at multiple resolutions. The key insight of this algorithm is to generate a set of super levels covering different density regions of phase space, then cluster each super level separately, and finally recombine this information into a single MSM. SHC is able to produce MSMs at different resolutions using different super density level sets. To demonstrate the power of this algorithm we apply it to a small RNA hairpin, generating MSMs at four different resolutions. We validate these MSMs by showing that they are able to reproduce the original simulation data. Furthermore, long time folding dynamics are extracted from these models. The results show that there are no metastable on-pathway intermediate states. Instead, the folded state serves as a hub directly connected to multiple unfolded/misfolded states which are separated from each other by large free energy barriers.

  4. Fermions as generalized Ising models

    Directory of Open Access Journals (Sweden)

    C. Wetterich

    2017-04-01

    Full Text Available We establish a general map between Grassmann functionals for fermions and probability or weight distributions for Ising spins. The equivalence between the two formulations is based on identical transfer matrices and expectation values of products of observables. The map preserves locality properties and can be realized for arbitrary dimensions. We present a simple example where a quantum field theory for free massless Dirac fermions in two-dimensional Minkowski space is represented by an asymmetric Ising model on a euclidean square lattice.

  5. Kinetic model for the coupling between allosteric transitions in GroEL and substrate protein folding and aggregation.

    Science.gov (United States)

    Tehver, Riina; Thirumalai, D

    2008-04-04

    The bacterial chaperonin GroEL and the co-chaperonin GroES assist in the folding of a number of structurally unrelated substrate proteins (SPs). In the absence of chaperonins, SP folds by the kinetic partitioning mechanism (KPM), according to which a fraction of unfolded molecules reaches the native state directly, while the remaining fraction gets trapped in a potentially aggregation-prone misfolded state. During the catalytic reaction cycle, GroEL undergoes a series of allosteric transitions (TR-->R"-->T) triggered by SP capture, ATP binding and hydrolysis, and GroES binding. We developed a general kinetic model that takes into account the coupling between the rates of the allosteric transitions and the folding and aggregation of the SP. Our model, in which the GroEL allosteric rates and SP-dependent folding and aggregation rates are independently varied without prior assumption, quantitatively fits the GroEL concentration-dependent data on the yield of native ribulose bisphosphate carboxylase/oxygenase (Rubisco) as a function of time. The extracted kinetic parameters for the GroEL reaction cycle are consistent with the available values from independent experiments. In addition, we also obtained physically reasonable parameters for the kinetic steps in the reaction cycle that are difficult to measure. If experimental values for GroEL allosteric rates are used, the time-dependent changes in native-state yield at eight GroEL concentrations can be quantitatively fit using only three SP-dependent parameters. The model predicts that the differences in the efficiencies (as measured by yields of the native state) of GroEL, single-ring mutant (SR1), and variants of SR1, in the rescue of mitochondrial malate dehydrogenase, citrate synthase, and Rubisco, are related to the large variations in the allosteric transition rates. We also show that GroEL/S mutants that efficiently fold one SP at the expense of all others are due to a decrease in the rate of a key step in the

  6. Modelling "reality" in tectonics: Simulation of the mechanical evolution of the Jura Mountains-Molasse Basin system, and routes to forward-inverse modelling of fold thrust belts.

    Science.gov (United States)

    Hindle, David; Kley, Jonas

    2016-04-01

    be dealt with by conditioning the top surface of the model to "trend" towards the present day topographic profile along the cross section, in a crude proxy for erosion. In the case of the Jura-Molasse fold thrust belt, the basal boundary condition also very likely plays a significant role in the thrust-belts evolution. A large, extra component of regional basement uplift appears to have occurred across the Swiss Molasse and Jura, according to geological indicators like the present day position and altitude of Miocene marine sedimentary units. In general, the Jura-Molasse example is thus highly instructive in the difficulties of incorporating all necessary geological realities into a numerical forward model of a specific geological situation. Despite all this, we find that using a numerical forward model of minimal complexity (three rheological layers as opposed to at least eight suggested by the rheological stratigraphy of the chain) with no pre-existing weaknesses to predetermine locations of faults, we easily achieve a good facsimile of at least the distribution of shortening across the Jura-Molasse system. Localisation of shortening occurs on approximately similar numbers of major faults as in reality, and their positions in the section are also broadly similar to those known from field data. Dynamic parameters like stress evolution, recovered from the model, are also in broad agreement with paleostress level indicators from the Jura-Molasse. In our first experiments, we have used a grid of variations of basic mechanical parameters (friction of basal layer and strength of main, limestone unit) to map the model responses over a range of parameter space and search for the best fitting response. The potential to automate such searches and continuously optimise the fit to real data is clearly also there, given sufficient computer capacity. Hence, we can envisage a time when cross section balancing will be combined with and improved by a subsequent stage of forward

  7. How the cortex gets its folds: an inside-out, connectivity-driven model for the scaling of mammalian cortical folding

    OpenAIRE

    Bruno eMota; Bruno eMota; Suzana eHerculano-Houzel; Suzana eHerculano-Houzel

    2012-01-01

    Larger mammalian cerebral cortices tend to have increasingly folded surfaces, often considered to result from the lateral expansion of the grey matter (GM), which, in a volume constrained by the cranium, causes mechanical compression that is relieved by inward folding of the white matter (WM), or to result from differential expansion of cortical layers. Across species, thinner cortices, presumably more pliable, would offer less resistance and hence become more folded than thicker cortices of ...

  8. Discrete gauge groups in F-theory models on genus-one fibered Calabi-Yau 4-folds without section

    Science.gov (United States)

    Kimura, Yusuke

    2017-04-01

    We determine the discrete gauge symmetries that arise in F-theory compactifications on examples of genus-one fibered Calabi-Yau 4-folds without a section. We construct genus-one fibered Calabi-Yau 4-folds using Fano manifolds, cyclic 3-fold covers of Fano 4-folds, and Segre embeddings of products of projective spaces. Discrete ℤ 5, ℤ 4, ℤ 3 and ℤ 2 symmetries arise in these constructions. We introduce a general method to obtain multisections for several constructions of genus-one fibered Calabi-Yau manifolds. The pullbacks of hyperplane classes under certain projections represent multisections to these genus-one fibrations. We determine the degrees of these multisections by computing the intersection numbers with fiber classes. As a result, we deduce the discrete gauge symmetries that arise in F-theory compactifications. This method applies to various Calabi-Yau genus-one fibrations.

  9. Self-oscillating Vocal Fold Model Mechanics: Healthy, Diseased, and Aging

    Science.gov (United States)

    Hiubler, Elizabeth P.; Pollok, Lucas F. E.; Apostoli, Adam G.; Hancock, Adrienne B.; Plesniak, Michael W.

    2014-11-01

    Voice disorders have been estimated to have a substantial economic impact of 2.5 billion annually. Approximately 30% of people will suffer from a voice disorder at some point in their lives. Life-sized, self-oscillating, synthetic vocal fold (VF) models are fabricated to exhibit material properties representative of human VFs. These models are created both with and without a polyp-like structure, a pathology that has been shown to produce rich viscous flow structures not normally observed for healthy VFs during normal phonation. Pressure measurements are acquired upstream of the VFs and high-speed images are captured at varying flow rates during VF oscillation to facilitate an understanding of the characteristics of healthy and diseased VFs. The images are analyzed using a videokymography line-scan technique. Clinically-relevant parameters calculated from the volume-velocity output of a circumferentially-vented mask (Rothenberg mask) are compared to human data collected from two groups of males aged 18-30 and 60-80. This study extends the use of synthetic VF models by assessing their ability to replicate behaviors observed in human subject data to advance a means of investigating changes associated with normal, pathological, and the aging voice. Supported by the GWU Institute for Biomedical Engineering (GWIBE) and GWU Center for Biomimetics and Bioinspired Engineering (COBRE).

  10. Irregular vocal fold dynamics incited by asymmetric fluid loading in a model of recurrent laryngeal nerve paralysis

    Science.gov (United States)

    Sommer, David; Erath, Byron D.; Zanartu, Matias; Peterson, Sean D.

    2011-11-01

    Voiced speech is produced by dynamic fluid-structure interactions in the larynx. Traditionally, reduced order models of speech have relied upon simplified inviscid flow solvers to prescribe the fluid loadings that drive vocal fold motion, neglecting viscous flow effects that occur naturally in voiced speech. Viscous phenomena, such as skewing of the intraglottal jet, have the most pronounced effect on voiced speech in cases of vocal fold paralysis where one vocal fold loses some, or all, muscular control. The impact of asymmetric intraglottal flow in pathological speech is captured in a reduced order two-mass model of speech by coupling a boundary-layer estimation of the asymmetric pressures with asymmetric tissue parameters that are representative of recurrent laryngeal nerve paralysis. Nonlinear analysis identifies the emergence of irregular and chaotic vocal fold dynamics at values representative of pathological speech conditions.

  11. A Summary of Coupled, Uncoupled, and Hybrid Tectonic Models for the Yakima Fold Belt--Topical Report

    Energy Technology Data Exchange (ETDEWEB)

    Chamness, Michele A.; Winsor, Kelsey; Unwin, Stephen D.

    2012-08-01

    This document is one in a series of topical reports compiled by the Pacific Northwest National Laboratory to summarize technical information on selected topics important to the performance of a probabilistic seismic hazard analysis of the Hanford Site. The purpose of this report is to summarize the range of opinions and supporting information expressed by the expert community regarding whether a coupled or uncoupled model, or a combination of both, best represents structures in the Yakima Fold Belt. This issue was assessed to have a high level of contention with up to moderate potential for impact on the hazard estimate. This report defines the alternative conceptual models relevant to this technical issue and the arguments and data that support those models. It provides a brief description of the technical issue and principal uncertainties; a general overview on the nature of the technical issue, along with alternative conceptual models, supporting arguments and information, and uncertainties; and finally, suggests some possible approaches for reducing uncertainties regarding this issue.

  12. Design of a rotamer library for coarse-grained models in protein-folding simulations.

    Science.gov (United States)

    Larriva, María; Rey, Antonio

    2014-01-27

    Rotamer libraries usually contain geometric information to trace an amino acid side chain, atom by atom, onto a protein backbone. These libraries have been widely used in protein design, structure refinement and prediction, homology modeling, and X-ray and NMR structure validation. However, they usually present too much information and are not always fully compatible with the coarse-grained models of the protein geometry that are frequently used to tackle the protein-folding problem through molecular simulation. In this work, we introduce a new backbone-dependent rotamer library for side chains compatible with low-resolution models in polypeptide chains. We have dispensed with an atomic description of proteins, representing each amino acid side chain by its geometric center (or centroid). The resulting rotamers have been estimated from a statistical analysis of a large structural database consisting of high-resolution X-ray protein structures. As additional information, each rotamer includes the frequency with which it has been found during the statistical analysis. More importantly, the library has been designed with a careful control to ensure that the vast majority of side chains in protein structures (at least 95% of residues) are properly represented. We have tested our library using an independent set of proteins, and our results support a good correlation between the reconstructed centroids from our rotamer library and those in the experimental structures. This new library can serve to improve the definition of side chain centroids in coarse-grained models, avoiding at the same time an excessive additional complexity in a geometric model for the polypeptide chain.

  13. Evaluation of Synthetic Self-Oscillating Models of the Vocal Folds

    Science.gov (United States)

    Hubler, Elizabeth P.; Weiland, Kelley S.; Hancock, Adrienne B.; Plesniak, Michael W.

    2013-11-01

    Approximately 30% of people will suffer from a voice disorder at some point in their lives. The probability doubles for those who rely heavily on their voice, such as teachers and singers. Synthetic vocal fold (VF) models are fabricated and evaluated experimentally in a vocal tract simulator to replicate physiological conditions. Pressure measurements are acquired along the vocal tract and high-speed images are captured at varying flow rates during VF oscillation to facilitate understanding of the characteristics of healthy and damaged VFs. The images are analyzed using a videokymography line-scan technique that has been used to examine VF motion and mucosal wave dynamics in vivo. Clinically relevant parameters calculated from the volume-velocity output of a circumferentially-vented mask (Rothenberg mask) are compared to patient data. This study integrates speech science with engineering and flow physics to overcome current limitations of synthetic VF models to properly replicate normal phonation in order to advance the understanding of resulting flow features, progression of pathological conditions, and medical techniques. Supported by the GW Institute for Biomedical Engineering (GWIBE) and GW Center for Biomimetics and Bioinspired Engineering (COBRE).

  14. Role of the osmolyte taurine on the folding of a model protein, hen egg white lysozyme, under a crowding condition.

    Science.gov (United States)

    Abe, Yoshito; Ohkuri, Takatoshi; Yoshitomi, Sachiko; Murakami, Shigeru; Ueda, Tadashi

    2015-05-01

    Taurine is one of the osmolytes that maintain the structure of proteins in cells exposed to denaturing environmental stressors. Recently, cryoelectron tomographic analysis of eukaryotic cells has revealed that their cytoplasms are crowded with proteins. Such crowding conditions would be expected to hinder the efficient folding of nascent polypeptide chains. Therefore, we examined the role of taurine on the folding of denatured and reduced lysozyme, as a model protein, under a crowding condition. The results confirmed that taurine had a better effect on protein folding than did β-alanine, which has a similar chemical structure, when the protein to be folded was present at submillimolar concentration. NMR analyses further revealed that under the crowding condition, taurine had more interactions than did β-alanine with the lysozyme molecule in both the folded and denatured states. We concluded that taurine improves the folding of the reduced lysozyme at submillimolar concentration to allow it to interact more favorably with the lysozyme molecule. Thus, the role of taurine, as an osmolyte in vivo, may be to assist in the efficient folding of proteins.

  15. A critical comparison of coarse-grained structure-based approaches and atomic models of protein folding.

    Science.gov (United States)

    Hu, Jie; Chen, Tao; Wang, Moye; Chan, Hue Sun; Zhang, Zhuqing

    2017-05-31

    Structure-based coarse-grained Gō-like models have been used extensively in deciphering protein folding mechanisms because of their simplicity and tractability. Meanwhile, explicit-solvent molecular dynamics (MD) simulations with physics-based all-atom force fields have been applied successfully to simulate folding/unfolding transitions for several small, fast-folding proteins. To explore the degree to which coarse-grained Gō-like models and their extensions to incorporate nonnative interactions are capable of producing folding processes similar to those in all-atom MD simulations, here we systematically compare the computed unfolded states, transition states, and transition paths obtained using coarse-grained models and all-atom explicit-solvent MD simulations. The conformations in the unfolded state in common Gō models are more extended, and are thus more in line with experiment, than those from all-atom MD simulations. Nevertheless, the structural features of transition states obtained by the two types of models are largely similar. In contrast, the folding transition paths are significantly more sensitive to modeling details. In particular, when common Gō-like models are augmented with nonnative interactions, the predicted dimensions of the unfolded conformations become similar to those computed using all-atom MD. With this connection, the large deviations of all-atom MD from simple diffusion theory are likely caused in part by the presence of significant nonnative effects in folding processes modelled by current atomic force fields. The ramifications of our findings to the application of coarse-grained modeling to more complex biomolecular systems are discussed.

  16. Protein folding optimization based on 3D off-lattice model via an improved artificial bee colony algorithm.

    Science.gov (United States)

    Li, Bai; Lin, Mu; Liu, Qiao; Li, Ya; Zhou, Changjun

    2015-10-01

    Protein folding is a fundamental topic in molecular biology. Conventional experimental techniques for protein structure identification or protein folding recognition require strict laboratory requirements and heavy operating burdens, which have largely limited their applications. Alternatively, computer-aided techniques have been developed to optimize protein structures or to predict the protein folding process. In this paper, we utilize a 3D off-lattice model to describe the original protein folding scheme as a simplified energy-optimal numerical problem, where all types of amino acid residues are binarized into hydrophobic and hydrophilic ones. We apply a balance-evolution artificial bee colony (BE-ABC) algorithm as the minimization solver, which is featured by the adaptive adjustment of search intensity to cater for the varying needs during the entire optimization process. In this work, we establish a benchmark case set with 13 real protein sequences from the Protein Data Bank database and evaluate the convergence performance of BE-ABC algorithm through strict comparisons with several state-of-the-art ABC variants in short-term numerical experiments. Besides that, our obtained best-so-far protein structures are compared to the ones in comprehensive previous literature. This study also provides preliminary insights into how artificial intelligence techniques can be applied to reveal the dynamics of protein folding. Graphical Abstract Protein folding optimization using 3D off-lattice model and advanced optimization techniques.

  17. Airflow visualization in a model of human glottis near the self-oscillating vocal folds model

    Czech Academy of Sciences Publication Activity Database

    Horáček, Jaromír; Uruba, Václav; Radolf, Vojtěch; Veselý, Jan; Bula, Vítězslav

    2011-01-01

    Roč. 5, č. 1 (2011), s. 21-28 ISSN 1802-680X R&D Projects: GA ČR GA101/08/1155 Institutional research plan: CEZ:AV0Z20760514 Keywords : biomechanics of human voice * voice production modelling * PIV measurement of streamline patterns Subject RIV: BI - Acoustics

  18. A cervid vocal fold model suggests greater glottal efficiency in calling at high frequencies.

    Directory of Open Access Journals (Sweden)

    Ingo R Titze

    2010-08-01

    Full Text Available Male Rocky Mountain elk (Cervus elaphus nelsoni produce loud and high fundamental frequency bugles during the mating season, in contrast to the male European Red Deer (Cervus elaphus scoticus who produces loud and low fundamental frequency roaring calls. A critical step in understanding vocal communication is to relate sound complexity to anatomy and physiology in a causal manner. Experimentation at the sound source, often difficult in vivo in mammals, is simulated here by a finite element model of the larynx and a wave propagation model of the vocal tract, both based on the morphology and biomechanics of the elk. The model can produce a wide range of fundamental frequencies. Low fundamental frequencies require low vocal fold strain, but large lung pressure and large glottal flow if sound intensity level is to exceed 70 dB at 10 m distance. A high-frequency bugle requires both large muscular effort (to strain the vocal ligament and high lung pressure (to overcome phonation threshold pressure, but at least 10 dB more intensity level can be achieved. Glottal efficiency, the ration of radiated sound power to aerodynamic power at the glottis, is higher in elk, suggesting an advantage of high-pitched signaling. This advantage is based on two aspects; first, the lower airflow required for aerodynamic power and, second, an acoustic radiation advantage at higher frequencies. Both signal types are used by the respective males during the mating season and probably serve as honest signals. The two signal types relate differently to physical qualities of the sender. The low-frequency sound (Red Deer call relates to overall body size via a strong relationship between acoustic parameters and the size of vocal organs and body size. The high-frequency bugle may signal muscular strength and endurance, via a 'vocalizing at the edge' mechanism, for which efficiency is critical.

  19. Multimodality pH imaging in a mouse dorsal skin fold window chamber model

    Science.gov (United States)

    Leung, Hui Min; Schafer, Rachel; Pagel, Mark M.; Robey, Ian F.; Gmitro, Arthur F.

    2013-03-01

    Upregulate levels of expression and activity of membrane H+ ion pumps in cancer cells drives the extracellular pH (pHe,) to values lower than normal. Furthermore, disregulated pH is indicative of the changes in glycolytic metabolism in tumor cells and has been shown to facilitate extracellular tissue remodeling during metastasis Therefore, measurement of pHe could be a useful cancer biomarker for diagnostic and therapy monitoring evaluation. Multimodality in-vivo imaging of pHe in tumorous tissue in a mouse dorsal skin fold window chamber (DSFWC) model is described. A custom-made plastic window chamber structure was developed that is compatible with both imaging optical and MR imaging modalities and provides a model system for continuous study of the same tissue microenvironment on multiple imaging platforms over a 3-week period. For optical imaging of pHe, SNARF-1 carboxylic acid is injected intravenously into a SCID mouse with an implanted tumor. A ratiometric measurement of the fluorescence signal captured on a confocal microscope reveals the pHe of the tissue visible within the window chamber. This imaging method was used in a preliminary study to evaluate sodium bicarbonate as a potential drug treatment to reverse tissue acidosis. For MR imaging of pHe the chemical exchange saturation transfer (CEST) was used as an alternative way of measuring pHe in a DSFWC model. ULTRAVIST®, a FDA approved x-ray/CT contrast agent has been shown to have a CEST effect that is pH dependent. A ratiometric analysis of water saturation at 5.6 and 4.2 ppm chemical shift provides a means to estimate the local pHe.

  20. Comparison of alternative representations of hydraulic-conductivity anisotropy in folded fractured-sedimentary rock: Modeling groundwater flow in the Shenandoah Valley (USA)

    Science.gov (United States)

    Yager, R.M.; Voss, C.I.; Southworth, S.

    2009-01-01

    A numerical representation that explicitly represents the generalized three-dimensional anisotropy of folded fractured-sedimentary rocks in a groundwater model best reproduces the salient features of the flow system in the Shenandoah Valley, USA. This conclusion results from a comparison of four alternative representations of anisotropy in which the hydraulic-conductivity tensor represents the bedrock structure as (model A) anisotropic with variable strikes and dips, (model B) horizontally anisotropic with a uniform strike, (model C) horizontally anisotropic with variable strikes, and (model D) isotropic. Simulations using the US Geological Survey groundwater flow and transport model SUTRA are based on a representation of hydraulic conductivity that conforms to bedding planes in a three-dimensional structural model of the valley that duplicates the pattern of folded sedimentary rocks. In the most general representation, (model A), the directions of maximum and medium hydraulic conductivity conform to the strike and dip of bedding, respectively, while the minimum hydraulic-conductivity direction is perpendicular to bedding. Model A produced a physically realistic flow system that reflects the underlying bedrock structure, with a flow field that is significantly different from those produced by the other three models. ?? Springer-Verlag 2009.

  1. Implementation of a 3d numerical model of a folded multilayer carbonate aquifer

    Science.gov (United States)

    Di Salvo, Cristina; Guyennon, Nicolas; Romano, Emanuele; Bruna Petrangeli, Anna; Preziosi, Elisabetta

    2016-04-01

    The main objective of this research is to present a case study of the numerical model implementation of a complex carbonate, structurally folded aquifer, with a finite difference, porous equivalent model. The case study aquifer (which extends over 235 km2 in the Apennine chain, Central Italy) provides a long term average of 3.5 m3/s of good quality groundwater to the surface river network, sustaining the minimum vital flow, and it is planned to be exploited in the next years for public water supply. In the downstream part of the river in the study area, a "Site of Community Importance" include the Nera River for its valuable aquatic fauna. However, the possible negative effects of the foreseen exploitation on groundwater dependent ecosystems are a great concern and model grounded scenarios are needed. This multilayer aquifer was conceptualized as five hydrostratigraphic units: three main aquifers (the uppermost unconfined, the central and the deepest partly confined), are separated by two locally discontinuous aquitards. The Nera river cuts through the two upper aquifers and acts as the main natural sink for groundwater. An equivalent porous medium approach was chosen. The complex tectonic structure of the aquifer requires several steps in defining the conceptual model; the presence of strongly dipping layers with very heterogeneous hydraulic conductivity, results in different thicknesses of saturated portions. Aquifers can have both unconfined or confined zones; drying and rewetting must be allowed when considering recharge/discharge cycles. All these characteristics can be included in the conceptual and numerical model; however, being the number of flow and head target scarce, the over-parametrization of the model must be avoided. Following the principle of parsimony, three steady state numerical models were developed, starting from a simple model, and then adding complexity: 2D (single layer), QUASI -3D (with leackage term simulating flow through aquitards) and

  2. ReFOLD: a server for the refinement of 3D protein models guided by accurate quality estimates.

    Science.gov (United States)

    Shuid, Ahmad N; Kempster, Robert; McGuffin, Liam J

    2017-07-03

    ReFOLD is a novel hybrid refinement server with integrated high performance global and local Accuracy Self Estimates (ASEs). The server attempts to identify and to fix likely errors in user supplied 3D models of proteins via successive rounds of refinement. The server is unique in providing output for multiple alternative refined models in a way that allows users to quickly visualize the key residue locations, which are likely to have been improved. This is important, as global refinement of a full chain model may not always be possible, whereas local regions, or individual domains, can often be much improved. Thus, users may easily compare the specific regions of the alternative refined models in which they are most interested e.g. key interaction sites or domains. ReFOLD was used to generate hundreds of alternative refined models for the CASP12 experiment, boosting our group's performance in the main tertiary structure prediction category. Our successful refinement of initial server models combined with our built-in ASEs were instrumental to our second place ranking on Template Based Modeling (TBM) and Free Modeling (FM)/TBM targets. The ReFOLD server is freely available at: http://www.reading.ac.uk/bioinf/ReFOLD/. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  3. Statistical dictionaries for hypothetical in silico model of the early-stage intermediate in protein folding

    Science.gov (United States)

    Kalinowska, Barbara; Fabian, Piotr; Stąpor, Katarzyna; Roterman, Irena

    2015-07-01

    The polypeptide chain folding process appears to be a multi-stage phenomenon. The scientific community has recently devoted much attention to early stages of this process, with numerous attempts at simulating them—either experimentally or in silico. This paper presents a comparative analysis of the predicted and observed results of folding simulations. The proposed technique, based on statistical dictionaries, yields a global accuracy of 57 %—a marked improvement over older approaches (with an accuracy of approximately 46 %).

  4. Fold-related-fracturing at the Livingstone River anticline (AB; Canada) by coupling field surveying and numerical modelling

    Science.gov (United States)

    Humair, Florian; Epard, Jean-Luc; Bauville, Arthur; Jaboyedoff, Michel; Pana, Dinu; Kaus, Boris; Schmalholz, Stefan

    2016-04-01

    The interpretation of fold-related joints and faults is of primary importance in terms of fluids prospection (e.g. water, oil, gas, C02) since anticlines are potential structural trap while fracturing can strongly influence the storage capacity as well as the migration pathways. Located at the front of the Foothills of the Rocky Mountains in Alberta (Canada), the Livingstone Range (LRA) is analogous to hydrocarbon reservoir that occur elsewhere in the Foothills (Cooley et al., 2011). The Livingstone Range fold system is related to the development of the Livingstone thrust that cuts around 1000m up-section from a regional decollement in the Palliser Formation (Devonian) to another in the Fernie Formation (Jurassic). Our study focuses on the detailed structural investigation of the Livingstone River anticline (northern part of the LRA). It aims at characterizing the anticline geometry as well as the fracturing pattern (orientation, mode, infilling, spacing, trace length, density, and cross-cutting relationships) in order to propose a kinematic interpretation of the fold-related fracturing genesis. The study area is investigated at different scales by combining field surveys with remote sensing (HR-Digital Elevation Model, Ground-based LiDAR, Gigapixel photography) and thin-sections analyses. In a second step we performed finite difference 3D numerical simulations in order to compute the evolution of local principal stress orientation during folding. We compared the fracture (or plastic bands) distribution in the field with 1) a dynamic numerical model of detachment folding; and 2) an instantaneous numerical model based on the final fold geometry. Cooley, M.A., Price, R.A., Dixon, J.M., Kyser, T.K. 2011. Along-strike variations and internal details of chevron-style flexural slip thrust-propagation folds within the southern Livingstone Range anticlinorium, a paleo-hydrocarbon reservoir in southern Alberta Foothills, Canada. AAPG bulletin, 95 (11), 1821-1849.

  5. Folding model using a bare elementary interaction for [sup 12]C+[sup 12]C elastic scattering

    Energy Technology Data Exchange (ETDEWEB)

    Qing-Run, L. (Chinese Center of Advanced Science and Technology (World Laboratory), Beijing (China) Institute of High Energy Physics, Academia Sinica, Beijing (China)); Yong-Xu, Y. (Department of Physics, Guangxi Normal University, Guilin (China))

    1993-05-01

    A folding potential for [sup 12]C+[sup 12]C scattering is constructed based on the [alpha]-particle model of the nucleus using a free [alpha]-[alpha] interaction. This potential gives a good description of the data in the energy region of 70--160 MeV. This report reveals a sort of nuclear system in which the elementary particle'' behaves as a free one and thus folding models can be tested more cleanly.''

  6. Generalization performance of regularized neural network models

    DEFF Research Database (Denmark)

    Larsen, Jan; Hansen, Lars Kai

    1994-01-01

    Architecture optimization is a fundamental problem of neural network modeling. The optimal architecture is defined as the one which minimizes the generalization error. This paper addresses estimation of the generalization performance of regularized, complete neural network models. Regularization...

  7. Dissecting electrostatic screening, specific ion binding, and ligand binding in an energetic model for glycine riboswitch folding

    Energy Technology Data Exchange (ETDEWEB)

    Lipfert, Jan; Sim, Adelene Y.L.; Herschlag, Daniel; Doniach, Sebastian (Stanford)

    2010-09-17

    Riboswitches are gene-regulating RNAs that are usually found in the 5{prime}-untranslated regions of messenger RNA. As the sugar-phosphate backbone of RNA is highly negatively charged, the folding and ligand-binding interactions of riboswitches are strongly dependent on the presence of cations. Using small angle X-ray scattering (SAXS) and hydroxyl radical footprinting, we examined the cation dependence of the different folding stages of the glycine-binding riboswitch from Vibrio cholerae. We found that the partial folding of the tandem aptamer of this riboswitch in the absence of glycine is supported by all tested mono- and divalent ions, suggesting that this transition is mediated by nonspecific electrostatic screening. Poisson-Boltzmann calculations using SAXS-derived low-resolution structural models allowed us to perform an energetic dissection of this process. The results showed that a model with a constant favorable contribution to folding that is opposed by an unfavorable electrostatic term that varies with ion concentration and valency provides a reasonable quantitative description of the observed folding behavior. Glycine binding, on the other hand, requires specific divalent ions binding based on the observation that Mg{sup 2+}, Ca{sup 2+}, and Mn{sup 2+} facilitated glycine binding, whereas other divalent cations did not. The results provide a case study of how ion-dependent electrostatic relaxation, specific ion binding, and ligand binding can be coupled to shape the energetic landscape of a riboswitch and can begin to be quantitatively dissected.

  8. Structural modeling of the Zagros fold-and-thrust belt (Iraq) combining field work and remote sensing techniques

    Science.gov (United States)

    Reif, D.; Grasemann, B.; Faber, R.; Lockhart, D.

    2009-04-01

    The Zagros fold-and-thrust belt is known for its spectacular fold trains, which have formed in detached Phanerozoic sedimentary cover rocks above a shortened crystalline Precambrian basement. Orogeny evolved through the Late Cretaceous to Miocene collision between the Arabian and Eurasian plate, during which the Neotethys oceanic basin was closed. Still active deformation shortening in the order of 2-2.5 cm/yr is partitioned in S-SW directed folding and thrusting of the Zagros fold-and-thrust belt and NW-SE to N-S trending dextral strike slip faults. The sub-cylindrical doubly-plunging fold trains with wavelengths of 5 - 10 km host more than half of the world's hydrocarbon reserves in mostly anticlinal traps. In this work we investigate the three dimensional structure of the Zagros fold-and-thrust belt in the Kurdistan region of Iraq. The mapped region is situated NE from the city of Erbil and comprises mainly Cretaceous to Cenozoic folded sediments consisting of mainly limestones, dolomites, sandstones, siltstones, claystones and conglomerates. Although the overall security situation in Kurdistan is much better than in the rest of Iraq, structural field mapping was restricted to sections along the main roads perpendicular to the strike of the fold trains, mainly because of the contamination of the area with landmines and unexploded ordnance, a problem that dates back to the end of World War Two. Landmines were also used by the central government in the 1960s and 1970s in order to subdue Kurdish groups. During the 1980-1988 Iran-Iraq War, the north was mined again. In order to extend the structural measurements statistically over the investigated area resulting in a three-dimensional model of the fold trains, we used the Fault Trace module of the WinGeol software (www.terramath.com). This package allows the interactive mapping and visualization of the spatial orientations (i.e. dip and strike) of geological finite planar structures (e.g. faults, lithological

  9. Use of integrated analogue and numerical modelling to predict tridimensional fracture intensity in fault-related-folds.

    Science.gov (United States)

    Pizzati, Mattia; Cavozzi, Cristian; Magistroni, Corrado; Storti, Fabrizio

    2016-04-01

    Fracture density pattern predictions with low uncertainty is a fundamental issue for constraining fluid flow pathways in thrust-related anticlines in the frontal parts of thrust-and-fold belts and accretionary prisms, which can also provide plays for hydrocarbon exploration and development. Among the drivers that concur to determine the distribution of fractures in fold-and-thrust-belts, the complex kinematic pathways of folded structures play a key role. In areas with scarce and not reliable underground information, analogue modelling can provide effective support for developing and validating reliable hypotheses on structural architectures and their evolution. In this contribution, we propose a working method that combines analogue and numerical modelling. We deformed a sand-silicone multilayer to eventually produce a non-cylindrical thrust-related anticline at the wedge toe, which was our test geological structure at the reservoir scale. We cut 60 serial cross-sections through the central part of the deformed model to analyze faults and folds geometry using dedicated software (3D Move). The cross-sections were also used to reconstruct the 3D geometry of reference surfaces that compose the mechanical stratigraphy thanks to the use of the software GoCad. From the 3D model of the experimental anticline, by using 3D Move it was possible to calculate the cumulative stress and strain underwent by the deformed reference layers at the end of the deformation and also in incremental steps of fold growth. Based on these model outputs it was also possible to predict the orientation of three main fractures sets (joints and conjugate shear fractures) and their occurrence and density on model surfaces. The next step was the upscaling of the fracture network to the entire digital model volume, to create DFNs.

  10. Comparison of a fiber-gel finite element model of vocal fold vibration to a transversely isotropic stiffness model.

    Science.gov (United States)

    Titze, Ingo R; Alipour, Fariborz; Blake, Douglas; Palaparthi, Anil

    2017-09-01

    A fiber-gel vocal fold model is compared to a transversely isotropic stiffness model in terms of normal mode vibration. The fiber-gel finite element model (FG-FEM) consists of a series of gel slices, each with a two-dimensional finite element mesh, in a plane transverse to the tissue fibers. The gel slices are coupled with fibers under tension in the anterior-posterior dimension. No vibrational displacement in the fiber-length direction is allowed, resulting in a plane strain state. This is consistent with the assumption of transverse displacement of a simple string, offering a wide range of natural frequencies (well into the kHz region) with variable tension. For low frequencies, the results compare favorably with the natural frequencies of a transversely isotropic elastic stiffness model (TISM) in which the shear modulus in the longitudinal plane is used to approximate the effect of fiber tension. For high frequencies, however, the natural frequencies do not approach the string mode frequencies unless plane strain is imposed on the TISM model. The simplifying assumption of plane strain, as well as the use of analytical closed-form shape functions, allow for substantial savings in computational time, which is important in clinical and exploratory applications of the FG-FEM model.

  11. Solution structures of proteins from NMR data and modeling: Alternative folds for neutrophil peptide 5

    International Nuclear Information System (INIS)

    Levy, R.M.; Bassolino, D.A.; Kitchen, D.B.; Pardi, A.

    1989-01-01

    The structure of neutrophil peptide 5 in solution has recently reported. The structure determination was accomplished by using a distance geometry algorithm and 107 interproton distances constrains obtained from 2D NMR data. In each of the eight independent solutions to the distance geometry equations, the overall fold of the polypeptide backbone was identical and the root mean square (rms) deviation between backbone atoms of the superimposed structures was small. In this paper the authors report additional NP-5 structures obtained by using a new structure generation algorithm: a Monte Carlo search in torsion angle space. These structures have a large rms backbone deviation from the distance geometry structures. The backbone topologies differ in significant respects from the distance geometry structures and from each other. Structures are found that are pseudo mirror images of part or all of the fold corresponding to that first obtained with the distance geometry procedure. The results demonstrate that the previously accepted criteria for defining the accuracy and precision of a peptide structure generated from NMR data are inadequate. An energetic analysis of structures corresponding to the different folding topologies has been carried out. The molecular mechanics energies obtained by minimization and molecular dynamics refinement provide sufficient information to eliminate certain alternative structures. On the basis of a careful comparison of the different trial structures with the experimental data, it is concluded that the NP-5 peptide fold which was originally reported is most consistent with the data

  12. Numerical Simulation of Interaction of Fluid Flow and Elastic Structure Modelling Vocal Fold

    Czech Academy of Sciences Publication Activity Database

    Valášek, J.; Sváček, P.; Horáček, Jaromír

    2016-01-01

    Roč. 821, č. 2016 (2016), s. 693-700 ISSN 1660-9336 R&D Projects: GA ČR(CZ) GAP101/11/0207 Institutional support: RVO:61388998 Keywords : finite element method * 2D Navier-Stokes equations * vocal folds * aeroelasticity Subject RIV: BI - Acoustics

  13. Geometry of human vocal folds and glottal channel for mathematical and biomechanical modeling of voice production

    Czech Academy of Sciences Publication Activity Database

    Šidlof, Petr; Švec, J. G.; Horáček, Jaromír; Veselý, Jan; Klepáček, I.; Havlík, R.

    2008-01-01

    Roč. 41, - (2008), s. 985-995 ISSN 0021-9290 R&D Projects: GA AV ČR IAA2076401 Institutional research plan: CEZ:AV0Z20760514 Keywords : vocal fold geometry * glottal channel shape * quantitative description Subject RIV: BI - Acoustics Impact factor: 2.784, year: 2008

  14. Finite element modeling of the vocal folds with deformable interface tracking

    DEFF Research Database (Denmark)

    Granados Corsellas, Alba; Brunskog, Jonas; Misztal, Marek Krzysztof

    2014-01-01

    Continuous and prolonged use of the sp eaking voice may lead to functional sp eech disorders that are not apparent for voice clinicians from high-sp eed imaging of the vo cal folds' vibration. However, it is hyp othesized that time dep endent tissue prop erties provide some insight into the injur...

  15. The human vocal fold layers. Their delineation inside vocal fold as a background to create 3D digital and synthetic glottal model

    Czech Academy of Sciences Publication Activity Database

    Klepáček, I.; Jirák, D.; Dušková-Smrčková, Miroslava; Janoušková, Olga; Vampola, T.

    2016-01-01

    Roč. 30, č. 5 (2016), s. 529-537 ISSN 0892-1997 R&D Projects: GA ČR(CZ) GAP101/12/1306 Institutional support: RVO:61389013 Keywords : human vocal fold * vocal ligamentous complex * lamina propria Subject RIV: CD - Macromolecular Chemistry Impact factor: 1.381, year: 2016

  16. Phonation threshold pressure and onset frequency in a two-layer physical model of the vocal folds.

    Science.gov (United States)

    Mendelsohn, Abie H; Zhang, Zhaoyan

    2011-11-01

    The influence of vocal fold geometry and stiffness on phonation onset was experimentally investigated using a body-cover physical model of the vocal folds. Results showed that a lower phonation threshold pressure and phonation onset frequency can be achieved by reducing body-layer or cover-layer stiffness, reducing medial surface thickness, or increasing cover-layer depth. Increasing body-layer stiffness also restricted vocal fold motion to the cover layer and reduced prephonatory glottal opening. Excitation of anterior-posterior modes was also observed, particularly for large values of the body-cover stiffness ratio. The results of this study were also discussed in relation to previous theoretical and experimental studies.

  17. Combination of Markov state models and kinetic networks for the analysis of molecular dynamics simulations of peptide folding.

    Science.gov (United States)

    Radford, Isolde H; Fersht, Alan R; Settanni, Giovanni

    2011-06-09

    Atomistic molecular dynamics simulations of the TZ1 beta-hairpin peptide have been carried out using an implicit model for the solvent. The trajectories have been analyzed using a Markov state model defined on the projections along two significant observables and a kinetic network approach. The Markov state model allowed for an unbiased identification of the metastable states of the system, and provided the basis for commitment probability calculations performed on the kinetic network. The kinetic network analysis served to extract the main transition state for folding of the peptide and to validate the results from the Markov state analysis. The combination of the two techniques allowed for a consistent and concise characterization of the dynamics of the peptide. The slowest relaxation process identified is the exchange between variably folded and denatured species, and the second slowest process is the exchange between two different subsets of the denatured state which could not be otherwise identified by simple inspection of the projected trajectory. The third slowest process is the exchange between a fully native and a partially folded intermediate state characterized by a native turn with a proximal backbone H-bond, and frayed side-chain packing and termini. The transition state for the main folding reaction is similar to the intermediate state, although a more native like side-chain packing is observed.

  18. Multivariate generalized linear mixed models using R

    CERN Document Server

    Berridge, Damon Mark

    2011-01-01

    Multivariate Generalized Linear Mixed Models Using R presents robust and methodologically sound models for analyzing large and complex data sets, enabling readers to answer increasingly complex research questions. The book applies the principles of modeling to longitudinal data from panel and related studies via the Sabre software package in R. A Unified Framework for a Broad Class of Models The authors first discuss members of the family of generalized linear models, gradually adding complexity to the modeling framework by incorporating random effects. After reviewing the generalized linear model notation, they illustrate a range of random effects models, including three-level, multivariate, endpoint, event history, and state dependence models. They estimate the multivariate generalized linear mixed models (MGLMMs) using either standard or adaptive Gaussian quadrature. The authors also compare two-level fixed and random effects linear models. The appendices contain additional information on quadrature, model...

  19. Geometric U-folds in four dimensions

    Science.gov (United States)

    Lazaroiu, C. I.; Shahbazi, C. S.

    2018-01-01

    We describe a general construction of geometric U-folds compatible with a non-trivial extension of the global formulation of four-dimensional extended supergravity on a differentiable spin manifold. The topology of geometric U-folds depends on certain flat fiber bundles which encode how supergravity fields are globally glued together. We show that smooth non-trivial U-folds of this type can exist only in theories where both the scalar and space-time manifolds have non-trivial fundamental group and in addition the scalar map of the solution is homotopically non-trivial. Consistency with string theory requires smooth geometric U-folds to be glued using subgroups of the effective discrete U-duality group, implying that the fundamental group of the scalar manifold of such solutions must be a subgroup of the latter. We construct simple examples of geometric U-folds in a generalization of the axion-dilaton model of \

  20. Generalized latent variable modeling multilevel, longitudinal, and structural equation models

    CERN Document Server

    Skrondal, Anders; Rabe-Hesketh, Sophia

    2004-01-01

    This book unifies and extends latent variable models, including multilevel or generalized linear mixed models, longitudinal or panel models, item response or factor models, latent class or finite mixture models, and structural equation models.

  1. General introduction to simulation models

    DEFF Research Database (Denmark)

    Hisham Beshara Halasa, Tariq; Boklund, Anette

    2012-01-01

    Monte Carlo simulation can be defined as a representation of real life systems to gain insight into their functions and to investigate the effects of alternative conditions or actions on the modeled system. Models are a simplification of a system. Most often, it is best to use experiments and fie...... as support decision making. However, several other factors affect decision making such as, ethics, politics and economics. Furthermore, the insight gained when models are build leads to point out areas where knowledge is lacking....... of FMD spread that can provide useful and trustworthy advises, there are four important issues, which the model should represent: 1) The herd structure of the country in question, 2) the dynamics of animal movements and contacts between herds, 3) the biology of the disease, and 4) the regulations...

  2. A case of craniofacial dysmorphism, congenital heart defects, coccygeal skin folds, generalized skeletal alterations, and hemihypertrophy with linear skin hypopigmentation: a new syndrome?

    Science.gov (United States)

    Nishimura, G; Nagai, T

    1998-01-01

    The case of a Japanese girl with a unique combination of congenital malformations is reported. The malformations include craniofacial dysmorphism, congenital heart defects, coccygeal skin folds, generalized skeletal alterations, and hemihypertrophy with linear skin hypopigmentation that indicated somatic mosaicism of a mutated gene or a submicroscopic chromosomal aberration. The phenotype in our patient overlapped significantly with, but was not completely consistent with, that of ter Haar syndrome, a recently elucidated malformation syndrome with an autosomal recessive trait. The present patient may have represented a previously undescribed malformation syndrome, or an atypical manifestation of ter Haar syndrome due to somatic mosaicism.

  3. How Kinetics within the Unfolded State Affects Protein Folding: an Analysis Based on Markov State Models and an Ultra-Long MD Trajectory

    Science.gov (United States)

    Deng, Nan-jie; Dai, Wei

    2013-01-01

    Understanding how kinetics in the unfolded state affects protein folding is a fundamentally important yet less well-understood issue. Here we employ three different models to analyze the unfolded landscape and folding kinetics of the miniprotein Trp-cage. The first is a 208 μs explicit solvent molecular dynamics (MD) simulation from D. E. Shaw Research containing tens of folding events. The second is a Markov state model (MSM-MD) constructed from the same ultra-long MD simulation; MSM-MD can be used to generate thousands of folding events. The third is a Markov state model built from temperature replica exchange MD simulations in implicit solvent (MSM-REMD). All the models exhibit multiple folding pathways, and there is a good correspondence between the folding pathways from direct MD and those computed from the MSMs. The unfolded populations interconvert rapidly between extended and collapsed conformations on time scales ≤ 40 ns, compared with the folding time of ≈ 5 μs. The folding rates are independent of where the folding is initiated from within the unfolded ensemble. About 90 % of the unfolded states are sampled within the first 40 μs of the ultra-long MD trajectory, which on average explores ~27 % of the unfolded state ensemble between consecutive folding events. We clustered the folding pathways according to structural similarity into “tubes”, and kinetically partitioned the unfolded state into populations that fold along different tubes. From our analysis of the simulations and a simple kinetic model, we find that when the mixing within the unfolded state is comparable to or faster than folding, the folding waiting times for all the folding tubes are similar and the folding kinetics is essentially single exponential despite the presence of heterogeneous folding paths with non-uniform barriers. When the mixing is much slower than folding, different unfolded populations fold independently leading to non-exponential kinetics. A kinetic partition of

  4. Modelling and Analysis of the Folding Principle used in Selv-Deployable Deorbiting Space Structures

    DEFF Research Database (Denmark)

    Nikolajsen, Jan Ánike; Lauridsen, Peter Riddersholm; Kristensen, Anders Schmidt

    2017-01-01

    An initial prototype of the Self-deployable Deorbiting Space Structure (SDSS) for semi-controlled debris removal was launched in 2014. The SDSS module consists of 3 main systems, i.e. the Drag Sail Unit (DSU), the Release Unit (RU) and the Housing Unit (HU). In the redesign, a storage lid is intr...... is introduced whereby the folded drag sail is completely separated from the HU during the release process. During the research, an updated version of the SDSS version is made for CubeSat. The prototype is for a CubeSat which will be scalable....

  5. A first-principles model of early evolution: emergence of gene families, species, and preferred protein folds.

    Directory of Open Access Journals (Sweden)

    Konstantin B Zeldovich

    2007-07-01

    Full Text Available In this work we develop a microscopic physical model of early evolution where phenotype--organism life expectancy--is directly related to genotype--the stability of its proteins in their native conformations-which can be determined exactly in the model. Simulating the model on a computer, we consistently observe the "Big Bang" scenario whereby exponential population growth ensues as soon as favorable sequence-structure combinations (precursors of stable proteins are discovered. Upon that, random diversity of the structural space abruptly collapses into a small set of preferred proteins. We observe that protein folds remain stable and abundant in the population at timescales much greater than mutation or organism lifetime, and the distribution of the lifetimes of dominant folds in a population approximately follows a power law. The separation of evolutionary timescales between discovery of new folds and generation of new sequences gives rise to emergence of protein families and superfamilies whose sizes are power-law distributed, closely matching the same distributions for real proteins. On the population level we observe emergence of species--subpopulations that carry similar genomes. Further, we present a simple theory that relates stability of evolving proteins to the sizes of emerging genomes. Together, these results provide a microscopic first-principles picture of how first-gene families developed in the course of early evolution.

  6. Actuarial statistics with generalized linear mixed models

    NARCIS (Netherlands)

    Antonio, K.; Beirlant, J.

    2007-01-01

    Over the last decade the use of generalized linear models (GLMs) in actuarial statistics has received a lot of attention, starting from the actuarial illustrations in the standard text by McCullagh and Nelder [McCullagh, P., Nelder, J.A., 1989. Generalized linear models. In: Monographs on Statistics

  7. Generalized Linear Models in Family Studies

    Science.gov (United States)

    Wu, Zheng

    2005-01-01

    Generalized linear models (GLMs), as defined by J. A. Nelder and R. W. M. Wedderburn (1972), unify a class of regression models for categorical, discrete, and continuous response variables. As an extension of classical linear models, GLMs provide a common body of theory and methodology for some seemingly unrelated models and procedures, such as…

  8. Parallel CFD simulation of flow in a 3D model of vibrating human vocal folds

    Czech Academy of Sciences Publication Activity Database

    Šidlof, Petr; Horáček, Jaromír; Řidký, V.

    2013-01-01

    Roč. 80, č. 1 (2013), s. 290-300 ISSN 0045-7930 R&D Projects: GA ČR(CZ) GAP101/11/0207 Institutional research plan: CEZ:AV0Z20760514 Keywords : numerical simulation * vocal folds * glottal airflow * inite volume method * parallel CFD Subject RIV: BI - Acoustics Impact factor: 1.532, year: 2013 http://www.sciencedirect.com/science?_ob=ArticleListURL&_method=list&_ArticleListID=-268060849&_sort=r&_st=13&view=c&_acct=C000034318&_version=1&_urlVersion=0&_userid=640952&md5=7c5b5539857ee9a02af5e690585b3126&searchtype=a

  9. Micro Data and General Equilibrium Models

    DEFF Research Database (Denmark)

    Browning, Martin; Hansen, Lars Peter; Heckman, James J.

    1999-01-01

    Dynamic general equilibrium models are required to evaluate policies applied at the national level. To use these models to make quantitative forecasts requires knowledge of an extensive array of parameter values for the economy at large. This essay describes the parameters required for different...... economic models, assesses the discordance between the macromodels used in policy evaluation and the microeconomic models used to generate the empirical evidence. For concreteness, we focus on two general equilibrium models: the stochastic growth model extended to include some forms of heterogeneity...

  10. Folding 19 proteins to their native state and stability of large proteins from a coarse-grained model.

    Science.gov (United States)

    Kapoor, Abhijeet; Travesset, Alex

    2014-03-01

    We develop an intermediate resolution model, where the backbone is modeled with atomic resolution but the side chain with a single bead, by extending our previous model (Proteins (2013) DOI: 10.1002/prot.24269) to properly include proline, preproline residues and backbone rigidity. Starting from random configurations, the model properly folds 19 proteins (including a mutant 2A3D sequence) into native states containing β sheet, α helix, and mixed α/β. As a further test, the stability of H-RAS (a 169 residue protein, critical in many signaling pathways) is investigated: The protein is stable, with excellent agreement with experimental B-factors. Despite that proteins containing only α helices fold to their native state at lower backbone rigidity, and other limitations, which we discuss thoroughly, the model provides a reliable description of the dynamics as compared with all atom simulations, but does not constrain secondary structures as it is typically the case in more coarse-grained models. Further implications are described. Copyright © 2013 Wiley Periodicals, Inc.

  11. Group theoretical classification of broken symmetry states of the two-fold degenerate Hubbard model on a triangular lattice

    International Nuclear Information System (INIS)

    Masago, Akira; Suzuki, Naoshi

    2001-01-01

    By a group theoretical procedure we derive the possible spontaneously broken-symmetry states for the two-fold degenerate Hubbard model on a two-dimensional triangular lattice. For ordering wave vectors corresponding to the points Γ and K in the first BZ we find 22 states which include 16 collinear and six non-collinear states. The collinear states include the usual SDW and CDW states which appear also in the single-band Hubbard model. The non-collinear states include exotic ordering states of orbitals and spins as well as the triangular arrangement of spins

  12. A general consumer-resource population model

    Science.gov (United States)

    Lafferty, Kevin D.; DeLeo, Giulio; Briggs, Cheryl J.; Dobson, Andrew P.; Gross, Thilo; Kuris, Armand M.

    2015-01-01

    Food-web dynamics arise from predator-prey, parasite-host, and herbivore-plant interactions. Models for such interactions include up to three consumer activity states (questing, attacking, consuming) and up to four resource response states (susceptible, exposed, ingested, resistant). Articulating these states into a general model allows for dissecting, comparing, and deriving consumer-resource models. We specify this general model for 11 generic consumer strategies that group mathematically into predators, parasites, and micropredators and then derive conditions for consumer success, including a universal saturating functional response. We further show how to use this framework to create simple models with a common mathematical lineage and transparent assumptions. Underlying assumptions, missing elements, and composite parameters are revealed when classic consumer-resource models are derived from the general model.

  13. Conformity and Dissonance in Generalized Voter Models

    Science.gov (United States)

    Page, Scott E.; Sander, Leonard M.; Schneider-Mizell, Casey M.

    2007-09-01

    We generalize the voter model to include social forces that produce conformity among voters and avoidance of cognitive dissonance of opinions within a voter. The time for both conformity and consistency (which we call the exit time) is, in general, much longer than for either process alone. We show that our generalized model can be applied quite widely: it is a form of Wright's island model of population genetics, and is related to problems in the physical sciences. We give scaling arguments, numerical simulations, and analytic estimates for the exit time for a range of relative strengths in the tendency to conform and to avoid dissonance.

  14. A Generalized Random Regret Minimization Model

    NARCIS (Netherlands)

    Chorus, C.G.

    2013-01-01

    This paper presents, discusses and tests a generalized Random Regret Minimization (G-RRM) model. The G-RRM model is created by replacing a fixed constant in the attribute-specific regret functions of the RRM model, by a regret-weight variable. Depending on the value of the regret-weights, the G-RRM

  15. Multiview Rectification of Folded Documents.

    Science.gov (United States)

    You, Shaodi; Matsushita, Yasuyuki; Sinha, Sudipta; Bou, Yusuke; Ikeuchi, Katsushi

    2018-02-01

    Digitally unwrapping images of paper sheets is crucial for accurate document scanning and text recognition. This paper presents a method for automatically rectifying curved or folded paper sheets from a few images captured from multiple viewpoints. Prior methods either need expensive 3D scanners or model deformable surfaces using over-simplified parametric representations. In contrast, our method uses regular images and is based on general developable surface models that can represent a wide variety of paper deformations. Our main contribution is a new robust rectification method based on ridge-aware 3D reconstruction of a paper sheet and unwrapping the reconstructed surface using properties of developable surfaces via conformal mapping. We present results on several examples including book pages, folded letters and shopping receipts.

  16. EOP MIT General Circulation Model (MITgcm)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data contains a regional implementation of the Massachusetts Institute of Technology general circulation model (MITgcm) at a 1-km spatial resolution for the...

  17. Generalized Reduced Order Model Generation, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — M4 Engineering proposes to develop a generalized reduced order model generation method. This method will allow for creation of reduced order aeroservoelastic state...

  18. Generalized Reduced Order Model Generation Project

    Data.gov (United States)

    National Aeronautics and Space Administration — M4 Engineering proposes to develop a generalized reduced order model generation method. This method will allow for creation of reduced order aeroservoelastic state...

  19. Empirical generalization assessment of neural network models

    DEFF Research Database (Denmark)

    Larsen, Jan; Hansen, Lars Kai

    1995-01-01

    competing models. Since all models are trained on the same data, a key issue is to take this dependency into account. The optimal split of the data set of size N into a cross-validation set of size Nγ and a training set of size N(1-γ) is discussed. Asymptotically (large data sees), γopt→1......This paper addresses the assessment of generalization performance of neural network models by use of empirical techniques. We suggest to use the cross-validation scheme combined with a resampling technique to obtain an estimate of the generalization performance distribution of a specific model....... This enables the formulation of a bulk of new generalization performance measures. Numerical results demonstrate the viability of the approach compared to the standard technique of using algebraic estimates like the FPE. Moreover, we consider the problem of comparing the generalization performance of different...

  20. Foundations of linear and generalized linear models

    CERN Document Server

    Agresti, Alan

    2015-01-01

    A valuable overview of the most important ideas and results in statistical analysis Written by a highly-experienced author, Foundations of Linear and Generalized Linear Models is a clear and comprehensive guide to the key concepts and results of linear statistical models. The book presents a broad, in-depth overview of the most commonly used statistical models by discussing the theory underlying the models, R software applications, and examples with crafted models to elucidate key ideas and promote practical model building. The book begins by illustrating the fundamentals of linear models,

  1. Perturbed generalized multicritical one-matrix models

    Science.gov (United States)

    Ambjørn, J.; Chekhov, L.; Makeenko, Y.

    2018-03-01

    We study perturbations around the generalized Kazakov multicritical one-matrix model. The multicritical matrix model has a potential where the coefficients of zn only fall off as a power 1 /n s + 1. This implies that the potential and its derivatives have a cut along the real axis, leading to technical problems when one performs perturbations away from the generalized Kazakov model. Nevertheless it is possible to relate the perturbed partition function to the tau-function of a KdV hierarchy and solve the model by a genus expansion in the double scaling limit.

  2. GENERALIZED VISCOPLASTIC MODELING OF DEBRIS FLOW.

    Science.gov (United States)

    Chen, Cheng-lung

    1988-01-01

    The earliest model developed by R. A. Bagnold was based on the concept of the 'dispersive' pressure generated by grain collisions. Some efforts have recently been made by theoreticians in non-Newtonian fluid mechanics to modify or improve Bagnold's concept or model. A viable rheological model should consist both of a rate-independent part and a rate-dependent part. A generalized viscoplastic fluid (GVF) model that has both parts as well as two major rheological properties (i. e. , the normal stress effect and soil yield criterion) is shown to be sufficiently accurate, yet practical for general use in debris-flow modeling. In fact, Bagnold's model is found to be only a particular case of the GVF model. analytical solutions for (steady) uniform debris flows in wide channels are obtained from the GVF model based on Bagnold's simplified assumption of constant grain concentration.

  3. NoFold: RNA structure clustering without folding or alignment.

    Science.gov (United States)

    Middleton, Sarah A; Kim, Junhyong

    2014-11-01

    Structures that recur across multiple different transcripts, called structure motifs, often perform a similar function-for example, recruiting a specific RNA-binding protein that then regulates translation, splicing, or subcellular localization. Identifying common motifs between coregulated transcripts may therefore yield significant insight into their binding partners and mechanism of regulation. However, as most methods for clustering structures are based on folding individual sequences or doing many pairwise alignments, this results in a tradeoff between speed and accuracy that can be problematic for large-scale data sets. Here we describe a novel method for comparing and characterizing RNA secondary structures that does not require folding or pairwise alignment of the input sequences. Our method uses the idea of constructing a distance function between two objects by their respective distances to a collection of empirical examples or models, which in our case consists of 1973 Rfam family covariance models. Using this as a basis for measuring structural similarity, we developed a clustering pipeline called NoFold to automatically identify and annotate structure motifs within large sequence data sets. We demonstrate that NoFold can simultaneously identify multiple structure motifs with an average sensitivity of 0.80 and precision of 0.98 and generally exceeds the performance of existing methods. We also perform a cross-validation analysis of the entire set of Rfam families, achieving an average sensitivity of 0.57. We apply NoFold to identify motifs enriched in dendritically localized transcripts and report 213 enriched motifs, including both known and novel structures. © 2014 Middleton and Kim; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  4. Structural models of intrinsically disordered and calcium-bound folded states of a protein adapted for secretion

    OpenAIRE

    O’Brien, Darragh P.; Hernandez, Belen; Durand, Dominique; Hourdel, Véronique; Sotomayor-Pérez, Ana-Cristina; Vachette, Patrice; Ghomi, Mahmoud; Chamot-Rooke, Julia; Ladant, Daniel; Brier, Sébastien; Chenal, Alexandre

    2016-01-01

    International audience; Many Gram-negative bacteria use Type I secretion systems, T1SS, to secrete virulence factors that contain calcium-binding Repeat-in-ToXin (RTX) motifs. Here, we present structural models of an RTX protein, RD, in both its intrinsically disordered calcium-free Apo-state and its folded calcium-bound Holo-state. Apo-RD behaves as a disordered polymer chain comprising several statistical elements that exhibit local rigidity with residual secondary structure. Holo-RD is a f...

  5. An extended Kalman filter approach to non-stationary Bayesian estimation of reduced-order vocal fold model parameters.

    Science.gov (United States)

    Hadwin, Paul J; Peterson, Sean D

    2017-04-01

    The Bayesian framework for parameter inference provides a basis from which subject-specific reduced-order vocal fold models can be generated. Previously, it has been shown that a particle filter technique is capable of producing estimates and associated credibility intervals of time-varying reduced-order vocal fold model parameters. However, the particle filter approach is difficult to implement and has a high computational cost, which can be barriers to clinical adoption. This work presents an alternative estimation strategy based upon Kalman filtering aimed at reducing the computational cost of subject-specific model development. The robustness of this approach to Gaussian and non-Gaussian noise is discussed. The extended Kalman filter (EKF) approach is found to perform very well in comparison with the particle filter technique at dramatically lower computational cost. Based upon the test cases explored, the EKF is comparable in terms of accuracy to the particle filter technique when greater than 6000 particles are employed; if less particles are employed, the EKF actually performs better. For comparable levels of accuracy, the solution time is reduced by 2 orders of magnitude when employing the EKF. By virtue of the approximations used in the EKF, however, the credibility intervals tend to be slightly underpredicted.

  6. Generalization of the quark rearrangement model

    International Nuclear Information System (INIS)

    Fields, T.; Chen, C.K.

    1976-01-01

    An extension and generalization of the quark rearrangement model of baryon annihilation is described which can be applied to all annihilation reactions and which incorporates some of the features of the highly successful quark parton model. Some p anti-p interactions are discussed

  7. Geometrical efficiency in computerized tomography: generalized model

    International Nuclear Information System (INIS)

    Costa, P.R.; Robilotta, C.C.

    1992-01-01

    A simplified model for producing sensitivity and exposure profiles in computerized tomographic system was recently developed allowing the forecast of profiles behaviour in the rotation center of the system. The generalization of this model for some point of the image plane was described, and the geometrical efficiency could be evaluated. (C.G.C.)

  8. Generalized linear model for partially ordered data.

    Science.gov (United States)

    Zhang, Qiang; Ip, Edward Haksing

    2012-01-13

    Within the rich literature on generalized linear models, substantial efforts have been devoted to models for categorical responses that are either completely ordered or completely unordered. Few studies have focused on the analysis of partially ordered outcomes, which arise in practically every area of study, including medicine, the social sciences, and education. To fill this gap, we propose a new class of generalized linear models--the partitioned conditional model--that includes models for both ordinal and unordered categorical data as special cases. We discuss the specification of the partitioned conditional model and its estimation. We use an application of the method to a sample of the National Longitudinal Study of Youth to illustrate how the new method is able to extract from partially ordered data useful information about smoking youths that is not possible using traditional methods. Copyright © 2011 John Wiley & Sons, Ltd.

  9. Combinatorial identities and quantum state densities of sigma models on N-folds

    International Nuclear Information System (INIS)

    Abdalla, M.C.B.; Bytsenko, A.A.; Guimaraes, M.E.X.

    2005-07-01

    There is a remarkable connection between the number of quantum states of conformal theories and the sequence of dimensions of Lie algebras. In this paper, we explore this connection by computing the asymptotic expansion of the elliptic genus and the microscopic entropy of black holes associated with (supersymmetric) sigma models. The new features of these results are the appearance of correct prefactors in the state density expansion and in the coefficient of the logarithmic correction to the entropy. (author)

  10. Impact stress in a self-oscillating model of human vocal folds

    Czech Academy of Sciences Publication Activity Database

    Horáček, Jaromír; Bula, Vítězslav; Radolf, Vojtěch; Šidlof, Petr

    2016-01-01

    Roč. 4, č. 3 (2016), s. 183-190 ISSN 2321-3558 R&D Projects: GA ČR(CZ) GAP101/12/1306 Institutional support: RVO:61388998 Keywords : fluid-structure interaction * flutter * biomechanics of voice modeling * phonation * aeroelasticity Subject RIV: BI - Acoustics Impact factor: 0.259, year: 2016 http://www.tvi-in.com/Journals/journaldetail.aspx?Id=2016062811045074383592dcc719793

  11. Diffusion maps, clustering and fuzzy Markov modeling in peptide folding transitions

    International Nuclear Information System (INIS)

    Nedialkova, Lilia V.; Amat, Miguel A.; Kevrekidis, Ioannis G.; Hummer, Gerhard

    2014-01-01

    Using the helix-coil transitions of alanine pentapeptide as an illustrative example, we demonstrate the use of diffusion maps in the analysis of molecular dynamics simulation trajectories. Diffusion maps and other nonlinear data-mining techniques provide powerful tools to visualize the distribution of structures in conformation space. The resulting low-dimensional representations help in partitioning conformation space, and in constructing Markov state models that capture the conformational dynamics. In an initial step, we use diffusion maps to reduce the dimensionality of the conformational dynamics of Ala5. The resulting pretreated data are then used in a clustering step. The identified clusters show excellent overlap with clusters obtained previously by using the backbone dihedral angles as input, with small—but nontrivial—differences reflecting torsional degrees of freedom ignored in the earlier approach. We then construct a Markov state model describing the conformational dynamics in terms of a discrete-time random walk between the clusters. We show that by combining fuzzy C-means clustering with a transition-based assignment of states, we can construct robust Markov state models. This state-assignment procedure suppresses short-time memory effects that result from the non-Markovianity of the dynamics projected onto the space of clusters. In a comparison with previous work, we demonstrate how manifold learning techniques may complement and enhance informed intuition commonly used to construct reduced descriptions of the dynamics in molecular conformation space

  12. Diffusion maps, clustering and fuzzy Markov modeling in peptide folding transitions

    Science.gov (United States)

    Nedialkova, Lilia V.; Amat, Miguel A.; Kevrekidis, Ioannis G.; Hummer, Gerhard

    2014-09-01

    Using the helix-coil transitions of alanine pentapeptide as an illustrative example, we demonstrate the use of diffusion maps in the analysis of molecular dynamics simulation trajectories. Diffusion maps and other nonlinear data-mining techniques provide powerful tools to visualize the distribution of structures in conformation space. The resulting low-dimensional representations help in partitioning conformation space, and in constructing Markov state models that capture the conformational dynamics. In an initial step, we use diffusion maps to reduce the dimensionality of the conformational dynamics of Ala5. The resulting pretreated data are then used in a clustering step. The identified clusters show excellent overlap with clusters obtained previously by using the backbone dihedral angles as input, with small—but nontrivial—differences reflecting torsional degrees of freedom ignored in the earlier approach. We then construct a Markov state model describing the conformational dynamics in terms of a discrete-time random walk between the clusters. We show that by combining fuzzy C-means clustering with a transition-based assignment of states, we can construct robust Markov state models. This state-assignment procedure suppresses short-time memory effects that result from the non-Markovianity of the dynamics projected onto the space of clusters. In a comparison with previous work, we demonstrate how manifold learning techniques may complement and enhance informed intuition commonly used to construct reduced descriptions of the dynamics in molecular conformation space.

  13. Diffusion maps, clustering and fuzzy Markov modeling in peptide folding transitions.

    Science.gov (United States)

    Nedialkova, Lilia V; Amat, Miguel A; Kevrekidis, Ioannis G; Hummer, Gerhard

    2014-09-21

    Using the helix-coil transitions of alanine pentapeptide as an illustrative example, we demonstrate the use of diffusion maps in the analysis of molecular dynamics simulation trajectories. Diffusion maps and other nonlinear data-mining techniques provide powerful tools to visualize the distribution of structures in conformation space. The resulting low-dimensional representations help in partitioning conformation space, and in constructing Markov state models that capture the conformational dynamics. In an initial step, we use diffusion maps to reduce the dimensionality of the conformational dynamics of Ala5. The resulting pretreated data are then used in a clustering step. The identified clusters show excellent overlap with clusters obtained previously by using the backbone dihedral angles as input, with small--but nontrivial--differences reflecting torsional degrees of freedom ignored in the earlier approach. We then construct a Markov state model describing the conformational dynamics in terms of a discrete-time random walk between the clusters. We show that by combining fuzzy C-means clustering with a transition-based assignment of states, we can construct robust Markov state models. This state-assignment procedure suppresses short-time memory effects that result from the non-Markovianity of the dynamics projected onto the space of clusters. In a comparison with previous work, we demonstrate how manifold learning techniques may complement and enhance informed intuition commonly used to construct reduced descriptions of the dynamics in molecular conformation space.

  14. Topics in the generalized vector dominance model

    International Nuclear Information System (INIS)

    Chavin, S.

    1976-01-01

    Two topics are covered in the generalized vector dominance model. In the first topic a model is constructed for dilepton production in hadron-hadron interactions based on the idea of generalized vector-dominance. It is argued that in the high mass region the generalized vector-dominance model and the Drell-Yan parton model are alternative descriptions of the same underlying physics. In the low mass regions the models differ; the vector-dominance approach predicts a greater production of dileptons. It is found that the high mass vector mesons which are the hallmark of the generalized vector-dominance model make little contribution to the large yield of leptons observed in the transverse-momentum range 1 less than p/sub perpendicular/ less than 6 GeV. The recently measured hadronic parameters lead one to believe that detailed fits to the data are possible under the model. The possibility was expected, and illustrated with a simple model the extreme sensitivity of the large-p/sub perpendicular/ lepton yield to the large-transverse-momentum tail of vector-meson production. The second topic is an attempt to explain the mysterious phenomenon of photon shadowing in nuclei utilizing the contribution of the longitudinally polarized photon. It is argued that if the scalar photon anti-shadows, it could compensate for the transverse photon, which is presumed to shadow. It is found in a very simple model that the scalar photon could indeed anti-shadow. The principal feature of the model is a cancellation of amplitudes. The scheme is consistent with scalar photon-nucleon data as well. The idea is tested with two simple GVDM models and finds that the anti-shadowing contribution of the scalar photon is not sufficient to compensate for the contribution of the transverse photon. It is found doubtful that the scalar photon makes a significant contribution to the total photon-nuclear cross section

  15. Increasing the stability of the bacteriophage endolysin PlyC using rationale-based FoldX computational modeling.

    Science.gov (United States)

    Heselpoth, Ryan D; Yin, Yizhou; Moult, John; Nelson, Daniel C

    2015-04-01

    Endolysins are bacteriophage-derived peptidoglycan hydrolases that represent an emerging class of proteinaceous therapeutics. While the streptococcal endolysin PlyC has been validated in vitro and in vivo for its therapeutic efficacy, the inherent thermosusceptible structure of the enzyme correlates to transient long-term stability, thereby hindering the feasibility of developing the enzyme as an antimicrobial. Here, we thermostabilized the cysteine, histidine-dependent amidohydrolase/peptidase (CHAP) domain of the PlyCA catalytic subunit of PlyC using a FoldX-driven computational protein engineering approach. Using a combination of FoldX and Rosetta algorithms, as well as visual inspection, a final list of PlyC point mutant candidates with predicted stabilizing ΔΔG values was assembled and thermally characterized. Five of the eight point mutations were found experimentally to be destabilizing, a result most likely attributable to computationally modeling a complex and dynamic nine-subunit holoenzyme with a corresponding 3.3-Å X-ray crystal structure. However, one of the mutants, PlyC (PlyCA) T406R, was shown experimentally to increase the thermal denaturation temperature by ∼2.2°C and kinetic stability 16-fold over wild type. This mutation is expected to introduce a thermally advantageous hydrogen bond between the Q106 side chain of the N-terminal glycosyl hydrolase domain and the R406 side chain of the C-terminal CHAP domain. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  16. Single-Molecule Protein Folding: A Study of the Surface-Mediated Conformational Dynamics of a Model Amphipathic Peptide

    Science.gov (United States)

    Cunningham, Joy; English, Douglas

    2004-03-01

    Most surface-active polypeptides, composed of 10-50 amino acids, are devoid of well-defined tertiary structure. The conformation of these proteins is greatly dependent upon their environment and may assume totally different characteristics in an aqueous environment, in a detergent micelle, or in an organic solvent. Most antimicrobial peptides are helix-forming and are activated upon interaction with a membrane-mimicking environment. We are seeking to physically characterize the mechanism of membrane-peptide interaction through studying a simple model peptide, MT-1. MT-1 was designed as a nonhomologous analogue of melittin, the principle component in bee venom. We are using single molecule spectroscopy to examine the induction of secondary structure upon interaction of MT-1 with various membrane-mimicking interfaces. Specifically, we monitor coil-to-helix transition through single molecule fluorescence resonance energy transfer (sm-FRET) to determine conformational distributions of folded and unfolded peptides at an interface. Studies with MT-1 will focus upon the biologically relevant issues of orientation, aggregation, and folding at surfaces using both ensemble and single molecule experiments.

  17. Generalizations of the noisy-or model

    Czech Academy of Sciences Publication Activity Database

    Vomlel, Jiří

    2015-01-01

    Roč. 51, č. 3 (2015), s. 508-524 ISSN 0023-5954 R&D Projects: GA ČR GA13-20012S Institutional support: RVO:67985556 Keywords : Bayesian networks * noisy-or model * classification * generalized linear models Subject RIV: JD - Computer Applications, Robotics Impact factor: 0.628, year: 2015 http://library.utia.cas.cz/separaty/2015/MTR/vomlel-0447357.pdf

  18. Toward General Analysis of Recursive Probability Models

    OpenAIRE

    Pless, Daniel; Luger, George

    2013-01-01

    There is increasing interest within the research community in the design and use of recursive probability models. Although there still remains concern about computational complexity costs and the fact that computing exact solutions can be intractable for many nonrecursive models and impossible in the general case for recursive problems, several research groups are actively developing computational techniques for recursive stochastic languages. We have developed an extension to the traditional...

  19. Impact of an interbedded viscous décollement on the structural and kinematic coupling in fold-and-thrust belts: Insights from analogue modeling

    Science.gov (United States)

    Borderie, Sandra; Graveleau, Fabien; Witt, César; Vendeville, Bruno C.

    2018-01-01

    Fold-and-thrust belts (FTBs) can be segmented both across and along strike because of various factors including tectonic and stratigraphic inheritance. In this study, we investigated along/across-strike structural interactions in a FTB propagating toward a foreland which displays contrasted lithological sequences. A set of analogue models was performed in a compressional box where a single viscous level of varying width was interbedded within a frictional series. The tectonic interaction between the viscous and the frictional provinces was tested both along and across strike. Results indicate that a frictional province influences the along-strike tectonic evolution of an adjacent viscous province. This influence decreases when the width of the viscous province increases. The frictional provinces control the taper, structural style, obliquity of the structures' trend and kinematics of the shallow deformation front of the viscous province. Results evidence how far a frictional province can impact the deformation of an adjacent viscous province. For frictional-viscous wedges, it appears that the critical taper theory, which is generally applied in 2-D, should be likely considered in terms of 3-D. Moreover, the kinematics of the deep deformation front shows mutual influences between the adjacent viscous and frictional provinces. Experimental results are compared to natural examples in the Kuqa Basin (Southern Tian Shan, China) and the Salt Range (Pakistan), and give an insight to a better understanding of the dynamics of fold-and-thrust belts bearing a viscous décollement, such as salt.

  20. General Equilibrium Models: Improving the Microeconomics Classroom

    Science.gov (United States)

    Nicholson, Walter; Westhoff, Frank

    2009-01-01

    General equilibrium models now play important roles in many fields of economics including tax policy, environmental regulation, international trade, and economic development. The intermediate microeconomics classroom has not kept pace with these trends, however. Microeconomics textbooks primarily focus on the insights that can be drawn from the…

  1. Reflex vocal fold adduction in the porcine model: the effects of stimuli delivered to various sensory nerves.

    Science.gov (United States)

    Woo, Jeong-Soo; Hundal, Jagdeep S; Sasaki, Clarence T; Abdelmessih, Mikhail W; Kelleher, Stephen P

    2008-10-01

    The aim of this study was to identify a panel of sensory nerves capable of eliciting an evoked glottic closure reflex (GCR) and to quantify the glottic closing force (GCF) of these responses in a porcine model. In 5 pigs, the internal branch of the superior laryngeal nerve (iSLN) and the trigeminal, pharyngeal plexus, glossopharyngeal, radial, and intercostal nerves were surgically isolated and electrically stimulated. During stimulation of each nerve, the GCR was detected by laryngeal electromyography and the GCF was measured with a pressure transducer. The only nerve that elicited the GCR in the 5 pigs was the iSLN. The average GCF was 288.9 mm Hg. This study demonstrates that the only afferent nerve that elicits the GCR in pigs is the iSLN, and that it should remain the focus of research for the rehabilitation of patients with absent or defective reflex vocal fold adduction.

  2. Comparison between the double folding model and the energy density approach for calculating the ion-ion potential

    International Nuclear Information System (INIS)

    Ismail, M.; Osman, M.; Guirguis, J.W.; Ramadan, Kh.A.; Zahra, H.A.

    1989-01-01

    In the present work, we use the energy density formalism derived from both the conventional Skyrme force with parameter sets SI, SII and SIII together with the extended Skyrme force with parameters SKE1, SKE2, SKE3 and SKE4 to study the real part of the ion-ion potential between different pairs of nuclei. We have first modified the Skyrme energy density to include the energy dependence of the ion-ion potential. Then we have calculated the interaction potential between different pairs of nuclei at the strong absorption radius. We have compared our results with those deduced from experiment and with the predictions of the double folding model with M3Y force. We found that our results, obtained using a suitable approximation of the kinetic energy density, agree satisfactorily with experiment. The agreement is better than the agreement found in other papers. (author)

  3. The Complexity of Folding Self-Folding Origami

    Directory of Open Access Journals (Sweden)

    Menachem Stern

    2017-12-01

    Full Text Available Why is it difficult to refold a previously folded sheet of paper? We show that even crease patterns with only one designed folding motion inevitably contain an exponential number of “distractor” folding branches accessible from a bifurcation at the flat state. Consequently, refolding a sheet requires finding the ground state in a glassy energy landscape with an exponential number of other attractors of higher energy, much like in models of protein folding (Levinthal’s paradox and other NP-hard satisfiability (SAT problems. As in these problems, we find that refolding a sheet requires actuation at multiple carefully chosen creases. We show that seeding successful folding in this way can be understood in terms of subpatterns that fold when cut out (“folding islands”. Besides providing guidelines for the placement of active hinges in origami applications, our results point to fundamental limits on the programmability of energy landscapes in sheets.

  4. The Complexity of Folding Self-Folding Origami

    Science.gov (United States)

    Stern, Menachem; Pinson, Matthew B.; Murugan, Arvind

    2017-10-01

    Why is it difficult to refold a previously folded sheet of paper? We show that even crease patterns with only one designed folding motion inevitably contain an exponential number of "distractor" folding branches accessible from a bifurcation at the flat state. Consequently, refolding a sheet requires finding the ground state in a glassy energy landscape with an exponential number of other attractors of higher energy, much like in models of protein folding (Levinthal's paradox) and other NP-hard satisfiability (SAT) problems. As in these problems, we find that refolding a sheet requires actuation at multiple carefully chosen creases. We show that seeding successful folding in this way can be understood in terms of subpatterns that fold when cut out ("folding islands"). Besides providing guidelines for the placement of active hinges in origami applications, our results point to fundamental limits on the programmability of energy landscapes in sheets.

  5. Determination of the elastic properties of rabbit vocal fold tissue using uniaxial tensile testing and a tailored finite element model.

    Science.gov (United States)

    Latifi, Neda; Miri, Amir K; Mongeau, Luc

    2014-11-01

    The aim of the present study was to quantify the effects of the specimen shape on the accuracy of mechanical properties determined from a shape-specific model generation strategy. Digital images of five rabbit vocal folds (VFs) in their initial undeformed conditions were used to build corresponding specific solid models. The displacement field of the VFs under uniaxial tensile test was then measured over the visible portion of the surface using digital image correlation. A three-dimensional finite element model was built, using ABAQUS, for each solid model, while imposing measured boundary conditions. An inverse-problem method was used, assuming a homogeneous isotropic linear elastic constitutive model. Unknown elastic properties were identified iteratively through an error minimization technique between simulated and measured force-time data. The longitudinal elastic moduli of the five rabbit VFs were calculated and compared to values from a simple analytical method and those obtained by approximating the cross-section as elliptical. The use of shape-specific models significantly reduced the standard deviation of the Young׳s moduli of the tested specimens. However, a non-parametric statistical analysis test, i.e., the Friedman test, yielded no statistically significant differences between the shape-specific method and the elliptic cylindrical finite element model. Considering the required procedures to reconstruct the shape-specific finite element model for each tissue specimen, it might be expedient to use the simpler method when large numbers of tissue specimens are to be compared regarding their Young׳s moduli. Copyright © 2014 Elsevier Ltd. All rights reserved.

  6. Teaching computers to fold proteins

    DEFF Research Database (Denmark)

    Winther, Ole; Krogh, Anders Stærmose

    2004-01-01

    A new general algorithm for optimization of potential functions for protein folding is introduced. It is based upon gradient optimization of the thermodynamic stability of native folds of a training set of proteins with known structure. The iterative update rule contains two thermodynamic averages...

  7. General regression and representation model for classification.

    Directory of Open Access Journals (Sweden)

    Jianjun Qian

    Full Text Available Recently, the regularized coding-based classification methods (e.g. SRC and CRC show a great potential for pattern classification. However, most existing coding methods assume that the representation residuals are uncorrelated. In real-world applications, this assumption does not hold. In this paper, we take account of the correlations of the representation residuals and develop a general regression and representation model (GRR for classification. GRR not only has advantages of CRC, but also takes full use of the prior information (e.g. the correlations between representation residuals and representation coefficients and the specific information (weight matrix of image pixels to enhance the classification performance. GRR uses the generalized Tikhonov regularization and K Nearest Neighbors to learn the prior information from the training data. Meanwhile, the specific information is obtained by using an iterative algorithm to update the feature (or image pixel weights of the test sample. With the proposed model as a platform, we design two classifiers: basic general regression and representation classifier (B-GRR and robust general regression and representation classifier (R-GRR. The experimental results demonstrate the performance advantages of proposed methods over state-of-the-art algorithms.

  8. Current definition and a generalized federbush model

    International Nuclear Information System (INIS)

    Singh, L.P.S.; Hagen, C.R.

    1978-01-01

    The Federbush model is studied, with particular attention being given to the definition of currents. Inasmuch as there is no a priori restriction of local gauge invariance, the currents in the interacting case can be defined more generally than in Q.E.D. It is found that two arbitrary parameters are thereby introduced into the theory. Lowest order perturbation calculations for the current correlation functions and the Fermion propagators indicate that the theory admits a whole class of solutions dependent upon these parameters with the closed solution of Federbush emerging as a special case. The theory is shown to be locally covariant, and a conserved energy--momentum tensor is displayed. One finds in addition that the generators of gauge transformations for the fields are conserved. Finally it is shown that the general theory yields the Federbush solution if suitable Thirring model type counterterms are added

  9. Generalized Additive Models for Nowcasting Cloud Shading

    Czech Academy of Sciences Publication Activity Database

    Brabec, Marek; Paulescu, M.; Badescu, V.

    2014-01-01

    Roč. 101, March (2014), s. 272-282 ISSN 0038-092X R&D Projects: GA MŠk LD12009 Grant - others:European Cooperation in Science and Technology(XE) COST ES1002 Institutional support: RVO:67985807 Keywords : sunshine number * nowcasting * generalized additive model * Markov chain Subject RIV: BB - Applied Statistics, Operational Research Impact factor: 3.469, year: 2014

  10. Generalized data stacking programming model with applications

    OpenAIRE

    Hala Samir Elhadidy; Rawya Yehia Rizk; Hassen Taher Dorrah

    2016-01-01

    Recent researches have shown that, everywhere in various sciences the systems are following stacked-based stored change behavior when subjected to events or varying environments “on and above” their normal situations. This paper presents a generalized data stack programming (GDSP) model which is developed to describe the system changes under varying environment. These changes which are captured with different ways such as sensor reading are stored in matrices. Extraction algorithm and identif...

  11. A General Business Model for Marine Reserves

    Science.gov (United States)

    Sala, Enric; Costello, Christopher; Dougherty, Dawn; Heal, Geoffrey; Kelleher, Kieran; Murray, Jason H.; Rosenberg, Andrew A.; Sumaila, Rashid

    2013-01-01

    Marine reserves are an effective tool for protecting biodiversity locally, with potential economic benefits including enhancement of local fisheries, increased tourism, and maintenance of ecosystem services. However, fishing communities often fear short-term income losses associated with closures, and thus may oppose marine reserves. Here we review empirical data and develop bioeconomic models to show that the value of marine reserves (enhanced adjacent fishing + tourism) may often exceed the pre-reserve value, and that economic benefits can offset the costs in as little as five years. These results suggest the need for a new business model for creating and managing reserves, which could pay for themselves and turn a profit for stakeholder groups. Our model could be expanded to include ecosystem services and other benefits, and it provides a general framework to estimate costs and benefits of reserves and to develop such business models. PMID:23573192

  12. Recovering kinetics from a simplified protein folding model using replica exchange simulations: a kinetic network and effective stochastic dynamics.

    Science.gov (United States)

    Zheng, Weihua; Andrec, Michael; Gallicchio, Emilio; Levy, Ronald M

    2009-08-27

    We present an approach to recover kinetics from a simplified protein folding model at different temperatures using the combined power of replica exchange (RE), a kinetic network, and effective stochastic dynamics. While RE simulations generate a large set of discrete states with the correct thermodynamics, kinetic information is lost due to the random exchange of temperatures. We show how we can recover the kinetics of a 2D continuous potential with an entropic barrier by using RE-generated discrete states as nodes of a kinetic network. By choosing the neighbors and the microscopic rates between the neighbors appropriately, the correct kinetics of the system can be recovered by running a kinetic simulation on the network. We fine-tune the parameters of the network by comparison with the effective drift velocities and diffusion coefficients of the system determined from short-time stochastic trajectories. One of the advantages of the kinetic network model is that the network can be built on a high-dimensional discretized state space, which can consist of multiple paths not consistent with a single reaction coordinate.

  13. RNA folding: structure prediction, folding kinetics and ion electrostatics.

    Science.gov (United States)

    Tan, Zhijie; Zhang, Wenbing; Shi, Yazhou; Wang, Fenghua

    2015-01-01

    Beyond the "traditional" functions such as gene storage, transport and protein synthesis, recent discoveries reveal that RNAs have important "new" biological functions including the RNA silence and gene regulation of riboswitch. Such functions of noncoding RNAs are strongly coupled to the RNA structures and proper structure change, which naturally leads to the RNA folding problem including structure prediction and folding kinetics. Due to the polyanionic nature of RNAs, RNA folding structure, stability and kinetics are strongly coupled to the ion condition of solution. The main focus of this chapter is to review the recent progress in the three major aspects in RNA folding problem: structure prediction, folding kinetics and ion electrostatics. This chapter will introduce both the recent experimental and theoretical progress, while emphasize the theoretical modelling on the three aspects in RNA folding.

  14. A generalized additive regression model for survival times

    DEFF Research Database (Denmark)

    Scheike, Thomas H.

    2001-01-01

    Additive Aalen model; counting process; disability model; illness-death model; generalized additive models; multiple time-scales; non-parametric estimation; survival data; varying-coefficient models......Additive Aalen model; counting process; disability model; illness-death model; generalized additive models; multiple time-scales; non-parametric estimation; survival data; varying-coefficient models...

  15. Generalized data stacking programming model with applications

    Directory of Open Access Journals (Sweden)

    Hala Samir Elhadidy

    2016-09-01

    Full Text Available Recent researches have shown that, everywhere in various sciences the systems are following stacked-based stored change behavior when subjected to events or varying environments “on and above” their normal situations. This paper presents a generalized data stack programming (GDSP model which is developed to describe the system changes under varying environment. These changes which are captured with different ways such as sensor reading are stored in matrices. Extraction algorithm and identification technique are proposed to extract the different layers between images and identify the stack class the object follows; respectively. The general multi-stacking network is presented including the interaction between various stack-based layering of some applications. The experiments prove that the concept of stack matrix gives average accuracy of 99.45%.

  16. Testing Parametric versus Semiparametric Modelling in Generalized Linear Models

    NARCIS (Netherlands)

    Härdle, W.K.; Mammen, E.; Müller, M.D.

    1996-01-01

    We consider a generalized partially linear model E(Y|X,T) = G{X'b + m(T)} where G is a known function, b is an unknown parameter vector, and m is an unknown function.The paper introduces a test statistic which allows to decide between a parametric and a semiparametric model: (i) m is linear, i.e.

  17. Modelling debris flows down general channels

    Directory of Open Access Journals (Sweden)

    S. P. Pudasaini

    2005-01-01

    Full Text Available This paper is an extension of the single-phase cohesionless dry granular avalanche model over curved and twisted channels proposed by Pudasaini and Hutter (2003. It is a generalisation of the Savage and Hutter (1989, 1991 equations based on simple channel topography to a two-phase fluid-solid mixture of debris material. Important terms emerging from the correct treatment of the kinematic and dynamic boundary condition, and the variable basal topography are systematically taken into account. For vanishing fluid contribution and torsion-free channel topography our new model equations exactly degenerate to the previous Savage-Hutter model equations while such a degeneration was not possible by the Iverson and Denlinger (2001 model, which, in fact, also aimed to extend the Savage and Hutter model. The model equations of this paper have been rigorously derived; they include the effects of the curvature and torsion of the topography, generally for arbitrarily curved and twisted channels of variable channel width. The equations are put into a standard conservative form of partial differential equations. From these one can easily infer the importance and influence of the pore-fluid-pressure distribution in debris flow dynamics. The solid-phase is modelled by applying a Coulomb dry friction law whereas the fluid phase is assumed to be an incompressible Newtonian fluid. Input parameters of the equations are the internal and bed friction angles of the solid particles, the viscosity and volume fraction of the fluid, the total mixture density and the pore pressure distribution of the fluid at the bed. Given the bed topography and initial geometry and the initial velocity profile of the debris mixture, the model equations are able to describe the dynamics of the depth profile and bed parallel depth-averaged velocity distribution from the initial position to the final deposit. A shock capturing, total variation diminishing numerical scheme is implemented to

  18. Thurstonian models for sensory discrimination tests as generalized linear models

    DEFF Research Database (Denmark)

    Brockhoff, Per B.; Christensen, Rune Haubo Bojesen

    2010-01-01

    as a so-called generalized linear model. The underlying sensory difference 6 becomes directly a parameter of the statistical model and the estimate d' and it's standard error becomes the "usual" output of the statistical analysis. The d' for the monadic A-NOT A method is shown to appear as a standard...... linear contrast in a generalized linear model using the probit link function. All methods developed in the paper are implemented in our free R-package sensR (http://www.cran.r-project.org/package=sensR/). This includes the basic power and sample size calculations for these four discrimination tests...

  19. The Generalized Quantum Episodic Memory Model.

    Science.gov (United States)

    Trueblood, Jennifer S; Hemmer, Pernille

    2017-11-01

    Recent evidence suggests that experienced events are often mapped to too many episodic states, including those that are logically or experimentally incompatible with one another. For example, episodic over-distribution patterns show that the probability of accepting an item under different mutually exclusive conditions violates the disjunction rule. A related example, called subadditivity, occurs when the probability of accepting an item under mutually exclusive and exhaustive instruction conditions sums to a number >1. Both the over-distribution effect and subadditivity have been widely observed in item and source-memory paradigms. These phenomena are difficult to explain using standard memory frameworks, such as signal-detection theory. A dual-trace model called the over-distribution (OD) model (Brainerd & Reyna, 2008) can explain the episodic over-distribution effect, but not subadditivity. Our goal is to develop a model that can explain both effects. In this paper, we propose the Generalized Quantum Episodic Memory (GQEM) model, which extends the Quantum Episodic Memory (QEM) model developed by Brainerd, Wang, and Reyna (2013). We test GQEM by comparing it to the OD model using data from a novel item-memory experiment and a previously published source-memory experiment (Kellen, Singmann, & Klauer, 2014) examining the over-distribution effect. Using the best-fit parameters from the over-distribution experiments, we conclude by showing that the GQEM model can also account for subadditivity. Overall these results add to a growing body of evidence suggesting that quantum probability theory is a valuable tool in modeling recognition memory. Copyright © 2016 Cognitive Science Society, Inc.

  20. The epistemological status of general circulation models

    Science.gov (United States)

    Loehle, Craig

    2017-05-01

    Forecasts of both likely anthropogenic effects on climate and consequent effects on nature and society are based on large, complex software tools called general circulation models (GCMs). Forecasts generated by GCMs have been used extensively in policy decisions related to climate change. However, the relation between underlying physical theories and results produced by GCMs is unclear. In the case of GCMs, many discretizations and approximations are made, and simulating Earth system processes is far from simple and currently leads to some results with unknown energy balance implications. Statistical testing of GCM forecasts for degree of agreement with data would facilitate assessment of fitness for use. If model results need to be put on an anomaly basis due to model bias, then both visual and quantitative measures of model fit depend strongly on the reference period used for normalization, making testing problematic. Epistemology is here applied to problems of statistical inference during testing, the relationship between the underlying physics and the models, the epistemic meaning of ensemble statistics, problems of spatial and temporal scale, the existence or not of an unforced null for climate fluctuations, the meaning of existing uncertainty estimates, and other issues. Rigorous reasoning entails carefully quantifying levels of uncertainty.

  1. Generalized continuous linear model of international trade

    Directory of Open Access Journals (Sweden)

    Kostenko Elena

    2014-01-01

    Full Text Available The probability-based approach to the linear model of international trade based on the theory of Markov processes with continuous time is analysed. A generalized continuous model of international trade is built, in which the transition of the system from state to state is described by linear differential equations. The methodology of how to obtain the intensity matrices, which are differential in nature, is shown, and the same is done for their corresponding transition matrices for processes of purchasing and selling. In the process of the creation of the continuous model, functions and operations of matrices were used in addition to the Laplace transform, which gave the analytical form of the transition matrices, and therefore the expressions for the state vectors of the system. The obtained expressions simplify analysis and calculations in comparison to other methods. The values of the continuous transition matrices include in themselves the results of discrete model of international trade at moments in time proportional to the time step. The continuous model improves the quality of planning and the effectiveness of control of international trade agreements.

  2. The epistemological status of general circulation models

    Science.gov (United States)

    Loehle, Craig

    2018-03-01

    Forecasts of both likely anthropogenic effects on climate and consequent effects on nature and society are based on large, complex software tools called general circulation models (GCMs). Forecasts generated by GCMs have been used extensively in policy decisions related to climate change. However, the relation between underlying physical theories and results produced by GCMs is unclear. In the case of GCMs, many discretizations and approximations are made, and simulating Earth system processes is far from simple and currently leads to some results with unknown energy balance implications. Statistical testing of GCM forecasts for degree of agreement with data would facilitate assessment of fitness for use. If model results need to be put on an anomaly basis due to model bias, then both visual and quantitative measures of model fit depend strongly on the reference period used for normalization, making testing problematic. Epistemology is here applied to problems of statistical inference during testing, the relationship between the underlying physics and the models, the epistemic meaning of ensemble statistics, problems of spatial and temporal scale, the existence or not of an unforced null for climate fluctuations, the meaning of existing uncertainty estimates, and other issues. Rigorous reasoning entails carefully quantifying levels of uncertainty.

  3. Experimental determination of folding factor of benign breast cancer cell (MCF10A) and its effect on contact models and 3D manipulation of biological particles.

    Science.gov (United States)

    Korayem, M H; Shahali, S; Rastegar, Z

    2017-12-02

    Plasma membrane of most cells is not smooth. The surfaces of both small and large micropermeable cells are folded and corrugated which makes mammalian cells to have a larger membrane surface than the supposed ideal mode, that is, the smooth sphere of the same volume. Since cancer is an anthropic disease, cancer cells tend to have a larger membrane area than normal cells. Therefore, cancer cells have higher folding factor and larger radius than normal and healthy cells. On the other hand, the prevalence of breast cancer has prompted researchers to improve the treatment options raised for the disease in the past. In this paper, the impact of folding factor of the cell surface has been investigated. Considering that AFM is one of the most effective tools in performing the tests at micro- and nanoscales, it was used to determine the topography of MCF10 cells and then the resulting images and results were used to experimentally extract the folding factor of cells. By applying this factor in the Hertz, DMT and JKR contact models in the elastic and viscoelastic states, these models have been modified and the simulation of the three models shows that the simulation results are closer to the experimental results by considering the folding in the calculations. Additionally, the simulation of 3D manipulation has been done in both elastic and viscoelastic states with and without consideration of folding. Finally, the results were compared to investigate the effects of folding of the cell surface to the critical force and critical time of sliding and rolling in contact with the substrate and AFM tip in the 3D manipulation model.

  4. Aspects of general linear modelling of migration.

    Science.gov (United States)

    Congdon, P

    1992-01-01

    "This paper investigates the application of general linear modelling principles to analysing migration flows between areas. Particular attention is paid to specifying the form of the regression and error components, and the nature of departures from Poisson randomness. Extensions to take account of spatial and temporal correlation are discussed as well as constrained estimation. The issue of specification bears on the testing of migration theories, and assessing the role migration plays in job and housing markets: the direction and significance of the effects of economic variates on migration depends on the specification of the statistical model. The application is in the context of migration in London and South East England in the 1970s and 1980s." excerpt

  5. Superconductivity in a generalized Hubbard model

    Science.gov (United States)

    Arrachea, Liliana; Aligia, A. A.

    1997-02-01

    We consider a Hubbard model in the square lattice, with a generalized hopping between nearest-neighbor sites for spin up (down), which depends on the total occupation nb of spin down (up) electrons on both sites. We call the hopping parameters tAA, tAB, and tBB for nb = 0, 1 or 2 respectively. Using the Hartree-Fock and Bardeen-Cooper-Schrieffer mean-field approximations to decouple the two-body and three-body interactions, we find that the model exhibits extended s-wave superconductivity in the electron-hole symmetric case tAB > tAA = tBB for small values of the Coulomb repulsion U or small band fillings. For moderate values of U, the antiferromagnetic normal (AFN) state has lower energy. The translationally invariant d-wave superconducting state has always larger energy than the AFN state.

  6. Functional methods in the generalized Dicke model

    International Nuclear Information System (INIS)

    Alcalde, M. Aparicio; Lemos, A.L.L. de; Svaiter, N.F.

    2007-01-01

    The Dicke model describes an ensemble of N identical two-level atoms (qubits) coupled to a single quantized mode of a bosonic field. The fermion Dicke model should be obtained by changing the atomic pseudo-spin operators by a linear combination of Fermi operators. The generalized fermion Dicke model is defined introducing different coupling constants between the single mode of the bosonic field and the reservoir, g 1 and g 2 for rotating and counter-rotating terms respectively. In the limit N -> ∞, the thermodynamic of the fermion Dicke model can be analyzed using the path integral approach with functional method. The system exhibits a second order phase transition from normal to superradiance at some critical temperature with the presence of a condensate. We evaluate the critical transition temperature and present the spectrum of the collective bosonic excitations for the general case (g 1 ≠ 0 and g 2 ≠ 0). There is quantum critical behavior when the coupling constants g 1 and g 2 satisfy g 1 + g 2 =(ω 0 Ω) 1/2 , where ω 0 is the frequency of the mode of the field and Ω is the energy gap between energy eigenstates of the qubits. Two particular situations are analyzed. First, we present the spectrum of the collective bosonic excitations, in the case g 1 ≠ 0 and g 2 ≠ 0, recovering the well known results. Second, the case g 1 ≠ 0 and g 2 ≠ 0 is studied. In this last case, it is possible to have a super radiant phase when only virtual processes are introduced in the interaction Hamiltonian. Here also appears a quantum phase transition at the critical coupling g 2 (ω 0 Ω) 1/2 , and for larger values for the critical coupling, the system enter in this super radiant phase with a Goldstone mode. (author)

  7. Chaos in generalized Jaynes-Cummings model

    Energy Technology Data Exchange (ETDEWEB)

    Chotorlishvili, L. [Institute for Physik, Martin-Luther-University Halle-Wittenberg, Heinrich-Damerow-Str. 4, 06120 Halle (Germany)], E-mail: lchotor33@yahoo.com; Toklikishvili, Z. [Physics Department of the Tbilisi State University, Chavchavadze av. 3, 0128 Tbilisi (Georgia)

    2008-04-14

    The possibility of chaos formation is studied in terms of a generalized Jaynes-Cummings model which is a key model in the quantum electrodynamics of resonators. In particular, the dynamics of a three-level optical atom which is under the action of the resonator field is considered. The specific feature of the considered problem consists in that not all transitions between the atom levels are permitted. This asymmetry of the system accounts for the complexity of the problem and makes it different from the three-level systems studied previously. We consider the most general case, where the interaction of the system with the resonator depends on the system coordinate inside the resonator. It is shown that, contrary to the commonly accepted opinion, the absence of resonance detuning does not guarantee the system state controllability. In the course of evolution the system performs an irreversible transition from the purely quantum-mechanical state to the mixed state. It is shown that the asymmetry of the system levels accounts for the fact that the upper excited level turns out to be the most populated one.

  8. A general phenomenological model for work function

    Science.gov (United States)

    Brodie, I.; Chou, S. H.; Yuan, H.

    2014-07-01

    A general phenomenological model is presented for obtaining the zero Kelvin work function of any crystal facet of metals and semiconductors, both clean and covered with a monolayer of electropositive atoms. It utilizes the known physical structure of the crystal and the Fermi energy of the two-dimensional electron gas assumed to form on the surface. A key parameter is the number of electrons donated to the surface electron gas per surface lattice site or adsorbed atom, which is taken to be an integer. Initially this is found by trial and later justified by examining the state of the valence electrons of the relevant atoms. In the case of adsorbed monolayers of electropositive atoms a satisfactory justification could not always be found, particularly for cesium, but a trial value always predicted work functions close to the experimental values. The model can also predict the variation of work function with temperature for clean crystal facets. The model is applied to various crystal faces of tungsten, aluminium, silver, and select metal oxides, and most demonstrate good fits compared to available experimental values.

  9. A general model of learning design objects

    Directory of Open Access Journals (Sweden)

    Azeddine Chikh

    2014-01-01

    Full Text Available Previous research on the development of learning objects has targeted either learners, as consumers of these objects, or instructors, as designers who reuse these objects in building new online courses. There is currently an urgent need for the sharing and reuse of both theoretical knowledge (literature reviews and practical knowledge (best practice in learning design. The primary aim of this paper is to develop a strategy for constructing a more powerful set of learning objects targeted at supporting instructors in designing their curricula. A key challenge in this work is the definition of a new class of learning design objects that combine two types of knowledge: (1 reusable knowledge, consisting of theoretical and practical information on education design, and (2 knowledge of reuse, which is necessary to describe the reusable knowledge using an extended learning object metadata language. In addition, we introduce a general model of learning design object repositories based on the Unified Modeling Language, and a learning design support framework is proposed based on the repository model. Finally, a first prototype is developed to provide a subjective evaluation of the new framework.

  10. Symplectic models for general insertion devices

    International Nuclear Information System (INIS)

    Wu, Y.; Forest, E.; Robin, D. S.; Nishimura, H.; Wolski, A.; Litvinenko, V. N.

    2001-01-01

    A variety of insertion devices (IDs), wigglers and undulators, linearly or elliptically polarized,are widely used as high brightness radiation sources at the modern light source rings. Long and high-field wigglers have also been proposed as the main source of radiation damping at next generation damping rings. As a result, it becomes increasingly important to understand the impact of IDs on the charged particle dynamics in the storage ring. In this paper, we report our recent development of a general explicit symplectic model for IDs with the paraxial ray approximation. High-order explicit symplectic integrators are developed to study real-world insertion devices with a number of wiggler harmonics and arbitrary polarizations

  11. New model for nucleon generalized parton distributions

    Energy Technology Data Exchange (ETDEWEB)

    Radyushkin, Anatoly V. [JLAB, Newport News, VA (United States)

    2014-01-01

    We describe a new type of models for nucleon generalized parton distributions (GPDs) H and E. They are heavily based on the fact nucleon GPDs require to use two forms of double distribution (DD) representations. The outcome of the new treatment is that the usual DD+D-term construction should be amended by an extra term, {xi} E{sub +}{sup 1} (x,{xi}) which has the DD structure {alpha}/{beta} e({beta},{alpha}, with e({beta},{alpha}) being the DD that generates GPD E(x,{xi}). We found that this function, unlike the D-term, has support in the whole -1 <= x <= 1 region. Furthermore, it does not vanish at the border points |x|={xi}.

  12. A Simple General Model of Evolutionary Dynamics

    Science.gov (United States)

    Thurner, Stefan

    Evolution is a process in which some variations that emerge within a population (of, e.g., biological species or industrial goods) get selected, survive, and proliferate, whereas others vanish. Survival probability, proliferation, or production rates are associated with the "fitness" of a particular variation. We argue that the notion of fitness is an a posteriori concept in the sense that one can assign higher fitness to species or goods that survive but one can generally not derive or predict fitness per se. Whereas proliferation rates can be measured, fitness landscapes, that is, the inter-dependence of proliferation rates, cannot. For this reason we think that in a physical theory of evolution such notions should be avoided. Here we review a recent quantitative formulation of evolutionary dynamics that provides a framework for the co-evolution of species and their fitness landscapes (Thurner et al., 2010, Physica A 389, 747; Thurner et al., 2010, New J. Phys. 12, 075029; Klimek et al., 2009, Phys. Rev. E 82, 011901 (2010). The corresponding model leads to a generic evolutionary dynamics characterized by phases of relative stability in terms of diversity, followed by phases of massive restructuring. These dynamical modes can be interpreted as punctuated equilibria in biology, or Schumpeterian business cycles (Schumpeter, 1939, Business Cycles, McGraw-Hill, London) in economics. We show that phase transitions that separate phases of high and low diversity can be approximated surprisingly well by mean-field methods. We demonstrate that the mathematical framework is suited to understand systemic properties of evolutionary systems, such as their proneness to collapse, or their potential for diversification. The framework suggests that evolutionary processes are naturally linked to self-organized criticality and to properties of production matrices, such as their eigenvalue spectra. Even though the model is phrased in general terms it is also practical in the sense

  13. Predicting pore pressure in active fold-thrust systems: An empirical model for the deepwater Sabah foldbelt

    Science.gov (United States)

    Couzens-Schultz, Brent A.; Azbel, Konstantin

    2014-12-01

    Measurements related to mudrock (shale and siltstone) porosity such as acoustic velocity, density or electrical resistivity, have traditionally been used to predict pore pressures in extensional stress settings. The underlying assumption is that burial and vertical effective stress (VES), which is the overburden minus the pore pressure, controls the compaction of these rocks through porosity loss. The dataset presented here compares VES and acoustic velocity of similar composition mudrocks in both an extensional and a compressional stress setting. In the extensional stress environment, the mudrocks follow a typical compaction trend with a porosity loss and increase in acoustic velocity that can be related to VES. In an active fold-thrust belt, the compressive stresses further reduce the porosity and increase the acoustic velocity of the mudrocks. First a layer-parallel shortening compacts sediments beyond what is observed for the VES. This additional compaction is further enhanced near thrust faults and in anticlinal forelimbs, presumably due to additional shear stress in these areas. The mudrocks located in folds that are buried by additional sedimentation do not compact again until the tectonic compaction is overridden by enough new burial. After that, the mudrocks follow the observed extensional setting compaction trend. In the fold-thrust belt, the observed reduction in porosity by stresses other than burial leads to an under-prediction of pore pressure using traditional methods. To account for this, we present a correction that can be applied to the acoustic velocity (or porosity) using two parameters: (a) proximity to thrust faults and anticlinal forelimbs and (b) the amount of burial after fold formation. With these corrections, the extensional velocity-VES compaction trend can be used to accurately predict pore pressure within the active fold-thrust belt. The correction is calibrated with well data and is empirical. None-the-less, it is a first step toward

  14. MODEL OF BRAZILIAN URBANIZATION: GENERAL NOTES

    Directory of Open Access Journals (Sweden)

    Leandro da Silva Guimarães

    2016-07-01

    Full Text Available The full text format seeks to analyze the social inequality in Brazil through the spatial process of that inequality in this sense it analyzes, scratching the edges of what is known of the Brazilian urbanization model and how this same model produced gentrification cities and exclusive. So search the text discuss the country’s urban exclusion through consolidation of what is conventionally called peripheral areas, or more generally, of peripheries. The text on screen is the result of research carried out at the Federal Fluminense University in Masters level. In this study, we tried to understand the genesis of an urban housing development located in São Gonçalo, Rio de Janeiro called Jardim Catarina. Understand what the problem space partner who originated it. In this sense, his analysis becomes consubstantial to understand the social and spatial inequalities in Brazil, as well as the role of the state as planning manager socio-spatial planning and principal agent in the solution of such problems. It is expected that with the realization of a study of greater amounts, from which this article is just a micro work can contribute subsidies that contribute to the arrangement and crystallization of public policies that give account of social inequalities and serve to leverage a country more fair and equitable cities.

  15. The Associative Memory, Water Mediated, Structure and Energy Model (AWSEM)-Amylometer: Predicting Amyloid Propensity and Fibril Topology Using an Optimized Folding Landscape Model.

    Science.gov (United States)

    Chen, Mingchen; Schafer, Nicholas P; Zheng, Weihua; Wolynes, Peter G

    2018-01-10

    Amyloids are fibrillar protein aggregates with simple repeated structural motifs in their cores, usually β-strands but sometimes α-helices. Identifying the amyloid-prone regions within protein sequences is important both for understanding the mechanisms of amyloid-associated diseases and for understanding functional amyloids. Based on the crystal structures of seven cross-β amyloidogenic peptides with different topologies and one recently solved cross-α fiber structure, we have developed a computational approach for identifying amyloidogenic segments in protein sequences using the Associative memory, Water mediated, Structure and Energy Model (AWSEM). The AWSEM-Amylometer performs favorably in comparison with other predictors in predicting aggregation-prone sequences in multiple data sets. The method also predicts well the specific topologies (the relative arrangement of β-strands in the core) of the amyloid fibrils. An important advantage of the AWSEM-Amylometer over other existing methods is its direct connection with an efficient, optimized protein folding simulation model, AWSEM. This connection allows one to combine efficient and accurate search of protein sequences for amyloidogenic segments with the detailed study of the thermodynamic and kinetic roles that these segments play in folding and aggregation in the context of the entire protein sequence. We present new simulation results that highlight the free energy landscapes of peptides that can take on multiple fibril topologies. We also demonstrate how the Amylometer methodology can be straightforwardly extended to the study of functional amyloids that have the recently discovered cross-α fibril architecture.

  16. General single phase wellbore flow model

    Energy Technology Data Exchange (ETDEWEB)

    Ouyang, Liang-Biao; Arbabi, S.; Aziz, K.

    1997-02-05

    A general wellbore flow model, which incorporates not only frictional, accelerational and gravitational pressure drops, but also the pressure drop caused by inflow, is presented in this report. The new wellbore model is readily applicable to any wellbore perforation patterns and well completions, and can be easily incorporated in reservoir simulators or analytical reservoir inflow models. Three dimensionless numbers, the accelerational to frictional pressure gradient ratio R{sub af}, the gravitational to frictional pressure gradient ratio R{sub gf}, and the inflow-directional to accelerational pressure gradient ratio R{sub da}, have been introduced to quantitatively describe the relative importance of different pressure gradient components. For fluid flow in a production well, it is expected that there may exist up to three different regions of the wellbore: the laminar flow region, the partially-developed turbulent flow region, and the fully-developed turbulent flow region. The laminar flow region is located near the well toe, the partially-turbulent flow region lies in the middle of the wellbore, while the fully-developed turbulent flow region is at the downstream end or the heel of the wellbore. Length of each region depends on fluid properties, wellbore geometry and flow rate. As the distance from the well toe increases, flow rate in the wellbore increases and the ratios R{sub af} and R{sub da} decrease. Consequently accelerational and inflow-directional pressure drops have the greatest impact in the toe region of the wellbore. Near the well heel the local wellbore flow rate becomes large and close to the total well production rate, here R{sub af} and R{sub da} are small, therefore, both the accelerational and inflow-directional pressure drops can be neglected.

  17. Evaluating the double Poisson generalized linear model.

    Science.gov (United States)

    Zou, Yaotian; Geedipally, Srinivas Reddy; Lord, Dominique

    2013-10-01

    The objectives of this study are to: (1) examine the applicability of the double Poisson (DP) generalized linear model (GLM) for analyzing motor vehicle crash data characterized by over- and under-dispersion and (2) compare the performance of the DP GLM with the Conway-Maxwell-Poisson (COM-Poisson) GLM in terms of goodness-of-fit and theoretical soundness. The DP distribution has seldom been investigated and applied since its first introduction two decades ago. The hurdle for applying the DP is related to its normalizing constant (or multiplicative constant) which is not available in closed form. This study proposed a new method to approximate the normalizing constant of the DP with high accuracy and reliability. The DP GLM and COM-Poisson GLM were developed using two observed over-dispersed datasets and one observed under-dispersed dataset. The modeling results indicate that the DP GLM with its normalizing constant approximated by the new method can handle crash data characterized by over- and under-dispersion. Its performance is comparable to the COM-Poisson GLM in terms of goodness-of-fit (GOF), although COM-Poisson GLM provides a slightly better fit. For the over-dispersed data, the DP GLM performs similar to the NB GLM. Considering the fact that the DP GLM can be easily estimated with inexpensive computation and that it is simpler to interpret coefficients, it offers a flexible and efficient alternative for researchers to model count data. Copyright © 2013 Elsevier Ltd. All rights reserved.

  18. A Note on the Identifiability of Generalized Linear Mixed Models

    DEFF Research Database (Denmark)

    Labouriau, Rodrigo

    2014-01-01

    I present here a simple proof that, under general regularity conditions, the standard parametrization of generalized linear mixed model is identifiable. The proof is based on the assumptions of generalized linear mixed models on the first and second order moments and some general mild regularity ...... conditions, and, therefore, is extensible to quasi-likelihood based generalized linear models. In particular, binomial and Poisson mixed models with dispersion parameter are identifiable when equipped with the standard parametrization...

  19. Application of a folding-model optical potential to analyzing inelastic pion–nucleus scattering and the in-medium effect on a pion–nucleon amplitude

    Energy Technology Data Exchange (ETDEWEB)

    Lukyanov, V. K., E-mail: lukyanov@theor.jinr.ru; Zemlyanaya, E. V.; Lukyanov, K. V. [Joint Institute for Nuclear Research (Russian Federation); Abdul-Magead, I. A. M. [Cairo University (Egypt)

    2016-11-15

    The folding-model optical potential is generalized in such a way as to apply it to calculating the cross sections for inelastic scattering of π{sup ±}-mesons on {sup 28}Si, {sup 40}Ca, {sup 58}Ni, and {sup 208}Pb nuclei at the energies of 162, 180, 226, and 291 MeV leading to the excitation of the 2{sup +} and 3{sup −} collective states. In doing this, use is made of known nucleon-density distributions in nuclei and the pion–nucleon scattering amplitude whose parameters were obtained previously by fitting the elastic scattering cross sections for the same nuclei. Thus, the values of quadrupole (β{sub 2}) and octupole (β{sub 3}) deformations of nuclei appear here as the only adjustable parameters. The scattering cross section is calculated by solving the relativistic wave equation, whereby effects of relativization and distortion in the entrance and exit scattering channels are taken exactly into account. The cross sections calculated in this way for inelastic scattering are in good agreement with respective experimental data. The importance of the inclusion of in-medium effects in choosing parameters of the pion–nucleon amplitude is emphasized.

  20. Sequencing and G-quadruplex folding of the canine proto-oncogene KIT promoter region: might dog be used as a model for human disease?

    Directory of Open Access Journals (Sweden)

    Silvia Da Ros

    Full Text Available Downregulation of gene expression by induction of non-canonical DNA structures at promotorial level is a novel attractive anticancer strategy. In human, two guanine-rich sequences (h_kit1 and h_kit2 were identified in the promotorial region of oncogene KIT. Their stabilization into G-quadruplex structures can find applications in the treatment of leukemias, mastocytosis, gastrointestinal stromal tumor, and lung carcinomas which are often associated to c-kit mis-regulation. Also the most common skin cancer in domestic dog, mast cell tumor, is linked to a mutation and/or to an over-expression of c-kit, thus supporting dog as an excellent animal model. In order to assess if the G-quadruplex mediated mechanism of regulation of c-kit expression is conserved among the two species, herein we cloned and sequenced the canine KIT promoter region and we compared it with the human one in terms of sequence and conformational equilibria in physiologically relevant conditions. Our results evidenced a general conserved promotorial sequence between the two species. As experimentally confirmed, this grants that the conformational features of the canine kit1 sequence are substantially shared with the human one. Conversely, two isoforms of the kit2 sequences were identified in the analyzed dog population. In comparison with the human counterpart, both of them showed an altered distribution among several folded conformations.

  1. Depletion of the chromatin looping proteins CTCF and cohesin causes chromatin compaction: insight into chromatin folding by polymer modelling

    NARCIS (Netherlands)

    Tark-Dame, M.; Jerabek, H.; Manders, E.M.M.; Heermann, D.W.; van Driel, R.

    2014-01-01

    Folding of the chromosomal fibre in interphase nuclei is an important element in the regulation of gene expression. For instance, physical contacts between promoters and enhancers are a key element in cell-type-specific transcription. We know remarkably little about the principles that control

  2. Autologous fat injection therapy including a high concentration of adipose-derived regenerative cells in a vocal fold paralysis model: animal pilot study.

    Science.gov (United States)

    Nishio, N; Fujimoto, Y; Suga, K; Iwata, Y; Toriyama, K; Takanari, K; Kamei, Y; Yamamoto, T; Gotoh, M

    2016-10-01

    To verify the effectiveness and safety of the addition of adipose-derived regenerative cells to autologous fat injection therapy. Unilateral vocal fold paralysis models were made by cutting the right recurrent laryngeal nerve in two pigs. At day 30, 0.5 ml adipose-derived regenerative cells mixed with 1 ml autologous fat was injected into the right vocal fold of one pig, with the other receiving 0.5 ml Ringer's solution mixed with 1 ml autologous fat. At day 120, fibrescopy, laser Doppler flowmeter, computed tomography, vocal function evaluation and histological assessment were conducted. Although histological assessment revealed atrophy of the thyroarytenoid muscle fibre in both pigs, there was remarkable hypertrophy of the thyroarytenoid muscle fibre in the area surrounding the adipose-derived regenerative cells injection site. The addition of a high concentration of adipose-derived regenerative cells to autologous fat injection therapy has the potential to improve the treatment outcome for unilateral vocal fold paralysis.

  3. Bayesian Subset Modeling for High-Dimensional Generalized Linear Models

    KAUST Repository

    Liang, Faming

    2013-06-01

    This article presents a new prior setting for high-dimensional generalized linear models, which leads to a Bayesian subset regression (BSR) with the maximum a posteriori model approximately equivalent to the minimum extended Bayesian information criterion model. The consistency of the resulting posterior is established under mild conditions. Further, a variable screening procedure is proposed based on the marginal inclusion probability, which shares the same properties of sure screening and consistency with the existing sure independence screening (SIS) and iterative sure independence screening (ISIS) procedures. However, since the proposed procedure makes use of joint information from all predictors, it generally outperforms SIS and ISIS in real applications. This article also makes extensive comparisons of BSR with the popular penalized likelihood methods, including Lasso, elastic net, SIS, and ISIS. The numerical results indicate that BSR can generally outperform the penalized likelihood methods. The models selected by BSR tend to be sparser and, more importantly, of higher prediction ability. In addition, the performance of the penalized likelihood methods tends to deteriorate as the number of predictors increases, while this is not significant for BSR. Supplementary materials for this article are available online. © 2013 American Statistical Association.

  4. Multivariate generalized linear model for genetic pleiotropy.

    Science.gov (United States)

    Schaid, Daniel J; Tong, Xingwei; Batzler, Anthony; Sinnwell, Jason P; Qing, Jiang; Biernacka, Joanna M

    2017-12-16

    When a single gene influences more than one trait, known as pleiotropy, it is important to detect pleiotropy to improve the biological understanding of a gene. This can lead to improved screening, diagnosis, and treatment of diseases. Yet, most current multivariate methods to evaluate pleiotropy test the null hypothesis that none of the traits are associated with a variant; departures from the null could be driven by just one associated trait. A formal test of pleiotropy should assume a null hypothesis that one or fewer traits are associated with a genetic variant. We recently developed statistical methods to analyze pleiotropy for quantitative traits having a multivariate normal distribution. We now extend this approach to traits that can be modeled by generalized linear models, such as analysis of binary, ordinal, or quantitative traits, or a mixture of these types of traits. Based on methods from estimating equations, we developed a new test for pleiotropy. We then extended the testing framework to a sequential approach to test the null hypothesis that $k+1$ traits are associated, given that the null of $k$ associated traits was rejected. This provides a testing framework to determine the number of traits associated with a genetic variant, as well as which traits, while accounting for correlations among the traits. By simulations, we illustrate the Type-I error rate and power of our new methods, describe how they are influenced by sample size, the number of traits, and the trait correlations, and apply the new methods to a genome-wide association study of multivariate traits measuring symptoms of major depression. Our new approach provides a quantitative assessment of pleiotropy, enhancing current analytic practice. © The Author 2017. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  5. A generalized model for homogenized reflectors

    International Nuclear Information System (INIS)

    Pogosbekyan, Leonid; Kim, Yeong Il; Kim, Young Jin; Joo, Hyung Kook

    1996-01-01

    A new concept of equivalent homogenization is proposed. The concept employs new set of homogenized parameters: homogenized cross sections (XS) and interface matrix (IM), which relates partial currents at the cell interfaces. The idea of interface matrix generalizes the idea of discontinuity factors (DFs), proposed and developed by K. Koebke and K. Smith. The method of K. Smith can be simulated within framework of new method, while the new method approximates hetero-geneous cell better in case of the steep flux gradients at the cell interfaces. The attractive shapes of new concept are:improved accuracy, simplicity of incorporation in the existing codes, equal numerical expenses in comparison to the K. Smith's approach. The new concept is useful for: (a) explicit reflector/baffle simulation; (b)control blades simulation; (c) mixed UO 2 /MOX core simulation. The offered model has been incorporated in the finite difference code and in the nodal code PANBOX. The numerical results show good accuracy of core calculations and insensitivity of homogenized parameters with respect to in-core conditions

  6. Cosmological models in the generalized Einstein action

    International Nuclear Information System (INIS)

    Arbab, A.I.

    2007-12-01

    We have studied the evolution of the Universe in the generalized Einstein action of the form R + β R 2 , where R is the scalar curvature and β = const. We have found exact cosmological solutions that predict the present cosmic acceleration. These models predict an inflationary de-Sitter era occurring in the early Universe. The cosmological constant (Λ) is found to decay with the Hubble constant (H) as, Λ ∝ H 4 . In this scenario the cosmological constant varies quadratically with the energy density (ρ), i.e., Λ ∝ ρ 2 . Such a variation is found to describe a two-component cosmic fluid in the Universe. One of the components accelerated the Universe in the early era, and the other in the present era. The scale factor of the Universe varies as a ∼ t n = 1/2 in the radiation era. The cosmological constant vanishes when n = 4/3 and n =1/2. We have found that the inclusion of the term R 2 mimics a cosmic matter that could substitute the ordinary matter. (author)

  7. Climatology of the HOPE-G global ocean general circulation model - Sea ice general circulation model

    Energy Technology Data Exchange (ETDEWEB)

    Legutke, S. [Deutsches Klimarechenzentrum (DKRZ), Hamburg (Germany); Maier-Reimer, E. [Max-Planck-Institut fuer Meteorologie, Hamburg (Germany)

    1999-12-01

    The HOPE-G global ocean general circulation model (OGCM) climatology, obtained in a long-term forced integration is described. HOPE-G is a primitive-equation z-level ocean model which contains a dynamic-thermodynamic sea-ice model. It is formulated on a 2.8 grid with increased resolution in low latitudes in order to better resolve equatorial dynamics. The vertical resolution is 20 layers. The purpose of the integration was both to investigate the models ability to reproduce the observed general circulation of the world ocean and to obtain an initial state for coupled atmosphere - ocean - sea-ice climate simulations. The model was driven with daily mean data of a 15-year integration of the atmosphere general circulation model ECHAM4, the atmospheric component in later coupled runs. Thereby, a maximum of the flux variability that is expected to appear in coupled simulations is included already in the ocean spin-up experiment described here. The model was run for more than 2000 years until a quasi-steady state was achieved. It reproduces the major current systems and the main features of the so-called conveyor belt circulation. The observed distribution of water masses is reproduced reasonably well, although with a saline bias in the intermediate water masses and a warm bias in the deep and bottom water of the Atlantic and Indian Oceans. The model underestimates the meridional transport of heat in the Atlantic Ocean. The simulated heat transport in the other basins, though, is in good agreement with observations. (orig.)

  8. Covering folded shapes

    Directory of Open Access Journals (Sweden)

    Oswin Aichholzer

    2014-05-01

    Full Text Available Can folding a piece of paper flat make it larger? We explore whether a shape S must be scaled to cover a flat-folded copy of itself. We consider both single folds and arbitrary folds (continuous piecewise isometries \\(S\\to\\mathbb{R}^2\\. The underlying problem is motivated by computational origami, and is related to other covering and fixturing problems, such as Lebesgue's universal cover problem and force closure grasps. In addition to considering special shapes (squares, equilateral triangles, polygons and disks, we give upper and lower bounds on scale factors for single folds of convex objects and arbitrary folds of simply connected objects.

  9. Application of Improved Radiation Modeling to General Circulation Models

    Energy Technology Data Exchange (ETDEWEB)

    Michael J Iacono

    2011-04-07

    This research has accomplished its primary objectives of developing accurate and efficient radiation codes, validating them with measurements and higher resolution models, and providing these advancements to the global modeling community to enhance the treatment of cloud and radiative processes in weather and climate prediction models. A critical component of this research has been the development of the longwave and shortwave broadband radiative transfer code for general circulation model (GCM) applications, RRTMG, which is based on the single-column reference code, RRTM, also developed at AER. RRTMG is a rigorously tested radiation model that retains a considerable level of accuracy relative to higher resolution models and measurements despite the performance enhancements that have made it possible to apply this radiation code successfully to global dynamical models. This model includes the radiative effects of all significant atmospheric gases, and it treats the absorption and scattering from liquid and ice clouds and aerosols. RRTMG also includes a statistical technique for representing small-scale cloud variability, such as cloud fraction and the vertical overlap of clouds, which has been shown to improve cloud radiative forcing in global models. This development approach has provided a direct link from observations to the enhanced radiative transfer provided by RRTMG for application to GCMs. Recent comparison of existing climate model radiation codes with high resolution models has documented the improved radiative forcing capability provided by RRTMG, especially at the surface, relative to other GCM radiation models. Due to its high accuracy, its connection to observations, and its computational efficiency, RRTMG has been implemented operationally in many national and international dynamical models to provide validated radiative transfer for improving weather forecasts and enhancing the prediction of global climate change.

  10. Noise Folding in Completely Perturbed Compressed Sensing

    Directory of Open Access Journals (Sweden)

    Limin Zhou

    2016-01-01

    Full Text Available This paper first presents a new generally perturbed compressed sensing (CS model y=(A+E(x+u+e, which incorporated a general nonzero perturbation E into sensing matrix A and a noise u into signal x simultaneously based on the standard CS model y=Ax+e and is called noise folding in completely perturbed CS model. Our construction mainly will whiten the new proposed CS model and explore in restricted isometry property (RIP and coherence of the new CS model under some conditions. Finally, we use OMP to give a numerical simulation which shows that our model is feasible although the recovered value of signal is not exact compared with original signal because of measurement noise e, signal noise u, and perturbation E involved.

  11. Efficient molecular mechanics simulations of the folding, orientation, and assembly of peptides in lipid bilayers using an implicit atomic solvation model

    Science.gov (United States)

    Bordner, Andrew J.; Zorman, Barry; Abagyan, Ruben

    2011-10-01

    Membrane proteins comprise a significant fraction of the proteomes of sequenced organisms and are the targets of approximately half of marketed drugs. However, in spite of their prevalence and biomedical importance, relatively few experimental structures are available due to technical challenges. Computational simulations can potentially address this deficit by providing structural models of membrane proteins. Solvation within the spatially heterogeneous membrane/solvent environment provides a major component of the energetics driving protein folding and association within the membrane. We have developed an implicit solvation model for membranes that is both computationally efficient and accurate enough to enable molecular mechanics predictions for the folding and association of peptides within the membrane. We derived the new atomic solvation model parameters using an unbiased fitting procedure to experimental data and have applied it to diverse problems in order to test its accuracy and to gain insight into membrane protein folding. First, we predicted the positions and orientations of peptides and complexes within the lipid bilayer and compared the simulation results with solid-state NMR structures. Additionally, we performed folding simulations for a series of host-guest peptides with varying propensities to form alpha helices in a hydrophobic environment and compared the structures with experimental measurements. We were also able to successfully predict the structures of amphipathic peptides as well as the structures for dimeric complexes of short hexapeptides that have experimentally characterized propensities to form beta sheets within the membrane. Finally, we compared calculated relative transfer energies with data from experiments measuring the effects of mutations on the free energies of translocon-mediated insertion of proteins into lipid bilayers and of combined folding and membrane insertion of a beta barrel protein.

  12. Multivariate statistical modelling based on generalized linear models

    CERN Document Server

    Fahrmeir, Ludwig

    1994-01-01

    This book is concerned with the use of generalized linear models for univariate and multivariate regression analysis. Its emphasis is to provide a detailed introductory survey of the subject based on the analysis of real data drawn from a variety of subjects including the biological sciences, economics, and the social sciences. Where possible, technical details and proofs are deferred to an appendix in order to provide an accessible account for non-experts. Topics covered include: models for multi-categorical responses, model checking, time series and longitudinal data, random effects models, and state-space models. Throughout, the authors have taken great pains to discuss the underlying theoretical ideas in ways that relate well to the data at hand. As a result, numerous researchers whose work relies on the use of these models will find this an invaluable account to have on their desks. "The basic aim of the authors is to bring together and review a large part of recent advances in statistical modelling of m...

  13. Origami-Inspired Folding of Thick, Rigid Panels

    Science.gov (United States)

    Trease, Brian P.; Thomson, Mark W.; Sigel, Deborah A.; Walkemeyer, Phillip E.; Zirbel, Shannon; Howell, Larry; Lang, Robert

    2014-01-01

    To achieve power of 250 kW or greater, a large compression ratio of stowed-to-deployed area is needed. Origami folding patterns were used to inspire the folding of a solar array to achieve synchronous deployment; however, origami models are generally created for near-zero-thickness material. Panel thickness is one of the main challenges of origami-inspired design. Three origami-inspired folding techniques (flasher, square twist, and map fold) were created with rigid panels and hinges. Hinge components are added to the model to enable folding of thick, rigid materials. Origami models are created assuming zero (or near zero) thickness. When a material with finite thickness is used, the panels are required to bend around an increasingly thick fold as they move away from the center of the model. The two approaches for dealing with material thickness are to use membrane hinges to connect the panels, or to add panel hinges, or hinges of the same thickness, at an appropriate width to enable folding.

  14. Fault-related-folding structure and reflection seismic sections. Construction of earth model using balanced cross section; Danso ga kaizaisuru shukyoku kozo no keitai to jishin tansa danmen. 1. Balanced cross section wo mochiita chika model no kochiku

    Energy Technology Data Exchange (ETDEWEB)

    Matsuoka, T.; Tamagawa, T. [Japan Petroleum Exploration Corp., Tokyo (Japan); Tsukui, R. [Japan National Oil Corp., Tokyo (Japan). Technology Research Center

    1997-05-27

    Pre-stacking depth migration treatment is studied for the estimation of the fold configuration from seismic survey cross sections. The estimation of a velocity structure is necessary for the execution of such treatment, and the utilization of structural-geological knowledge is required for its interpretation. The concept of balanced cross section in relation to the fault-bend fold constructs a stratum structure model under conditions that the deformation during fold and fault formation is a planar strain, that there is no change in volume due to deformation, and that a fold is a parallel fold. In addition to the above geometric and kinetic approach, there is another fold formation process simulation model using a Newtonian fluid for study from the viewpoint of dynamics. This simulation stands on the presumption that the boundary contains a ramp that had been in presence before fold formation and that an incompressible viscous matter is mounted on the top surface. The viscous matter flows and deforms for the formation of an anticline on the ramp. Such enables the reproduction of a fault-bend fold formation process, and helpful discussion may be furthered on the dynamic aspect of this simulation. 5 refs., 4 figs.

  15. The ECHAM3 atmospheric general circulation model

    International Nuclear Information System (INIS)

    1993-09-01

    The ECHAM model has been developed from the ECMWF model (cycle 31, November 1988). It contains several changes, mostly in the parameterization, in order to adjust the model for climate simulations. The technical details of the ECHAM operational model are described. (orig./KW)

  16. From Holonomy of the Ising Model Form Factors to n-Fold Integrals and the Theory of Elliptic Curves

    Directory of Open Access Journals (Sweden)

    Salah Boukraa

    2007-10-01

    Full Text Available We recall the form factors $f^(j_{N,N}$ corresponding to the $lambda$-extension $C(N,N; lambda$ of the two-point diagonal correlation function of the Ising model on the square lattice and their associated linear differential equations which exhibit both a "Russian-doll" nesting, and a decomposition of the linear differential operators as a direct sum of operators (equivalent to symmetric powers of the differential operator of the complete elliptic integral $E$. The scaling limit of these differential operators breaks the direct sum structure but not the "Russian doll" structure, the "scaled" linear differential operators being no longer Fuchsian. We then introduce some multiple integrals of the Ising class expected to have the same singularities as the singularities of the $n$-particle contributions $chi^{(n}$ to the susceptibility of the square lattice Ising model. We find the Fuchsian linear differential equations satisfied by these multiple integrals for $n = 1, 2, 3, 4$ and, only modulo a prime, for $n = 5$ and 6, thus providing a large set of (possible new singularities of the $chi^{(n}$. We get the location of these singularities by solving the Landau conditions. We discuss the mathematical, as well as physical, interpretation of these new singularities. Among the singularities found, we underline the fact that the quadratic polynomial condition $1 + 3w + 4w^2 = 0$, that occurs in the linear differential equation of $chi^{(3}$, actually corresponds to the occurrence of complex multiplication for elliptic curves. The interpretation of complex multiplication for elliptic curves as complex fixed points of generators of the exact renormalization group is sketched. The other singularities occurring in our multiple integrals are not related to complex multiplication situations, suggesting a geometric interpretation in terms of more general (motivic mathematical structures beyond the theory of elliptic curves. The scaling limit of the (lattice

  17. PREFACE Protein folding: lessons learned and new frontiers Protein folding: lessons learned and new frontiers

    Science.gov (United States)

    Pappu, Rohit V.; Nussinov, Ruth

    2009-03-01

    In appropriate physiological milieux proteins spontaneously fold into their functional three-dimensional structures. The amino acid sequences of functional proteins contain all the information necessary to specify the folds. This remarkable observation has spawned research aimed at answering two major questions. (1) Of all the conceivable structures that a protein can adopt, why is the ensemble of native-like structures the most favorable? (2) What are the paths by which proteins manage to robustly and reproducibly fold into their native structures? Anfinsen's thermodynamic hypothesis has guided the pursuit of answers to the first question whereas Levinthal's paradox has influenced the development of models for protein folding dynamics. Decades of work have led to significant advances in the folding problem. Mean-field models have been developed to capture our current, coarse grain understanding of the driving forces for protein folding. These models are being used to predict three-dimensional protein structures from sequence and stability profiles as a function of thermodynamic and chemical perturbations. Impressive strides have also been made in the field of protein design, also known as the inverse folding problem, thereby testing our understanding of the determinants of the fold specificities of different sequences. Early work on protein folding pathways focused on the specific sequence of events that could lead to a simplification of the search process. However, unifying principles proved to be elusive. Proteins that show reversible two-state folding-unfolding transitions turned out to be a gift of natural selection. Focusing on these simple systems helped researchers to uncover general principles regarding the origins of cooperativity in protein folding thermodynamics and kinetics. On the theoretical front, concepts borrowed from polymer physics and the physics of spin glasses led to the development of a framework based on energy landscape theories. These

  18. General problems of modeling for accelerators

    International Nuclear Information System (INIS)

    Luccio, A.

    1991-01-01

    In this presentation the author only discusses problems of modeling for circular accelerators and bases the examples on the AGS Booster Synchrotron presently being commissioned at BNL. A model is a platonic representation of an accelerator. With algorithms, implemented through computer codes, the model is brought to life. At the start of a new accelerator project, the model and the real machine are taking shape somewhat apart. They get closer and closer as the project goes on. Ideally, the modeler is only satisfied when the model or the machine cannot be distinguished. Accelerator modeling for real time control has specific problems. If one wants fast responses, algorithms may be implemented in hardware or by parallel computation, perhaps by neural networks. Algorithms and modeling is not only for accelerator control. It is also for: accelerator parameter measurement; hardware problem debugging, perhaps with some help of artificial intelligence; operator training, much like a flight simulator

  19. generalized constitutive model for stabilized quick clay

    African Journals Online (AJOL)

    QUICK CLAY. PANCRAS MUGISHAGWE BUJULU AND GUSTAV GRIMSTAD. ABSTRACT. An experimentally-based two yield surface constitutive model for cemented quick clay has been ... Clay Model, the Koiter Rule and two Mapping Rules. .... models, where a mobilization formulation is used, this is independent of q.

  20. Towards a General Model of Temporal Discounting

    Science.gov (United States)

    van den Bos, Wouter; McClure, Samuel M.

    2013-01-01

    Psychological models of temporal discounting have now successfully displaced classical economic theory due to the simple fact that many common behavior patterns, such as impulsivity, were unexplainable with classic models. However, the now dominant hyperbolic model of discounting is itself becoming increasingly strained. Numerous factors have…

  1. Development of a generalized integral jet model

    DEFF Research Database (Denmark)

    Duijm, Nijs Jan; Kessler, A.; Markert, Frank

    2017-01-01

    model is needed to describe the rapid combustion of the flammable part of the plume (flash fire) and a third model has to be applied for the remaining jet fire. The objective of this paper is to describe the first steps of the development of an integral-type model describing the transient development...

  2. A guide to developing resource selection functions from telemetry data using generalized estimating equations and generalized linear mixed models

    Directory of Open Access Journals (Sweden)

    Nicola Koper

    2012-03-01

    Full Text Available Resource selection functions (RSF are often developed using satellite (ARGOS or Global Positioning System (GPS telemetry datasets, which provide a large amount of highly correlated data. We discuss and compare the use of generalized linear mixed-effects models (GLMM and generalized estimating equations (GEE for using this type of data to develop RSFs. GLMMs directly model differences among caribou, while GEEs depend on an adjustment of the standard error to compensate for correlation of data points within individuals. Empirical standard errors, rather than model-based standard errors, must be used with either GLMMs or GEEs when developing RSFs. There are several important differences between these approaches; in particular, GLMMs are best for producing parameter estimates that predict how management might influence individuals, while GEEs are best for predicting how management might influence populations. As the interpretation, value, and statistical significance of both types of parameter estimates differ, it is important that users select the appropriate analytical method. We also outline the use of k-fold cross validation to assess fit of these models. Both GLMMs and GEEs hold promise for developing RSFs as long as they are used appropriately.

  3. Fold-structure analysis of paleozoic rocks in the Variscan Harz Mountains (Lautenthal, Central Germany) based on laserscanning and 3D modelling

    Science.gov (United States)

    Wagner, Bianca; Leiss, Bernd; Stöpler, Ralf; Zahnow, Fabian

    2017-04-01

    Folded paleozoic sedimentary rocks of Upper Devonian to Lower Carboniferous age are very well exposed in the abandoned chert quarry of Lautenthal in the western Harz Mountains. The outcrop represents typical structures of the Rhenohercynian thrust and fold belt of the Variscan orogen and therefore allows quantitative studies for the understanding of e.g. fold mechanisms and the amount of shortening. The sequence is composed of alternating beds of cherts, shales and tuffites, which show varying thicknesses, undulating and thinning out of certain layers. Irregularly occurring lenses of greywackes are interpreted as sedimentary intrusions. The compressive deformation style is expressed by different similar and parallel fold structures at varying scales as well as small-scale reverse faults and triangle structures. An accurate mapping of the outcrop in the classical way is very challenging due to distant and unconnected outcrop parts with differing elevations and orientations. Furthermore, the visibility is limited because of nearby trees, diffuse vegetation cover and no available total view. Therefore, we used a FARO 120 3D laserscanner and Trimble GNSS device to generate a referenced and drawn to scale point cloud of the complete quarry. Based on the point cloud a geometric 3D model of prominent horizons and structural features of various sizes was constructed. Thereafter, we analyzed the structures in matters of orientation and deformation mechanisms. Finally, we applied a retrodeformation algorithm on the model to restore the original sedimentary sequence and to calculate shortening including the amount of pressure solution. Only digital mapping allows such a time-saving, accurate and especially complete 3D survey of this excellent study object. We demonstrated that such 3D-models enable spatial correlations with other complex structures cropping out in the area. Moreover, we confirmed that a structural upscaling to the 100 to 1000 m scale is much easier and much

  4. generalized constitutive model for stabilized quick clay

    African Journals Online (AJOL)

    An experimentally-based two yield surface constitutive model for cemented quick clay has been developed at NTNU, Norway, to reproduce the mechanical behavior of the stabilized quick clay in the triaxial p'-q stress space. The model takes into account the actual mechanical properties of the stabilized material, such as ...

  5. Stratospheric General Circulation with Chemistry Model (SGCCM)

    Science.gov (United States)

    Rood, Richard B.; Douglass, Anne R.; Geller, Marvin A.; Kaye, Jack A.; Nielsen, J. Eric; Rosenfield, Joan E.; Stolarski, Richard S.

    1990-01-01

    In the past two years constituent transport and chemistry experiments have been performed using both simple single constituent models and more complex reservoir species models. Winds for these experiments have been taken from the data assimilation effort, Stratospheric Data Analysis System (STRATAN).

  6. Equilibrium in Generalized Cournot and Stackelberg Models

    NARCIS (Netherlands)

    Bulavsky, V.A.; Kalashnikov, V.V.

    1999-01-01

    A model of an oligopolistic market with a homogeneous product is examined. Each subject of the model uses a conjecture about the market response to variations of its production volume. The conjecture value depends upon both the current total volume of production at the market and the subject's

  7. Generalized coupling in the Kuramoto model

    DEFF Research Database (Denmark)

    Filatrella, G.; Pedersen, Niels Falsig; Wiesenfeld, K.

    2007-01-01

    We propose a modification of the Kuramoto model to account for the effective change in the coupling constant among the oscillators, as suggested by some experiments on Josephson junction, laser arrays, and mechanical systems, where the active elements are turned on one by one. The resulting model...... with the behavior of Josephson junctions coupled via a cavity....

  8. Multiloop functional renormalization group for general models

    Science.gov (United States)

    Kugler, Fabian B.; von Delft, Jan

    2018-02-01

    We present multiloop flow equations in the functional renormalization group (fRG) framework for the four-point vertex and self-energy, formulated for a general fermionic many-body problem. This generalizes the previously introduced vertex flow [F. B. Kugler and J. von Delft, Phys. Rev. Lett. 120, 057403 (2018), 10.1103/PhysRevLett.120.057403] and provides the necessary corrections to the self-energy flow in order to complete the derivative of all diagrams involved in the truncated fRG flow. Due to its iterative one-loop structure, the multiloop flow is well suited for numerical algorithms, enabling improvement of many fRG computations. We demonstrate its equivalence to a solution of the (first-order) parquet equations in conjunction with the Schwinger-Dyson equation for the self-energy.

  9. Generalized Path Analysis and Generalized Simultaneous Equations Model for Recursive Systems with Responses of Mixed Types

    Science.gov (United States)

    Tsai, Tien-Lung; Shau, Wen-Yi; Hu, Fu-Chang

    2006-01-01

    This article generalizes linear path analysis (PA) and simultaneous equations models (SiEM) to deal with mixed responses of different types in a recursive or triangular system. An efficient instrumental variable (IV) method for estimating the structural coefficients of a 2-equation partially recursive generalized path analysis (GPA) model and…

  10. Description of the General Equilibrium Model of Ecosystem Services (GEMES)

    Science.gov (United States)

    Travis Warziniack; David Finnoff; Jenny Apriesnig

    2017-01-01

    This paper serves as documentation for the General Equilibrium Model of Ecosystem Services (GEMES). GEMES is a regional computable general equilibrium model that is composed of values derived from natural capital and ecosystem services. It models households, producing sectors, and governments, linked to one another through commodity and factor markets. GEMES was...

  11. The Five-Factor Model: General Overview

    Directory of Open Access Journals (Sweden)

    A A Vorobyeva

    2011-12-01

    Full Text Available The article describes the five-factor model (FFM, giving an overview of its history, basic dimensions, cross-cultural research conducted on the model and highlights some practical studies based on the FFM, including the studies on job performance, leader performance and daily social interactions. An overview of the recent five-factor theory is also provided. According to the theory, the five factors are encoded in human genes, therefore it is almost impossible to change the basic factors themselves, but a person's behavior might be changed due to characteristic adaptations which do not alter personality dimensions, only a person's behavior.

  12. Esperanto: A Unique Model for General Linguistics.

    Science.gov (United States)

    Dulichenko, Aleksandr D.

    1988-01-01

    Esperanto presents a unique model for linguistic research by allowing the study of language development from project to fully functioning language. Esperanto provides insight into the growth of polysemy and redundancy, as well as into language universals and the phenomenon of social control. (Author/CB)

  13. A standardized fold change method for microarray differential expression analysis used to reveal genes involved in acute rejection in murine allograft models.

    Science.gov (United States)

    Zhou, Weichen; Wang, Yi; Fujino, Masayuki; Shi, Leming; Jin, Li; Li, Xiao-Kang; Wang, Jiucun

    2018-03-01

    Murine transplantation models are used extensively to research immunological rejection and tolerance. Here we studied both murine heart and liver allograft models using microarray technology. We had difficulty in identifying genes related to acute rejections expressed in both heart and liver transplantation models using two standard methodologies: Student's t test and linear models for microarray data (Limma). Here we describe a new method, standardized fold change (SFC), for differential analysis of microarray data. We estimated the performance of SFC, the t test and Limma by generating simulated microarray data 100 times. SFC performed better than the t test and showed a higher sensitivity than Limma where there is a larger value for fold change of expression. SFC gave better reproducibility than Limma and the t test with real experimental data from the MicroArray Quality Control platform and expression data from a mouse cardiac allograft. Eventually, a group of significant overlapping genes was detected by SFC in the expression data of mouse cardiac and hepatic allografts and further validated with the quantitative RT-PCR assay. The group included genes for important reactions of transplantation rejection and revealed functional changes of the immune system in both heart and liver of the mouse model. We suggest that SFC can be utilized to stably and effectively detect differential gene expression and to explore microarray data in further studies.

  14. Practical likelihood analysis for spatial generalized linear mixed models

    DEFF Research Database (Denmark)

    Bonat, W. H.; Ribeiro, Paulo Justiniano

    2016-01-01

    , respectively, examples of binomial and count datasets modeled by spatial generalized linear mixed models. Our results show that the Laplace approximation provides similar estimates to Markov Chain Monte Carlo likelihood, Monte Carlo expectation maximization, and modified Laplace approximation. Some advantages...

  15. Development of independent generalized probabilistic models for regulatory activities

    International Nuclear Information System (INIS)

    Gashev, M.Kh.; Zinchenko, Yu.A.; Stefanishin, N.A.

    2012-01-01

    The paper discusses the development of probabilistic models to be used in regulatory activities. Results from the development of independent generalized PSA-1 models for purposes of SNRIU risk-informed regulation are presented

  16. Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction

    Science.gov (United States)

    Das, Payel; Moll, Mark; Stamati, Hernán; Kavraki, Lydia E.; Clementi, Cecilia

    2006-01-01

    The definition of reaction coordinates for the characterization of a protein-folding reaction has long been a controversial issue, even for the “simple” case in which one single free-energy barrier separates the folded and unfolded ensemble. We propose a general approach to this problem to obtain a few collective coordinates by using nonlinear dimensionality reduction. We validate the usefulness of this method by characterizing the folding landscape associated with a coarse-grained protein model of src homology 3 as sampled by molecular dynamics simulations. The folding free-energy landscape projected on the few relevant coordinates emerging from the dimensionality reduction can correctly identify the transition-state ensemble of the reaction. The first embedding dimension efficiently captures the evolution of the folding process along the main folding route. These results clearly show that the proposed method can efficiently find a low-dimensional representation of a complex process such as protein folding. PMID:16785435

  17. Modeling electrokinetics in ionic liquids: General

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Chao [Physical and Computational Science Directorate, Pacific Northwest National Laboratory, Richland WA USA; Bao, Jie [Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland WA USA; Pan, Wenxiao [Department of Mechanical Engineering, University of Wisconsin-Madison, Madison WI USA; Sun, Xin [Physical and Computational Science Directorate, Pacific Northwest National Laboratory, Richland WA USA

    2017-04-07

    Using direct numerical simulations we provide a thorough study on the electrokinetics of ionic liquids. In particular, the modfied Poisson-Nernst-Planck (MPNP) equations are solved to capture the crowding and overscreening effects that are the characteristics of an ionic liquid. For modeling electrokinetic flows in an ionic liquid, the MPNP equations are coupled with the Navier-Stokes equations to study the coupling of ion transport, hydrodynamics, and electrostatic forces. Specifically, we consider the ion transport between two parallel plates, charging dynamics in a 2D straight-walled pore, electro-osmotic ow in a nano-channel, electroconvective instability on a plane ion-selective surface, and electroconvective ow on a curved ion-selective surface. We discuss how the crowding and overscreening effects and their interplay affect the electrokinetic behaviors of ionic liquids in these application problems.

  18. Systematic comparison of barriers for heavy-ion fusion calculated on the basis of the double-folding model by employing two versions of nucleon–nucleon interaction

    Energy Technology Data Exchange (ETDEWEB)

    Gontchar, I. I. [Omsk State Transport University (Russian Federation); Chushnyakova, M. V., E-mail: maria.chushnyakova@gmail.com [Omsk State Technical University (Russian Federation)

    2016-07-15

    A systematic calculation of barriers for heavy-ion fusion was performed on the basis of the double-folding model by employing two versions of an effective nucleon–nucleon interaction: M3Y interaction and Migdal interaction. The results of calculations by the Hartree–Fockmethod with the SKX coefficients were taken for nuclear densities. The calculations reveal that the fusion barrier is higher in the case of employing theMigdal interaction than in the case of employing the Ðœ3Y interaction. In view of this, the use of the Migdal interaction in describing heavy-ion fusion is questionable.

  19. Folding model analysis of 32S+32S elastic scattering at 70, 90, 97.09, 120 and 160 MeV

    International Nuclear Information System (INIS)

    Bilwes, B.; Bilwes, R.; Stuttge, L.; Ballester, F.; Diaz, J.; Ferrero, J.L.; Roldan, C.; Sanchez, F.

    1987-01-01

    Angular distributions for the 32 S( 32 S, 32 S) elastic scattering have been measured at 70, 90, 97.09, 120 and 160 MeV incident lab-energies. The data have been analyzed with the folding model, using the M3Y and DDD interactions. A good reproduction of the data is obtained if a renormalization coefficient for the real part of the optical potential is introduced. Moreover the application of the dispersion relation proposed by Mahaux et al. and which uses the imaganary part does not seem to give renormalization coefficients as important as those found in the analysis of the data. (orig.)

  20. Anisotropic cosmological models and generalized scalar tensor theory

    Indian Academy of Sciences (India)

    physics pp. 669–673. Anisotropic cosmological models and generalized scalar tensor theory. SUBENOY CHAKRABORTY1,*, BATUL CHANDRA SANTRA2 and ... Anisotropic cosmological models; general scalar tensor theory; inflation. PACS Nos 98.80.Hw; 04.50.+h; 98.80.Cq. 1. Introduction. Brans–Dicke theory [1] (BD ...

  1. Model-free adaptive sliding mode controller design for generalized ...

    Indian Academy of Sciences (India)

    L M WANG

    2017-08-16

    Aug 16, 2017 ... A novel model-free adaptive sliding mode strategy is proposed for a generalized projective synchronization (GPS) ... the neural network theory, a model-free adaptive sliding mode controller is designed to guarantee asymptotic stability of the generalized ..... following optimization parameters are needed: ⎧.

  2. Managing heteroscedasticity in general linear models.

    Science.gov (United States)

    Rosopa, Patrick J; Schaffer, Meline M; Schroeder, Amber N

    2013-09-01

    Heteroscedasticity refers to a phenomenon where data violate a statistical assumption. This assumption is known as homoscedasticity. When the homoscedasticity assumption is violated, this can lead to increased Type I error rates or decreased statistical power. Because this can adversely affect substantive conclusions, the failure to detect and manage heteroscedasticity could have serious implications for theory, research, and practice. In addition, heteroscedasticity is not uncommon in the behavioral and social sciences. Thus, in the current article, we synthesize extant literature in applied psychology, econometrics, quantitative psychology, and statistics, and we offer recommendations for researchers and practitioners regarding available procedures for detecting heteroscedasticity and mitigating its effects. In addition to discussing the strengths and weaknesses of various procedures and comparing them in terms of existing simulation results, we describe a 3-step data-analytic process for detecting and managing heteroscedasticity: (a) fitting a model based on theory and saving residuals, (b) the analysis of residuals, and (c) statistical inferences (e.g., hypothesis tests and confidence intervals) involving parameter estimates. We also demonstrate this data-analytic process using an illustrative example. Overall, detecting violations of the homoscedasticity assumption and mitigating its biasing effects can strengthen the validity of inferences from behavioral and social science data.

  3. How the genome folds

    Science.gov (United States)

    Lieberman Aiden, Erez

    2012-02-01

    I describe Hi-C, a novel technology for probing the three-dimensional architecture of whole genomes by coupling proximity-based ligation with massively parallel sequencing. Working with collaborators at the Broad Institute and UMass Medical School, we used Hi-C to construct spatial proximity maps of the human genome at a resolution of 1Mb. These maps confirm the presence of chromosome territories and the spatial proximity of small, gene-rich chromosomes. We identified an additional level of genome organization that is characterized by the spatial segregation of open and closed chromatin to form two genome-wide compartments. At the megabase scale, the chromatin conformation is consistent with a fractal globule, a knot-free conformation that enables maximally dense packing while preserving the ability to easily fold and unfold any genomic locus. The fractal globule is distinct from the more commonly used globular equilibrium model. Our results demonstrate the power of Hi-C to map the dynamic conformations of whole genomes.

  4. A generalized model via random walks for information filtering

    Energy Technology Data Exchange (ETDEWEB)

    Ren, Zhuo-Ming, E-mail: zhuomingren@gmail.com [Department of Physics, University of Fribourg, Chemin du Musée 3, CH-1700, Fribourg (Switzerland); Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, ChongQing, 400714 (China); Kong, Yixiu [Department of Physics, University of Fribourg, Chemin du Musée 3, CH-1700, Fribourg (Switzerland); Shang, Ming-Sheng, E-mail: msshang@cigit.ac.cn [Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, ChongQing, 400714 (China); Zhang, Yi-Cheng [Department of Physics, University of Fribourg, Chemin du Musée 3, CH-1700, Fribourg (Switzerland)

    2016-08-06

    There could exist a simple general mechanism lurking beneath collaborative filtering and interdisciplinary physics approaches which have been successfully applied to online E-commerce platforms. Motivated by this idea, we propose a generalized model employing the dynamics of the random walk in the bipartite networks. Taking into account the degree information, the proposed generalized model could deduce the collaborative filtering, interdisciplinary physics approaches and even the enormous expansion of them. Furthermore, we analyze the generalized model with single and hybrid of degree information on the process of random walk in bipartite networks, and propose a possible strategy by using the hybrid degree information for different popular objects to toward promising precision of the recommendation. - Highlights: • We propose a generalized recommendation model employing the random walk dynamics. • The proposed model with single and hybrid of degree information is analyzed. • A strategy with the hybrid degree information improves precision of recommendation.

  5. A generalized model via random walks for information filtering

    International Nuclear Information System (INIS)

    Ren, Zhuo-Ming; Kong, Yixiu; Shang, Ming-Sheng; Zhang, Yi-Cheng

    2016-01-01

    There could exist a simple general mechanism lurking beneath collaborative filtering and interdisciplinary physics approaches which have been successfully applied to online E-commerce platforms. Motivated by this idea, we propose a generalized model employing the dynamics of the random walk in the bipartite networks. Taking into account the degree information, the proposed generalized model could deduce the collaborative filtering, interdisciplinary physics approaches and even the enormous expansion of them. Furthermore, we analyze the generalized model with single and hybrid of degree information on the process of random walk in bipartite networks, and propose a possible strategy by using the hybrid degree information for different popular objects to toward promising precision of the recommendation. - Highlights: • We propose a generalized recommendation model employing the random walk dynamics. • The proposed model with single and hybrid of degree information is analyzed. • A strategy with the hybrid degree information improves precision of recommendation.

  6. Vocal Fold Paralysis

    Science.gov (United States)

    ... decades-long project to develop an electrical stimulation technology to help people avoid having a tracheotomy when both vocal folds are paralyzed. The device, which currently is being tested in animals and people, uses an implanted pacemaker to stimulate ...

  7. General Friction Model Extended by the Effect of Strain Hardening

    DEFF Research Database (Denmark)

    Nielsen, Chris V.; Martins, Paulo A.F.; Bay, Niels

    2016-01-01

    An extension to the general friction model proposed by Wanheim and Bay [1] to include the effect of strain hardening is proposed. The friction model relates the friction stress to the fraction of real contact area by a friction factor under steady state sliding. The original model for the real...... contact area as function of the normalized contact pressure is based on slip-line analysis and hence on the assumption of rigid-ideally plastic material behavior. In the present work, a general finite element model is established to, firstly, reproduce the original model under the assumption of rigid......-ideally plastic material, and secondly, to extend the solution by the influence of material strain hardening. This corresponds to adding a new variable and, therefore, a new axis to the general friction model. The resulting model is presented in a combined function suitable for e.g. finite element modeling...

  8. Swelling pressure induced phase-volume transition in hybrid biopolymer gels caused by unfolding of folded crosslinks: A model

    Czech Academy of Sciences Publication Activity Database

    Dušek, Karel; Dušková, Miroslava; Ilavský, Michal; Steward, R.; Kopeček, J.

    2003-01-01

    Roč. 4, č. 6 (2003), s. 1818-1826 ISSN 1525-7797 R&D Projects: GA AV ČR KSK4050111 Keywords : thermodynamic model * swelling transitions * hybrid gels Subject RIV: CD - Macromolecular Chemistry Impact factor: 2.824, year: 2003

  9. RNA 3D Structure Modeling by Combination of Template-Based Method ModeRNA, Template-Free Folding with SimRNA, and Refinement with QRNAS.

    Science.gov (United States)

    Piatkowski, Pawel; Kasprzak, Joanna M; Kumar, Deepak; Magnus, Marcin; Chojnowski, Grzegorz; Bujnicki, Janusz M

    2016-01-01

    RNA encompasses an essential part of all known forms of life. The functions of many RNA molecules are dependent on their 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. To address this problem, computational structure prediction methods were developed that either utilize information derived from known structures of other RNA molecules (by way of template-based modeling) or attempt to simulate the physical process of RNA structure formation (by way of template-free modeling). All computational methods suffer from various limitations that make theoretical models less reliable than high-resolution experimentally determined structures. This chapter provides a protocol for computational modeling of RNA 3D structure that overcomes major limitations by combining two complementary approaches: template-based modeling that is capable of predicting global architectures based on similarity to other molecules but often fails to predict local unique features, and template-free modeling that can predict the local folding, but is limited to modeling the structure of relatively small molecules. Here, we combine the use of a template-based method ModeRNA with a template-free method SimRNA. ModeRNA requires a sequence alignment of the target RNA sequence to be modeled with a template of the known structure; it generates a model that predicts the structure of a conserved core and provides a starting point for modeling of variable regions. SimRNA can be used to fold small RNAs (models for larger RNAs that have a correctly modeled core. ModeRNA can be either downloaded, compiled and run locally or run through a web interface at http://genesilico.pl/modernaserver/ . SimRNA is currently available to download for local use as a precompiled software package at http://genesilico.pl/software/stand-alone/simrna and as a

  10. Reliability assessment of competing risks with generalized mixed shock models

    International Nuclear Information System (INIS)

    Rafiee, Koosha; Feng, Qianmei; Coit, David W.

    2017-01-01

    This paper investigates reliability modeling for systems subject to dependent competing risks considering the impact from a new generalized mixed shock model. Two dependent competing risks are soft failure due to a degradation process, and hard failure due to random shocks. The shock process contains fatal shocks that can cause hard failure instantaneously, and nonfatal shocks that impact the system in three different ways: 1) damaging the unit by immediately increasing the degradation level, 2) speeding up the deterioration by accelerating the degradation rate, and 3) weakening the unit strength by reducing the hard failure threshold. While the first impact from nonfatal shocks comes from each individual shock, the other two impacts are realized when the condition for a new generalized mixed shock model is satisfied. Unlike most existing mixed shock models that consider a combination of two shock patterns, our new generalized mixed shock model includes three classic shock patterns. According to the proposed generalized mixed shock model, the degradation rate and the hard failure threshold can simultaneously shift multiple times, whenever the condition for one of these three shock patterns is satisfied. An example using micro-electro-mechanical systems devices illustrates the effectiveness of the proposed approach with sensitivity analysis. - Highlights: • A rich reliability model for systems subject to dependent failures is proposed. • The degradation rate and the hard failure threshold can shift simultaneously. • The shift is triggered by a new generalized mixed shock model. • The shift can occur multiple times under the generalized mixed shock model.

  11. Fold and Fit: Space Conserving Shape Editing

    KAUST Repository

    Ibrahim, Mohamed

    2017-09-01

    We present a framework that folds man-made objects in a structure-aware manner for space-conserving storage and transportation. Given a segmented 3D mesh of a man-made object, our framework jointly optimizes for joint locations, the folding order, and folding angles for each part of the model, enabling it to transform into a spatially efficient configuration while keeping its original functionality as intact as possible. That is, if a model is supposed to withstand several forces in its initial state to serve its functionality, our framework places the joints between the parts of the model such that the model can withstand forces with magnitudes that are comparable to the magnitudes applied on the unedited model. Furthermore, if the folded shape is not compact, our framework proposes further segmentation of the model to improve its compactness in its folded state.

  12. Model Reduction of Switched Systems Based on Switching Generalized Gramians

    DEFF Research Database (Denmark)

    Shaker, Hamid Reza; Wisniewski, Rafal

    2012-01-01

    In this paper, a general method for model order reduction of discrete-time switched linear systems is presented. The proposed technique uses switching generalized gramians. It is shown that several classical reduction methods can be developed into the generalized gramian framework for the model...... reduction of linear systems and for the reduction of switched systems. Discrete-time balanced reduction within a specified frequency interval is taken as an example within this framework. To avoid numerical instability and to increase the numerical efficiency, a generalized gramian-based Petrov...

  13. A General Polygon-based Deformable Model for Object Recognition

    DEFF Research Database (Denmark)

    Jensen, Rune Fisker; Carstensen, Jens Michael

    1999-01-01

    We propose a general scheme for object localization and recognition based on a deformable model. The model combines shape and image properties by warping a arbitrary prototype intensity template according to the deformation in shape. The shape deformations are constrained by a probabilistic...... distribution, which combined with a match of the warped intensity template and the image form the final criteria used for localization and recognition of a given object. The chosen representation gives the model an ability to model an almost arbitrary object. Beside the actual model a full general scheme...

  14. Generalized Linear Models with Applications in Engineering and the Sciences

    CERN Document Server

    Myers, Raymond H; Vining, G Geoffrey; Robinson, Timothy J

    2012-01-01

    Praise for the First Edition "The obvious enthusiasm of Myers, Montgomery, and Vining and their reliance on their many examples as a major focus of their pedagogy make Generalized Linear Models a joy to read. Every statistician working in any area of applied science should buy it and experience the excitement of these new approaches to familiar activities."-Technometrics Generalized Linear Models: With Applications in Engineering and the Sciences, Second Edition continues to provide a clear introduction to the theoretical foundations and key applications of generalized linear models (GLMs). Ma

  15. Folded supersymmetry with a twist

    Energy Technology Data Exchange (ETDEWEB)

    Cohen, Timothy [Department of Physics, Princeton University,Princeton, NJ 08544 (United States); School of Natural Sciences, Institute for Advanced Study,Princeton, NJ 08540 (United States); Institute of Theoretical Science, University of Oregon,Eugene, OR 97403 (United States); Craig, Nathaniel [Department of Physics, University of California,Santa Barbara, CA 93106 (United States); Lou, Hou Keong [Department of Physics, Princeton University,Princeton, NJ 08544 (United States); Pinner, David [Princeton Center for Theoretical Science, Princeton University,Princeton, NJ 08544 (United States)

    2016-03-30

    Folded supersymmetry (f-SUSY) stabilizes the weak scale against radiative corrections from the top sector via scalar partners whose gauge quantum numbers differ from their Standard Model counterparts. This non-trivial pairing of states can be realized in extra-dimensional theories with appropriate supersymmetry-breaking boundary conditions. We present a class of calculable f-SUSY models that are parametrized by a non-trivial twist in 5D boundary conditions and can accommodate the observed Higgs mass and couplings. Although the distinctive phenomenology associated with the novel folded states should provide strong evidence for this mechanism, the most stringent constraints are currently placed by conventional supersymmetry searches. These models remain minimally fine-tuned in light of LHC8 data and provide a range of both standard and exotic signatures accessible at LHC13.

  16. A comparison of RNA folding measures

    DEFF Research Database (Denmark)

    Freyhult, E.; Gardner, P. P.; Moulton, V.

    2005-01-01

    Background In the last few decades there has been a great deal of discussion concerning whether or not noncoding RNA sequences (ncRNAs) fold in a more well-defined manner than random sequences. In this paper, we investigate several existing measures for how well an RNA sequence folds, and compare...... the behaviour of these measures over a large range of Rfam ncRNA families. Such measures can be useful in, for example, identifying novel ncRNAs, and indicating the presence of alternate RNA foldings. Results Our analysis shows that ncRNAs, but not mRNAs, in general have lower minimal free energy (MFE) than...... random sequences with the same dinucleotide frequency. Moreover, even when the MFE is significant, many ncRNAs appear to not have a unique fold, but rather several alternative folds, at least when folded in silico. Furthermore, we find that the six investigated measures are correlated to varying degrees...

  17. RNA secondary structures in a polymer-zeta model how foldings should be shaped for sparsification to establish a linear speedup

    DEFF Research Database (Denmark)

    Jin, Emma Yu; Nebel, M. E.

    2016-01-01

    algorithm. In this paper we discuss the application of the polymer-zeta property for the analysis of sparsification, showing that it must be applied conditionally on first and last positions to pair. Afterwards, we will investigate the combinatorics of RNA secondary structures assuming......Various tools used to predict the secondary structure for a given RNA sequence are based on dynamic programming used to compute a conformation of minimum free energy. For structures without pseudoknots, a worst-case runtime proportional to n3, with n being the length of the sequence, results since...... that the corresponding conditional probabilities behave according to a polymer-zeta probability model. We show that even if some of the structural parameters exhibit an almost realistic behavior on average, the expected shape of a folding in that model must be assumed to highly differ from those observed in nature. More...

  18. Linear and Generalized Linear Mixed Models and Their Applications

    CERN Document Server

    Jiang, Jiming

    2007-01-01

    This book covers two major classes of mixed effects models, linear mixed models and generalized linear mixed models, and it presents an up-to-date account of theory and methods in analysis of these models as well as their applications in various fields. The book offers a systematic approach to inference about non-Gaussian linear mixed models. Furthermore, it has included recently developed methods, such as mixed model diagnostics, mixed model selection, and jackknife method in the context of mixed models. The book is aimed at students, researchers and other practitioners who are interested

  19. Simulation modelling in agriculture: General considerations. | R.I. ...

    African Journals Online (AJOL)

    The computer does all the necessary arithmetic when the hypothesis is invoked to predict the future behaviour of the simulated system under given conditions.A general ... in the advisory service. Keywords: agriculture; botany; computer simulation; modelling; simulation model; simulation modelling; south africa; techniques ...

  20. A Duality Result for the Generalized Erlang Risk Model

    Directory of Open Access Journals (Sweden)

    Lanpeng Ji

    2014-11-01

    Full Text Available In this article, we consider the generalized Erlang risk model and its dual model. By using a conditional measure-preserving correspondence between the two models, we derive an identity for two interesting conditional probabilities. Applications to the discounted joint density of the surplus prior to ruin and the deficit at ruin are also discussed.

  1. Critical Comments on the General Model of Instructional Communication

    Science.gov (United States)

    Walton, Justin D.

    2014-01-01

    This essay presents a critical commentary on McCroskey et al.'s (2004) general model of instructional communication. In particular, five points are examined which make explicit and problematize the meta-theoretical assumptions of the model. Comments call attention to the limitations of the model and argue for a broader approach to…

  2. Hierarchical Generalized Linear Models for the Analysis of Judge Ratings

    Science.gov (United States)

    Muckle, Timothy J.; Karabatsos, George

    2009-01-01

    It is known that the Rasch model is a special two-level hierarchical generalized linear model (HGLM). This article demonstrates that the many-faceted Rasch model (MFRM) is also a special case of the two-level HGLM, with a random intercept representing examinee ability on a test, and fixed effects for the test items, judges, and possibly other…

  3. A PROPOSAL FOR GENERALIZATION OF 3D MODELS

    Directory of Open Access Journals (Sweden)

    A. Uyar

    2017-11-01

    Full Text Available In recent years, 3D models have been created of many cities around the world. Most of the 3D city models have been introduced as completely graphic or geometric models, and the semantic and topographic aspects of the models have been neglected. In order to use 3D city models beyond the task, a generalization is necessary. CityGML is an open data model and XML-based format for the storage and exchange of virtual 3D city models. Level of Details (LoD which is an important concept for 3D modelling, can be defined as outlined degree or prior representation of real-world objects. The paper aim is first describes some requirements of 3D model generalization, then presents problems and approaches that have been developed in recent years. In conclude the paper will be a summary and outlook on problems and future work.

  4. a Proposal for Generalization of 3d Models

    Science.gov (United States)

    Uyar, A.; Ulugtekin, N. N.

    2017-11-01

    In recent years, 3D models have been created of many cities around the world. Most of the 3D city models have been introduced as completely graphic or geometric models, and the semantic and topographic aspects of the models have been neglected. In order to use 3D city models beyond the task, a generalization is necessary. CityGML is an open data model and XML-based format for the storage and exchange of virtual 3D city models. Level of Details (LoD) which is an important concept for 3D modelling, can be defined as outlined degree or prior representation of real-world objects. The paper aim is first describes some requirements of 3D model generalization, then presents problems and approaches that have been developed in recent years. In conclude the paper will be a summary and outlook on problems and future work.

  5. The DINA model as a constrained general diagnostic model: Two variants of a model equivalency.

    Science.gov (United States)

    von Davier, Matthias

    2014-02-01

    The 'deterministic-input noisy-AND' (DINA) model is one of the more frequently applied diagnostic classification models for binary observed responses and binary latent variables. The purpose of this paper is to show that the model is equivalent to a special case of a more general compensatory family of diagnostic models. Two equivalencies are presented. Both project the original DINA skill space and design Q-matrix using mappings into a transformed skill space as well as a transformed Q-matrix space. Both variants of the equivalency produce a compensatory model that is mathematically equivalent to the (conjunctive) DINA model. This equivalency holds for all DINA models with any type of Q-matrix, not only for trivial (simple-structure) cases. The two versions of the equivalency presented in this paper are not implied by the recently suggested log-linear cognitive diagnosis model or the generalized DINA approach. The equivalencies presented here exist independent of these recently derived models since they solely require a linear - compensatory - general diagnostic model without any skill interaction terms. Whenever it can be shown that one model can be viewed as a special case of another more general one, conclusions derived from any particular model-based estimates are drawn into question. It is widely known that multidimensional models can often be specified in multiple ways while the model-based probabilities of observed variables stay the same. This paper goes beyond this type of equivalency by showing that a conjunctive diagnostic classification model can be expressed as a constrained special case of a general compensatory diagnostic modelling framework. © 2013 The British Psychological Society.

  6. Graphical tools for model selection in generalized linear models.

    Science.gov (United States)

    Murray, K; Heritier, S; Müller, S

    2013-11-10

    Model selection techniques have existed for many years; however, to date, simple, clear and effective methods of visualising the model building process are sparse. This article describes graphical methods that assist in the selection of models and comparison of many different selection criteria. Specifically, we describe for logistic regression, how to visualize measures of description loss and of model complexity to facilitate the model selection dilemma. We advocate the use of the bootstrap to assess the stability of selected models and to enhance our graphical tools. We demonstrate which variables are important using variable inclusion plots and show that these can be invaluable plots for the model building process. We show with two case studies how these proposed tools are useful to learn more about important variables in the data and how these tools can assist the understanding of the model building process. Copyright © 2013 John Wiley & Sons, Ltd.

  7. General classical solutions in the noncommutative CPN-1 model

    International Nuclear Information System (INIS)

    Foda, O.; Jack, I.; Jones, D.R.T.

    2002-01-01

    We give an explicit construction of general classical solutions for the noncommutative CP N-1 model in two dimensions, showing that they correspond to integer values for the action and topological charge. We also give explicit solutions for the Dirac equation in the background of these general solutions and show that the index theorem is satisfied

  8. Parameter Estimation for a Computable General Equilibrium Model

    DEFF Research Database (Denmark)

    Arndt, Channing; Robinson, Sherman; Tarp, Finn

    We introduce a maximum entropy approach to parameter estimation for computable general equilibrium (CGE) models. The approach applies information theory to estimating a system of nonlinear simultaneous equations. It has a number of advantages. First, it imposes all general equilibrium constraints...

  9. Parameter Estimation for a Computable General Equilibrium Model

    DEFF Research Database (Denmark)

    Arndt, Channing; Robinson, Sherman; Tarp, Finn

    2002-01-01

    We introduce a maximum entropy approach to parameter estimation for computable general equilibrium (CGE) models. The approach applies information theory to estimating a system of non-linear simultaneous equations. It has a number of advantages. First, it imposes all general equilibrium constraints...

  10. Evaluating realized seed dispersal across fragmented tropical landscapes: a two-fold approach using parentage analysis and the neighbourhood model.

    Science.gov (United States)

    Ismail, Sascha A; Ghazoul, Jaboury; Ravikanth, Gudasalamani; Kushalappa, Cheppudira G; Uma Shaanker, Ramanan; Kettle, Chris J

    2017-05-01

    Despite the importance of seed dispersal for survival of plant species in fragmented landscapes, data on seed dispersal at landscape scales remain sparse. Effective seed dispersal among fragments determines recolonization and plant species persistence in such landscapes. We present the first large-scale (216-km 2 ) direct estimates of realized seed dispersal of a high-value timber tree (Dysoxylum malabaricum) across an agro-forest landscape in the Western Ghats, India. Based upon an exhaustive inventory of adult trees and a sample of 488 seedlings all genotyped at 10 microsatellite loci, we estimated realized seed dispersal using parentage analysis and the neighbourhood model. Our estimates found that most realized seed dispersal was within 200 m, which is insufficient to effectively bridge the distances between forest patches. We conclude that using mobility of putative animal dispersers can be misleading when estimating tropical tree species vulnerability to habitat fragmentation. This raises serious concerns about the potential of many tropical trees to recolonize isolated forest patches where high-value tree species have already been removed. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

  11. Onset of airflow limitation in a collapsible tube model: impact of surrounding pressure, longitudinal strain, and wall folding geometry.

    Science.gov (United States)

    Amatoury, Jason; Kairaitis, Kristina; Wheatley, John R; Bilston, Lynne E; Amis, Terence C

    2010-11-01

    We studied the impact of wall strain and surrounding pressure on the onset of airflow limitation in a thin-walled "floppy" tube model. A vacuum source-generated steady-state (baseline) airflow (0-350 ml/s) through a thin-walled latex tube (length 80 mm, wall thickness 0.23 mm) enclosed within a rigid, sealed, air-filled, cylindrical chamber while upstream minus downstream pressure, chamber pressure (Pc), and lumen geometry [in-line digital camera; segmentation (Amira 5.2.2) and analysis (Rhinoceros 4) software] were monitored. Longitudinal strain (S; 0-62.5%) and Pc (0-20 cmH(2)O) combinations were imposed, and Pc associated with onset of 1) reduced airflow and 2) fully developed airflow limitation recorded. At any strain, increasing Pc resulted in a decrease in airflow. Across all baseline airflow, threshold pressure was 1-7 cmH(2)O for S cmH(2)O at S = 25% and 37.5%, and 5-7 cmH(2)O at S = 50% and 62.5%. Pc associated with fully developed airflow limitation was 4-6 cmH(2)O for S 20 cmH(2)O at S = 25% (i.e., no flow limitation), 18 cmH(2)O at S = 37.5%, and 8-12 cmH(2)O at S = 50% and 62.5%. Lumen area decreased with increasing Pc but was 1) larger at S = 25% and 2) characterized by bifold narrowing at S < 25% and trifold narrowing at S ≥ 25%. In conclusion, tube function was modulated by Pc vs. S interactions, with S = 25% producing trifold lumen narrowing, maximal patency, and no airflow limitation. Findings may have implications for understanding peripharyngeal tissue pressure and pharyngeal wall strain effects on passive pharyngeal airway function in humans.

  12. General Computational Model for Human Musculoskeletal System of Spine

    Directory of Open Access Journals (Sweden)

    Kyungsoo Kim

    2012-01-01

    Full Text Available A general computational model of the human lumbar spine and trunk muscles including optimization formulations was provided. For a given condition, the trunk muscle forces could be predicted considering the human physiology including the follower load concept. The feasibility of the solution could be indirectly validated by comparing the compressive force, the shear force, and the joint moment. The presented general computational model and optimization technology can be fundamental tools to understand the control principle of human trunk muscles.

  13. Specific and General Human Capital in an Endogenous Growth Model

    OpenAIRE

    Evangelia Vourvachaki; Vahagn Jerbashian; : Sergey Slobodyan

    2014-01-01

    In this article, we define specific (general) human capital in terms of the occupations whose use is spread in a limited (wide) set of industries. We analyze the growth impact of an economy's composition of specific and general human capital, in a model where education and research and development are costly and complementary activities. The model suggests that a declining share of specific human capital, as observed in the Czech Republic, can be associated with a lower rate of long-term grow...

  14. Pricing Participating Products under a Generalized Jump-Diffusion Model

    Directory of Open Access Journals (Sweden)

    Tak Kuen Siu

    2008-01-01

    Full Text Available We propose a model for valuing participating life insurance products under a generalized jump-diffusion model with a Markov-switching compensator. It also nests a number of important and popular models in finance, including the classes of jump-diffusion models and Markovian regime-switching models. The Esscher transform is employed to determine an equivalent martingale measure. Simulation experiments are conducted to illustrate the practical implementation of the model and to highlight some features that can be obtained from our model.

  15. 2-D seismic modeling of the Variscan foreland thrust and fold belt crust in NW Spain from ESCIN-1 deep seismic reflection data

    Science.gov (United States)

    Gallastegui, J.; Pulgar, J. A.; Alvarez-Marrón, J.

    1997-01-01

    The foreland thrust and fold belt (Cantabrian Zone) of the Variscan Belt in NW Spain and the transition to the hinterland (Westasturian-Leonese Zone) was the location of a seismic experiment in 1991. The seismic reflection profile (ESCIN-1) is 140 km long and runs in an E-W direction. The interpretation and seismic modeling of the main reflective interfaces in the profile were made integrating available geological and geophysical data including surface geology, deep seismic reflection data from ESCIN-1, transmission velocities from a borehole, refraction and laboratory data. The geological and velocity model of the crust was tested obtaining synthetic seismograms and can be correlated with surface geology. The velocity model images the main crustal structures interpreted from ESCIN-1. The basal detachment of the foreland thrust and fold belt dips gently from 12 km in the easternmost part of the profile to 16 km in the transition to the hinterland to the west. A new interpretation is proposed for the structure above the basal detachment in the eastern end of the profile, where the basal detachment, at a depth of 12 km, is duplicated at 6.5 km by a N-dipping Alpine thrust that also duplicates part of the basement. In the western part, two deep reflective bands dip westward and the most conspicuous one can be followed from 16-27 km depth. The two bands, previously interpreted as crustal ramps, join a reflective lower crust that is located between 25 and 29 km and fades westwards. A reflective Moho interpreted at the base of the reflective lower crust dips and fades in the same direction from 30-34 km.

  16. Generalized continua as models for classical and advanced materials

    CERN Document Server

    Forest, Samuel

    2016-01-01

    This volume is devoted to an actual topic which is the focus world-wide of various research groups. It contains contributions describing the material behavior on different scales, new existence and uniqueness theorems, the formulation of constitutive equations for advanced materials. The main emphasis of the contributions is directed on the following items - Modelling and simulation of natural and artificial materials with significant microstructure, - Generalized continua as a result of multi-scale models, - Multi-field actions on materials resulting in generalized material models, - Theories including higher gradients, and - Comparison with discrete modelling approaches.

  17. Extending the generalized Chaplygin gas model by using geometrothermodynamics

    Science.gov (United States)

    Aviles, Alejandro; Bastarrachea-Almodovar, Aztlán; Campuzano, Lorena; Quevedo, Hernando

    2012-09-01

    We use the formalism of geometrothermodynamics to derive fundamental thermodynamic equations that are used to construct general relativistic cosmological models. In particular, we show that the simplest possible fundamental equation, which corresponds in geometrothermodynamics to a system with no internal thermodynamic interaction, describes the different fluids of the standard model of cosmology. In addition, a particular fundamental equation with internal thermodynamic interaction is shown to generate a new cosmological model that correctly describes the dark sector of the Universe and contains as a special case the generalized Chaplygin gas model.

  18. A Semi-Tychonic Model in General relativity

    Science.gov (United States)

    Murphy, George L.

    1998-10-01

    In the sixteenth century Tycho Brahe proposed a geocentric model of the solar system kinematically equivalent to the heliocentric Copernican model. There has been disagreement even among prominent relativists over whether or not relativity validates use of a geocentric model. Tycho's desire for a non-rotating earth cannot be satisfied, but we demonstrate here dynamical equivalence between a Copernican and a "semi-Tychonic" model by using an appropriate accelerated reference frame in general relativity. (The idea of absolute space in Newtonian mechanics makes use of Einstein's theory desirable even in the Newtonian approximation.) Optical questions are easily dealt with. Our treatment provides a satisfactory answer for the important historical question concerning geocentric and heliocentric models, and is also of pedagogic value. In addition, it gives insights into the real generality of general relativity, the nature of the relativistic equations of motion, and the analogy between coordinate and gauge transformations.

  19. Folds and Etudes

    Science.gov (United States)

    Bean, Robert

    2007-01-01

    In this article, the author talks about "Folds" and "Etudes" which are images derived from anonymous typing exercises that he found in a used copy of "Touch Typing Made Simple". "Etudes" refers to the musical tradition of studies for a solo instrument, which is a typewriter. Typing exercises are repetitive attempts to type words and phrases…

  20. Folding worlds between pages

    CERN Document Server

    Meier, Matthias

    2010-01-01

    "We all remember pop-up books form our childhood. As fascinated as we were back then, we probably never imagined how much engineering know-how went into these books. Pop-up engineer Anton Radevsky has even managed to fold a 27-kilometre particle accelerator into a book" (4 pages)

  1. Generalized entropy formalism and a new holographic dark energy model

    Science.gov (United States)

    Sayahian Jahromi, A.; Moosavi, S. A.; Moradpour, H.; Morais Graça, J. P.; Lobo, I. P.; Salako, I. G.; Jawad, A.

    2018-05-01

    Recently, the Rényi and Tsallis generalized entropies have extensively been used in order to study various cosmological and gravitational setups. Here, using a special type of generalized entropy, a generalization of both the Rényi and Tsallis entropy, together with holographic principle, we build a new model for holographic dark energy. Thereinafter, considering a flat FRW universe, filled by a pressureless component and the new obtained dark energy model, the evolution of cosmos has been investigated showing satisfactory results and behavior. In our model, the Hubble horizon plays the role of IR cutoff, and there is no mutual interaction between the cosmos components. Our results indicate that the generalized entropy formalism may open a new window to become more familiar with the nature of spacetime and its properties.

  2. A generalized model via random walks for information filtering

    Science.gov (United States)

    Ren, Zhuo-Ming; Kong, Yixiu; Shang, Ming-Sheng; Zhang, Yi-Cheng

    2016-08-01

    There could exist a simple general mechanism lurking beneath collaborative filtering and interdisciplinary physics approaches which have been successfully applied to online E-commerce platforms. Motivated by this idea, we propose a generalized model employing the dynamics of the random walk in the bipartite networks. Taking into account the degree information, the proposed generalized model could deduce the collaborative filtering, interdisciplinary physics approaches and even the enormous expansion of them. Furthermore, we analyze the generalized model with single and hybrid of degree information on the process of random walk in bipartite networks, and propose a possible strategy by using the hybrid degree information for different popular objects to toward promising precision of the recommendation.

  3. Folding model study of the charge-exchange scattering to the isobaric analog state and implication for the nuclear symmetry energy

    Energy Technology Data Exchange (ETDEWEB)

    Khoa, Dao T.; Thang, Dang Ngoc [VINATOM, Institute for Nuclear Science and Technique, Hanoi (Viet Nam); Loc, Bui Minh [VINATOM, Institute for Nuclear Science and Technique, Hanoi (Viet Nam); University of Pedagogy, Ho Chi Minh City (Viet Nam)

    2014-02-15

    The Fermi transition (ΔL = ΔS = 0 and ΔT = 1) between the nuclear isobaric analog states (IAS), induced by the charge-exchange (p, n) or ({sup 3}He, t) reaction, can be considered as ''elastic'' scattering of proton or {sup 3}He by the isovector term of the optical potential (OP) that flips the projectile isospin. The accurately measured (p, n) or ({sup 3}He, t) scattering cross section to the IAS can be used, therefore, to probe the isospin dependence of the proton or {sup 3}He optical potential. Within the folding model, the isovector part of the OP is determined exclusively by the neutron-proton difference in the nuclear densities and the isospin dependence of the effective nucleon-nucleon (NN) interaction. Because the isovector coupling explicitly links the isovector part of the proton or {sup 3}He optical potential to the cross section of the charge-exchange (p, n) or ({sup 3}He, t) scattering to the IAS, the isospin dependence of the effective (in-medium) NN interaction can be well tested in the folding model analysis of these charge-exchange reactions. On the other hand, the same isospin- and density-dependent NN interaction can also be used in a Hartree-Fock calculation of asymmetric nuclear matter, to estimate the nuclear matter energy and its asymmetry part (the nuclear symmetry energy). As a result, the fine-tuning of the isospin dependence of the effective NN interaction against the measured (p, n) or ({sup 3}He, t) cross sections should allow us to make some realistic prediction of the nuclear symmetry energy and its density dependence. (orig.)

  4. Folding model study of the charge-exchange scattering to the isobaric analog state and implication for the nuclear symmetry energy

    International Nuclear Information System (INIS)

    Khoa, Dao T.; Thang, Dang Ngoc; Loc, Bui Minh

    2014-01-01

    The Fermi transition (ΔL = ΔS = 0 and ΔT = 1) between the nuclear isobaric analog states (IAS), induced by the charge-exchange (p, n) or ( 3 He, t) reaction, can be considered as ''elastic'' scattering of proton or 3 He by the isovector term of the optical potential (OP) that flips the projectile isospin. The accurately measured (p, n) or ( 3 He, t) scattering cross section to the IAS can be used, therefore, to probe the isospin dependence of the proton or 3 He optical potential. Within the folding model, the isovector part of the OP is determined exclusively by the neutron-proton difference in the nuclear densities and the isospin dependence of the effective nucleon-nucleon (NN) interaction. Because the isovector coupling explicitly links the isovector part of the proton or 3 He optical potential to the cross section of the charge-exchange (p, n) or ( 3 He, t) scattering to the IAS, the isospin dependence of the effective (in-medium) NN interaction can be well tested in the folding model analysis of these charge-exchange reactions. On the other hand, the same isospin- and density-dependent NN interaction can also be used in a Hartree-Fock calculation of asymmetric nuclear matter, to estimate the nuclear matter energy and its asymmetry part (the nuclear symmetry energy). As a result, the fine-tuning of the isospin dependence of the effective NN interaction against the measured (p, n) or ( 3 He, t) cross sections should allow us to make some realistic prediction of the nuclear symmetry energy and its density dependence. (orig.)

  5. Spherical images and inextensible curved folding

    Science.gov (United States)

    Seffen, Keith A.

    2018-02-01

    In their study, Duncan and Duncan [Proc. R. Soc. London A 383, 191 (1982), 10.1098/rspa.1982.0126] calculate the shape of an inextensible surface folded in two about a general curve. They find the analytical relationships between pairs of generators linked across the fold curve, the shape of the original path, and the fold angle variation along it. They present two special cases of generator layouts for which the fold angle is uniform or the folded curve remains planar, for simplifying practical folding in sheet-metal processes. We verify their special cases by a graphical treatment according to a method of Gauss. We replace the fold curve by a piecewise linear path, which connects vertices of intersecting pairs of hinge lines. Inspired by the d-cone analysis by Farmer and Calladine [Int. J. Mech. Sci. 47, 509 (2005), 10.1016/j.ijmecsci.2005.02.013], we construct the spherical images for developable folding of successive vertices: the operating conditions of the special cases in Duncan and Duncan are then revealed straightforwardly by the geometric relationships between the images. Our approach may be used to synthesize folding patterns for novel deployable and shape-changing surfaces without need of complex calculation.

  6. On the general ontological foundations of conceptual modeling

    NARCIS (Netherlands)

    Guizzardi, G.; Herre, Heinrich; Wagner, Gerd; Spaccapietra, Stefano; March, Salvatore T.; Kambayashi, Yahiko

    2002-01-01

    As pointed out in the pioneering work of [WSW99,EW01], an upper level ontology allows to evaluate the ontological correctness of a conceptual model and to develop guidelines how the constructs of a conceptual modeling language should be used. In this paper we adopt the General Ontological Language

  7. General Separations Area (GSA) Groundwater Flow Model Update: Hydrostratigraphic Data

    Energy Technology Data Exchange (ETDEWEB)

    Bagwell, L. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL); Bennett, P. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL); Flach, G. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL)

    2017-02-21

    This document describes the assembly, selection, and interpretation of hydrostratigraphic data for input to an updated groundwater flow model for the General Separations Area (GSA; Figure 1) at the Department of Energy’s (DOE) Savannah River Site (SRS). This report is one of several discrete but interrelated tasks that support development of an updated groundwater model (Bagwell and Flach, 2016).

  8. A MIXTURE LIKELIHOOD APPROACH FOR GENERALIZED LINEAR-MODELS

    NARCIS (Netherlands)

    WEDEL, M; DESARBO, WS

    1995-01-01

    A mixture model approach is developed that simultaneously estimates the posterior membership probabilities of observations to a number of unobservable groups or latent classes, and the parameters of a generalized linear model which relates the observations, distributed according to some member of

  9. Response of an ocean general circulation model to wind and ...

    Indian Academy of Sciences (India)

    The stretched-coordinate ocean general circulation model has been designed to study the observed variability due to wind and thermodynamic forcings. The model domain extends from 60°N to 60°S and cyclically continuous in the longitudinal direction. The horizontal resolution is 5° × 5° and 9 discrete vertical levels.

  10. Bianchi type IX string cosmological model in general relativity

    Indian Academy of Sciences (India)

    Abstract. We have investigated Bianchi type IX string cosmological models in general relativity. To get a determinate solution, we have assumed a condition p = λ i.e. rest energy density for a cloud of strings is equal to the string tension density. The various physical and geometrical aspects of the models are also discussed.

  11. Stability analysis for a general age-dependent vaccination model

    International Nuclear Information System (INIS)

    El Doma, M.

    1995-05-01

    An SIR epidemic model of a general age-dependent vaccination model is investigated when the fertility, mortality and removal rates depends on age. We give threshold criteria of the existence of equilibriums and perform stability analysis. Furthermore a critical vaccination coverage that is sufficient to eradicate the disease is determined. (author). 12 refs

  12. Bianchi type IX string cosmological model in general relativity

    Indian Academy of Sciences (India)

    We have investigated Bianchi type IX string cosmological models in general relativity. To get a determinate solution, we have assumed a condition ρ= i.e. rest energy density for a cloud of strings is equal to the string tension density. The various physical and geometrical aspects of the models are also discussed.

  13. Thin‐ or thick‐skinned faulting in the Yakima fold and thrust belt (WA)? Constraints from kinematic modeling of the saddle mountains anticline

    Science.gov (United States)

    Casale, Gabriele; Pratt, Thomas L.

    2015-01-01

    The Yakima fold and thrust belt (YFTB) deforms the Columbia River Basalt Group flows of Washington State. The YFTB fault geometries and slip rates are crucial parameters for seismic‐hazard assessments of nearby dams and nuclear facilities, yet there are competing models for the subsurface fault geometry involving shallowly rooted versus deeply rooted fault systems. The YFTB is also thought to be analogous to the evenly spaced wrinkle ridges found on other terrestrial planets. Using seismic reflection data, borehole logs, and surface geologic data, we tested two proposed kinematic end‐member thick‐ and thin‐skinned fault models beneath the Saddle Mountains anticline of the YFTB. Observed subsurface geometry can be produced by 600–800 m of heave along a single listric‐reverse fault or ∼3.5  km of slip along two superposed low‐angle thrust faults. Both models require decollement slip between 7 and 9 km depth, resulting in greater fault areas than sometimes assumed in hazard assessments. Both models require initial slip much earlier than previously thought and may provide insight into the subsurface geometry of analogous comparisons to wrinkle ridges observed on other planets.

  14. Double generalized linear compound poisson models to insurance claims data

    DEFF Research Database (Denmark)

    Andersen, Daniel Arnfeldt; Bonat, Wagner Hugo

    2017-01-01

    This paper describes the specification, estimation and comparison of double generalized linear compound Poisson models based on the likelihood paradigm. The models are motivated by insurance applications, where the distribution of the response variable is composed by a degenerate distribution...... in a finite sample framework. The simulation studies are also used to validate the fitting algorithms and check the computational implementation. Furthermore, we investigate the impact of an unsuitable choice for the response variable distribution on both mean and dispersion parameter estimates. We provide R...... implementation and illustrate the application of double generalized linear compound Poisson models using a data set about car insurances....

  15. Physically-Derived Dynamical Cores in Atmospheric General Circulation Models

    Science.gov (United States)

    Rood, Richard B.; Lin, Shian-Kiann

    1999-01-01

    The algorithm chosen to represent the advection in atmospheric models is often used as the primary attribute to classify the model. Meteorological models are generally classified as spectral or grid point, with the term grid point implying discretization using finite differences. These traditional approaches have a number of shortcomings that render them non-physical. That is, they provide approximate solutions to the conservation equations that do not obey the fundamental laws of physics. The most commonly discussed shortcomings are overshoots and undershoots which manifest themselves most overtly in the constituent continuity equation. For this reason many climate models have special algorithms to model water vapor advection. This talk focuses on the development of an atmospheric general circulation model which uses a consistent physically-based advection algorithm in all aspects of the model formulation. The shallow-water model of Lin and Rood (QJRMS, 1997) is generalized to three dimensions and combined with the physics parameterizations of NCAR's Community Climate Model. The scientific motivation for the development is to increase the integrity of the underlying fluid dynamics so that the physics terms can be more effectively isolated, examined, and improved. The expected benefits of the new model are discussed and results from the initial integrations will be presented.

  16. A general model for membrane-based separation processes

    DEFF Research Database (Denmark)

    Soni, Vipasha; Abildskov, Jens; Jonsson, Gunnar Eigil

    2009-01-01

    behaviour will play an important role. In this paper, modelling of membrane-based processes for separation of gas and liquid mixtures are considered. Two general models, one for membrane-based liquid separation processes (with phase change) and another for membrane-based gas separation are presented....... The separation processes covered are: membrane-based gas separation processes, pervaporation and various types of membrane distillation processes. The specific model for each type of membrane-based process is generated from the two general models by applying the specific system descriptions and the corresponding......A separation process could be defined as a process that transforms a given mixture of chemicals into two or more compositionally distinct end-use products. One way to design these separation processes is to employ a model-based approach, where mathematical models that reliably predict the process...

  17. Flexible Approaches to Computing Mediated Effects in Generalized Linear Models: Generalized Estimating Equations and Bootstrapping

    Science.gov (United States)

    Schluchter, Mark D.

    2008-01-01

    In behavioral research, interest is often in examining the degree to which the effect of an independent variable X on an outcome Y is mediated by an intermediary or mediator variable M. This article illustrates how generalized estimating equations (GEE) modeling can be used to estimate the indirect or mediated effect, defined as the amount by…

  18. QCD Sum Rules and Models for Generalized Parton Distributions

    Energy Technology Data Exchange (ETDEWEB)

    Anatoly Radyushkin

    2004-10-01

    I use QCD sum rule ideas to construct models for generalized parton distributions. To this end, the perturbative parts of QCD sum rules for the pion and nucleon electromagnetic form factors are interpreted in terms of GPDs and two models are discussed. One of them takes the double Borel transform at adjusted value of the Borel parameter as a model for nonforward parton densities, and another is based on the local duality relation. Possible ways of improving these Ansaetze are briefly discussed.

  19. Generalized Tensor Analysis Model for Multi-Subcarrier Analog Optical Systems

    DEFF Research Database (Denmark)

    Zhao, Ying; Yu, Xianbin; Zheng, Xiaoping

    2011-01-01

    We propose and develop a general tensor analysis framework for a subcarrier multiplex analog optical fiber link for applications in microwave photonics. The goal of this work is to construct an uniform method to address nonlinear distortions of a discrete frequency transmission system. We employ....... In addition, it is demonstrated that each corresponding tensor is formally determined by device structures, which allows for a synthesized study of device combinations more systematically. For implementing numerical methods, the practical significance of the tensor model is it simplifies the derivation...... details compared with series-based approaches by hiding the underlying multi-fold summation and index operation. The integrity of the proposed methodology is validated by investigating the classical intensity modulated system. Furthermore, to give an application model of the tensor formalism, we make...

  20. Protein folding and wring resonances

    DEFF Research Database (Denmark)

    Bohr, Jakob; Bohr, Henrik; Brunak, Søren

    1997-01-01

    The polypeptide chain of a protein is shown to obey topological contraints which enable long range excitations in the form of wring modes of the protein backbone. Wring modes of proteins of specific lengths can therefore resonate with molecular modes present in the cell. It is suggested...... that protein folding takes place when the amplitude of a wring excitation becomes so large that it is energetically favorable to bend the protein backbone. The condition under which such structural transformations can occur is found, and it is shown that both cold and hot denaturation (the unfolding...... of proteins) are natural consequences of the suggested wring mode model. Native (folded) proteins are found to possess an intrinsic standing wring mode....

  1. Estimating and Forecasting Generalized Fractional Long Memory Stochastic Volatility Models

    Directory of Open Access Journals (Sweden)

    Shelton Peiris

    2017-12-01

    Full Text Available This paper considers a flexible class of time series models generated by Gegenbauer polynomials incorporating the long memory in stochastic volatility (SV components in order to develop the General Long Memory SV (GLMSV model. We examine the corresponding statistical properties of this model, discuss the spectral likelihood estimation and investigate the finite sample properties via Monte Carlo experiments. We provide empirical evidence by applying the GLMSV model to three exchange rate return series and conjecture that the results of out-of-sample forecasts adequately confirm the use of GLMSV model in certain financial applications.

  2. Earthquakes and aseismic creep associated with growing fault-related folds

    Science.gov (United States)

    Burke, C. C.; Johnson, K. M.

    2017-12-01

    Blind thrust faults overlain by growing anticlinal folds pose a seismic risk to many urban centers in the world. A large body of research has focused on using fold and growth strata geometry to infer the rate of slip on the causative fault and the distribution of off-fault deformation. However, because we have had few recorded large earthquakes on blind faults underlying folds, it remains unclear how much of the folding occurs during large earthquakes or during the interseismic period accommodated by aseismic creep. Numerous kinematic and mechanical models as well as field observations demonstrate that flexural slip between sedimentary layering is an important mechanism of fault-related folding. In this study, we run boundary element models of flexural-slip fault-related folding to examine the extent to which energy is released seismically or aseismically throughout the evolution of the fold and fault. We assume a fault imbedded in viscoelastic mechanical layering under frictional contact. We assign depth-dependent frictional properties and adopt a rate-state friction formulation to simulate slip over time. We find that in many cases, a large percentage (greater than 50%) of fold growth is accomplished by aseismic creep at bedding and fault contacts. The largest earthquakes tend to occur on the fault, but a significant portion of the seismicity is distributed across bedding contacts through the fold. We are currently working to quantify these results using a large number of simulations with various fold and fault geometries. Result outputs include location, duration, and magnitude of events. As more simulations are completed, these results from different fold and fault geometries will provide insight into how much folding occurs from these slip events. Generalizations from these simulations can be compared with observations of active fault-related folds and used in the future to inform seismic hazard studies.

  3. The Folded Horn Antenna

    Science.gov (United States)

    Farr, E. G.; Bowen, L. H.; Baum, C. E.; Prather, W. D.

    Antennas for radiating high-power mesoband (medium-bandwidth) electromagnetic signals are critical to the mission of upsetting electronics at a distance. When operated at frequencies of a few hundred megahertz, RF weapons require highly efficient antennas that can fit into a small volume. Most of the existing antennas, such as pyramidal horns, are too large to fit onto certain platforms of interest. To address this challenge, we investigate the folded horn, which has aperture dimensions of 0.5 × 2 wavelengths, and a depth of 1.5-2 wavelengths. This antenna has a nearly focused aperture field, due to a parabolic fold in the H-plane. We report here on the fabrication and testing of the first folded horn, operating at 3 GHz. After a number of iterations, we obtained a realized gain of at least 10 dBi over 3-5 GHz, an aperture efficiency of 80%, and a return loss below -10 dB over 2.8-3.35 GHz. This design could be adapted to high-voltages, and it could work well in a two-antenna array, with two antennas positioned back to back, driven by a differential source.

  4. Generalized heat-transport equations: parabolic and hyperbolic models

    Science.gov (United States)

    Rogolino, Patrizia; Kovács, Robert; Ván, Peter; Cimmelli, Vito Antonio

    2018-03-01

    We derive two different generalized heat-transport equations: the most general one, of the first order in time and second order in space, encompasses some well-known heat equations and describes the hyperbolic regime in the absence of nonlocal effects. Another, less general, of the second order in time and fourth order in space, is able to describe hyperbolic heat conduction also in the presence of nonlocal effects. We investigate the thermodynamic compatibility of both models by applying some generalizations of the classical Liu and Coleman-Noll procedures. In both cases, constitutive equations for the entropy and for the entropy flux are obtained. For the second model, we consider a heat-transport equation which includes nonlocal terms and study the resulting set of balance laws, proving that the corresponding thermal perturbations propagate with finite speed.

  5. Australian and overseas models of general practice training.

    Science.gov (United States)

    Hays, Richard B; Morgan, Simon

    2011-06-06

    General practice training in Australia continues to evolve. It is now the responsibility of an independent organisation, is delivered by regional training providers, and comprises a structured training program. Overseas, general practice varies in its importance to health care systems, and training models differ considerably. In some cases training is mandatory, in others voluntary, but the aim is always similar--to improve the quality of care delivered to the large majority of populations that access health care through primary care. We review the current status of vocational general practice training in Australia, compare it with selected training programs in international contexts, and describe how the local model is well placed to address future challenges. Challenges include changes in population demographics, increasing comorbidity, increasing costs of technology-based health care, increasing globalisation of health, and workforce shortages. Although general practice training in Australia is strong, it can improve further by learning from other training programs to meet these challengers.

  6. GEMFsim: A Stochastic Simulator for the Generalized Epidemic Modeling Framework

    OpenAIRE

    Sahneh, Faryad Darabi; Vajdi, Aram; Shakeri, Heman; Fan, Futing; Scoglio, Caterina

    2016-01-01

    The recently proposed generalized epidemic modeling framework (GEMF) \\cite{sahneh2013generalized} lays the groundwork for systematically constructing a broad spectrum of stochastic spreading processes over complex networks. This article builds an algorithm for exact, continuous-time numerical simulation of GEMF-based processes. Moreover the implementation of this algorithm, GEMFsim, is available in popular scientific programming platforms such as MATLAB, R, Python, and C; GEMFsim facilitates ...

  7. Modeling the brain morphology distribution in the general aging population

    Science.gov (United States)

    Huizinga, W.; Poot, D. H. J.; Roshchupkin, G.; Bron, E. E.; Ikram, M. A.; Vernooij, M. W.; Rueckert, D.; Niessen, W. J.; Klein, S.

    2016-03-01

    Both normal aging and neurodegenerative diseases such as Alzheimer's disease cause morphological changes of the brain. To better distinguish between normal and abnormal cases, it is necessary to model changes in brain morphology owing to normal aging. To this end, we developed a method for analyzing and visualizing these changes for the entire brain morphology distribution in the general aging population. The method is applied to 1000 subjects from a large population imaging study in the elderly, from which 900 were used to train the model and 100 were used for testing. The results of the 100 test subjects show that the model generalizes to subjects outside the model population. Smooth percentile curves showing the brain morphology changes as a function of age and spatiotemporal atlases derived from the model population are publicly available via an interactive web application at agingbrain.bigr.nl.

  8. A general maximum likelihood analysis of variance components in generalized linear models.

    Science.gov (United States)

    Aitkin, M

    1999-03-01

    This paper describes an EM algorithm for nonparametric maximum likelihood (ML) estimation in generalized linear models with variance component structure. The algorithm provides an alternative analysis to approximate MQL and PQL analyses (McGilchrist and Aisbett, 1991, Biometrical Journal 33, 131-141; Breslow and Clayton, 1993; Journal of the American Statistical Association 88, 9-25; McGilchrist, 1994, Journal of the Royal Statistical Society, Series B 56, 61-69; Goldstein, 1995, Multilevel Statistical Models) and to GEE analyses (Liang and Zeger, 1986, Biometrika 73, 13-22). The algorithm, first given by Hinde and Wood (1987, in Longitudinal Data Analysis, 110-126), is a generalization of that for random effect models for overdispersion in generalized linear models, described in Aitkin (1996, Statistics and Computing 6, 251-262). The algorithm is initially derived as a form of Gaussian quadrature assuming a normal mixing distribution, but with only slight variation it can be used for a completely unknown mixing distribution, giving a straightforward method for the fully nonparametric ML estimation of this distribution. This is of value because the ML estimates of the GLM parameters can be sensitive to the specification of a parametric form for the mixing distribution. The nonparametric analysis can be extended straightforwardly to general random parameter models, with full NPML estimation of the joint distribution of the random parameters. This can produce substantial computational saving compared with full numerical integration over a specified parametric distribution for the random parameters. A simple method is described for obtaining correct standard errors for parameter estimates when using the EM algorithm. Several examples are discussed involving simple variance component and longitudinal models, and small-area estimation.

  9. Generalized eigenstate typicality in translation-invariant quasifree fermionic models

    Science.gov (United States)

    Riddell, Jonathon; Müller, Markus P.

    2018-01-01

    We demonstrate a generalized notion of eigenstate thermalization for translation-invariant quasifree fermionic models: the vast majority of eigenstates satisfying a finite number of suitable constraints (e.g., fixed energy and particle number) have the property that their reduced density matrix on small subsystems approximates the corresponding generalized Gibbs ensemble. To this end, we generalize analytic results by H. Lai and K. Yang [Phys. Rev. B 91, 081110(R) (2015), 10.1103/PhysRevB.91.081110] and illustrate the claim numerically by example of the Jordan-Wigner transform of the XX spin chain.

  10. A general diagnostic model applied to language testing data.

    Science.gov (United States)

    von Davier, Matthias

    2008-11-01

    Probabilistic models with one or more latent variables are designed to report on a corresponding number of skills or cognitive attributes. Multidimensional skill profiles offer additional information beyond what a single test score can provide, if the reported skills can be identified and distinguished reliably. Many recent approaches to skill profile models are limited to dichotomous data and have made use of computationally intensive estimation methods such as Markov chain Monte Carlo, since standard maximum likelihood (ML) estimation techniques were deemed infeasible. This paper presents a general diagnostic model (GDM) that can be estimated with standard ML techniques and applies to polytomous response variables as well as to skills with two or more proficiency levels. The paper uses one member of a larger class of diagnostic models, a compensatory diagnostic model for dichotomous and partial credit data. Many well-known models, such as univariate and multivariate versions of the Rasch model and the two-parameter logistic item response theory model, the generalized partial credit model, as well as a variety of skill profile models, are special cases of this GDM. In addition to an introduction to this model, the paper presents a parameter recovery study using simulated data and an application to real data from the field test for TOEFL Internet-based testing.

  11. Dynamic generalized linear models for monitoring endemic diseases

    DEFF Research Database (Denmark)

    Lopes Antunes, Ana Carolina; Jensen, Dan; Hisham Beshara Halasa, Tariq

    2016-01-01

    The objective was to use a Dynamic Generalized Linear Model (DGLM) based on abinomial distribution with a linear trend, for monitoring the PRRS (Porcine Reproductive and Respiratory Syndrome sero-prevalence in Danish swine herds. The DGLM was described and its performance for monitoring control...... in sero-prevalence. Based on this, it was possible to detect variations in the growth model component. This study is a proof-of-concept, demonstrating the use of DGLMs for monitoring endemic diseases. In addition, the principles stated might be useful in general research on monitoring and surveillance...

  12. Generalized memory associativity in a network model for the neuroses

    Science.gov (United States)

    Wedemann, Roseli S.; Donangelo, Raul; de Carvalho, Luís A. V.

    2009-03-01

    We review concepts introduced in earlier work, where a neural network mechanism describes some mental processes in neurotic pathology and psychoanalytic working-through, as associative memory functioning, according to the findings of Freud. We developed a complex network model, where modules corresponding to sensorial and symbolic memories interact, representing unconscious and conscious mental processes. The model illustrates Freud's idea that consciousness is related to symbolic and linguistic memory activity in the brain. We have introduced a generalization of the Boltzmann machine to model memory associativity. Model behavior is illustrated with simulations and some of its properties are analyzed with methods from statistical mechanics.

  13. Impact of Thermostats on Folding and Aggregation Properties of Peptides Using the Optimized Potential for Efficient Structure Prediction Coarse-Grained Model.

    Science.gov (United States)

    Spill, Yannick G; Pasquali, Samuela; Derreumaux, Philippe

    2011-05-10

    The simulation of amyloid fibril formation is impossible if one takes into account all chemical details of the amino acids and their detailed interactions with the solvent. We investigate the folding and aggregation of two model peptides using the optimized potential for efficient structure prediction (OPEP) coarse-grained model and replica exchange molecular dynamics (REMD) simulations coupled with either the Langevin or the Berendsen thermostat. For both the monomer of blocked penta-alanine and the trimer of the 25-35 fragment of the Alzheimer's amyloid β protein, we find little variations in the equilibrium structures and heat capacity curves using the two thermostats. Despite this high similarity, we detect significant differences in the populations of the dominant conformations at low temperatures, whereas the configurational distributions remain the same in proximity of the melting temperature. Aβ25-35 trimers at 300 K have an averaged β-sheet content of 12% and are primarily characterized by fully disordered peptides or a small curved two-stranded β-sheet stabilized by a disordered peptide. In addition, OPEP molecular dynamics simulations of Aβ25-35 hexamers at 300 K with a small curved six-stranded antiparallel β-sheet do not show any extension of the β-sheet content. These data support the idea that the mechanism of Aβ25-35 amyloid formation does not result from a high fraction of extended β-sheet-rich trimers and hexamers.

  14. Seasonal predictability of Kiremt rainfall in coupled general circulation models

    Science.gov (United States)

    Gleixner, Stephanie; Keenlyside, Noel S.; Demissie, Teferi D.; Counillon, François; Wang, Yiguo; Viste, Ellen

    2017-11-01

    The Ethiopian economy and population is strongly dependent on rainfall. Operational seasonal predictions for the main rainy season (Kiremt, June-September) are based on statistical approaches with Pacific sea surface temperatures (SST) as the main predictor. Here we analyse dynamical predictions from 11 coupled general circulation models for the Kiremt seasons from 1985-2005 with the forecasts starting from the beginning of May. We find skillful predictions from three of the 11 models, but no model beats a simple linear prediction model based on the predicted Niño3.4 indices. The skill of the individual models for dynamically predicting Kiremt rainfall depends on the strength of the teleconnection between Kiremt rainfall and concurrent Pacific SST in the models. Models that do not simulate this teleconnection fail to capture the observed relationship between Kiremt rainfall and the large-scale Walker circulation.

  15. Estimating classification images with generalized linear and additive models.

    Science.gov (United States)

    Knoblauch, Kenneth; Maloney, Laurence T

    2008-12-22

    Conventional approaches to modeling classification image data can be described in terms of a standard linear model (LM). We show how the problem can be characterized as a Generalized Linear Model (GLM) with a Bernoulli distribution. We demonstrate via simulation that this approach is more accurate in estimating the underlying template in the absence of internal noise. With increasing internal noise, however, the advantage of the GLM over the LM decreases and GLM is no more accurate than LM. We then introduce the Generalized Additive Model (GAM), an extension of GLM that can be used to estimate smooth classification images adaptively. We show that this approach is more robust to the presence of internal noise, and finally, we demonstrate that GAM is readily adapted to estimation of higher order (nonlinear) classification images and to testing their significance.

  16. Automation of electroweak NLO corrections in general models

    Energy Technology Data Exchange (ETDEWEB)

    Lang, Jean-Nicolas [Universitaet Wuerzburg (Germany)

    2016-07-01

    I discuss the automation of generation of scattering amplitudes in general quantum field theories at next-to-leading order in perturbation theory. The work is based on Recola, a highly efficient one-loop amplitude generator for the Standard Model, which I have extended so that it can deal with general quantum field theories. Internally, Recola computes off-shell currents and for new models new rules for off-shell currents emerge which are derived from the Feynman rules. My work relies on the UFO format which can be obtained by a suited model builder, e.g. FeynRules. I have developed tools to derive the necessary counterterm structures and to perform the renormalization within Recola in an automated way. I describe the procedure using the example of the two-Higgs-doublet model.

  17. Improved Generalized Force Model considering the Comfortable Driving Behavior

    Directory of Open Access Journals (Sweden)

    De-Jie Xu

    2015-01-01

    Full Text Available This paper presents an improved generalized force model (IGFM that considers the driver’s comfortable driving behavior. Through theoretical analysis, we propose the calculation methods of comfortable driving distance and velocity. Then the stability condition of the model is obtained by the linear stability analysis. The problems of the unrealistic acceleration of the leading car existing in the previous models were solved. Furthermore, the simulation results show that IGFM can predict correct delay time of car motion and kinematic wave speed at jam density, and it can exactly describe the driver’s behavior under an urgent case, where no collision occurs. The dynamic properties of IGFM also indicate that stability has improved compared to the generalized force model.

  18. The folding mechanism and key metastable state identification of the PrP127-147 monomer studied by molecular dynamics simulations and Markov state model analysis.

    Science.gov (United States)

    Zhou, Shuangyan; Wang, Qianqian; Wang, Yuwei; Yao, Xiaojun; Han, Wei; Liu, Huanxiang

    2017-05-10

    The structural transition of prion proteins from a native α-helix (PrP C ) to a misfolded β-sheet-rich conformation (PrP Sc ) is believed to be the main cause of a number of prion diseases in humans and animals. Understanding the molecular basis of misfolding and aggregation of prion proteins will be valuable for unveiling the etiology of prion diseases. However, due to the limitation of conventional experimental techniques and the heterogeneous property of oligomers, little is known about the molecular architecture of misfolded PrP Sc and the mechanism of structural transition from PrP C to PrP Sc . The prion fragment 127-147 (PrP127-147) has been reported to be a critical region for PrP Sc formation in Gerstmann-Straussler-Scheinker (GSS) syndrome and thus has been used as a model for the study of prion aggregation. In the present study, we employ molecular dynamics (MD) simulation techniques to study the conformational change of this fragment that could be relevant to the PrP C -PrP Sc transition. Employing extensive replica exchange molecular dynamics (REMD) and conventional MD simulations, we sample a huge number of conformations of PrP127-147. Using the Markov state model (MSM), we identify the metastable conformational states of this fragment and the kinetic network of transitions between the states. The resulting MSM reveals that disordered random-coiled conformations are the dominant structures. A key metastable folded state with typical extended β-sheet structures is identified with Pro137 being located in a turn region, consistent with a previous experimental report. Conformational analysis reveals that intrapeptide hydrophobic interaction and two key residue interactions, including Arg136-His140 and Pro137-His140, contribute a lot to the formation of ordered extended β-sheet states. However, network pathway analysis from the most populated disordered state indicates that the formation of extended β-sheet states is quite slow (at the millisecond

  19. A general model framework for multisymbol number comparison.

    Science.gov (United States)

    Huber, Stefan; Nuerk, Hans-Christoph; Willmes, Klaus; Moeller, Korbinian

    2016-11-01

    Different models have been proposed for the processing of multisymbol numbers like two- and three-digit numbers but also for negative numbers and decimals. However, these multisymbol numbers are assembled from the same set of Arabic digits and comply with the place-value structure of the Arabic number system. Considering these shared properties, we suggest that the processing of multisymbol numbers can be described in one general model framework. Accordingly, we first developed a computational model framework realizing componential representations of multisymbol numbers and evaluated its validity by simulating standard empirical effects of number magnitude comparison. We observed that the model framework successfully accounted for most of these effects. Moreover, our simulations provided first evidence supporting the notion of a fully componential processing of multisymbol numbers for the specific case of comparing two negative numbers. Thus, our general model framework indicates that the processing of different kinds of multisymbol integer and decimal numbers shares common characteristics (e.g., componential representation). The relevance and applicability of our model goes beyond the case of basic number processing. In particular, we also successfully simulated effects from applied marketing and consumer research by accounting for the left-digit effect found in processing of prices. Finally, we provide evidence that our model framework can be integrated into the more general context of multiattribute decision making. In sum, this indicates that our model framework captures a general scheme of separate processing of different attributes weighted by their saliency for the task at hand. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

  20. SELECTION MOMENTS AND GENERALIZED METHOD OF MOMENTS FOR HETEROSKEDASTIC MODELS

    Directory of Open Access Journals (Sweden)

    Constantin ANGHELACHE

    2016-06-01

    Full Text Available In this paper, the authors describe the selection methods for moments and the application of the generalized moments method for the heteroskedastic models. The utility of GMM estimators is found in the study of the financial market models. The selection criteria for moments are applied for the efficient estimation of GMM for univariate time series with martingale difference errors, similar to those studied so far by Kuersteiner.

  1. Contextual interactions in a generalized energy model of complex cells

    OpenAIRE

    Dellen, Babette; Clark, John W.; Wessel, Ralf

    2009-01-01

    We propose a generalized energy model of complex cells to describe modulatory contextual influences on the responses of neurons in the primary visual cortex (V1). Many orientationselective cells in V1 respond to contrast of orientation and motion of stimuli exciting the classical receptive field (CRF) and the non-CRF, or surround. In the proposed model, a central spatiotemporal filter, defining the CRF, is nonlinearly combined with a spatiotemporal filter extending into the non- ...

  2. Study of the properties of general relativistic Kink model (GRK)

    International Nuclear Information System (INIS)

    Oliveira, L.C.S. de.

    1980-01-01

    The stability of the general relativistic Kink model (GRK) is studied. It is shown that the model is stable at least against radial perturbations. Furthermore, the Dirac field in the background of the geometry generated by the GRK is studied. It is verified that the GRK localizes the Dirac field, around the region of largest curvature. The physical interpretation of this system (the Dirac field in the GRK background) is discussed. (Author) [pt

  3. On the Use of Generalized Volume Scattering Models for the Improvement of General Polarimetric Model-Based Decomposition

    Directory of Open Access Journals (Sweden)

    Qinghua Xie

    2017-01-01

    Full Text Available Recently, a general polarimetric model-based decomposition framework was proposed by Chen et al., which addresses several well-known limitations in previous decomposition methods and implements a simultaneous full-parameter inversion by using complete polarimetric information. However, it only employs four typical models to characterize the volume scattering component, which limits the parameter inversion performance. To overcome this issue, this paper presents two general polarimetric model-based decomposition methods by incorporating the generalized volume scattering model (GVSM or simplified adaptive volume scattering model, (SAVSM proposed by Antropov et al. and Huang et al., respectively, into the general decomposition framework proposed by Chen et al. By doing so, the final volume coherency matrix structure is selected from a wide range of volume scattering models within a continuous interval according to the data itself without adding unknowns. Moreover, the new approaches rely on one nonlinear optimization stage instead of four as in the previous method proposed by Chen et al. In addition, the parameter inversion procedure adopts the modified algorithm proposed by Xie et al. which leads to higher accuracy and more physically reliable output parameters. A number of Monte Carlo simulations of polarimetric synthetic aperture radar (PolSAR data are carried out and show that the proposed method with GVSM yields an overall improvement in the final accuracy of estimated parameters and outperforms both the version using SAVSM and the original approach. In addition, C-band Radarsat-2 and L-band AIRSAR fully polarimetric images over the San Francisco region are also used for testing purposes. A detailed comparison and analysis of decomposition results over different land-cover types are conducted. According to this study, the use of general decomposition models leads to a more accurate quantitative retrieval of target parameters. However, there

  4. Probing folding free energy landscape of small proteins through ...

    Indian Academy of Sciences (India)

    Unknown

    lattice and off-lattice models of proteins have been used to study the statistical and dynamical aspects of folding.12,13 Levitt pioneered in the computational studies of protein folding using off-lattice protein models.14 A recent off-lattice model study of HP-36 based on hydrophobicity tried to correlate the folding with many ...

  5. The general class of Bianchi cosmological models with dark energy ...

    Indian Academy of Sciences (India)

    The general class of Bianchi cosmological models with dark energy in the form of modified Chaplygin gas with variable Λ and G and bulk viscosity have been considered. We discuss three types of average scalefactor by using a special law for deceleration parameter which is linear in time with negative slope. The exact ...

  6. A general circulation model (GCM) parameterization of Pinatubo aerosols

    Energy Technology Data Exchange (ETDEWEB)

    Lacis, A.A.; Carlson, B.E.; Mishchenko, M.I. [NASA Goddard Institute for Space Studies, New York, NY (United States)

    1996-04-01

    The June 1991 volcanic eruption of Mt. Pinatubo is the largest and best documented global climate forcing experiment in recorded history. The time development and geographical dispersion of the aerosol has been closely monitored and sampled. Based on preliminary estimates of the Pinatubo aerosol loading, general circulation model predictions of the impact on global climate have been made.

  7. A generalized quarter car modelling approach with frame flexibility ...

    Indian Academy of Sciences (India)

    HUSAIN KANCHWALA

    ground-wheel contacts at three other locations. A Matlab code for obtaining the generalized quarter-car model is provided towards the end of this paper. The code enables a user to perform fairly quick parametric studies. An example of such a parametric study is presented there as well. The role of other wheels, in particular, ...

  8. Anisotropic cosmological models and generalized scalar tensor theory

    Indian Academy of Sciences (India)

    Abstract. In this paper generalized scalar tensor theory has been considered in the background of anisotropic cosmological models, namely, axially symmetric Bianchi-I, Bianchi-III and Kortowski–. Sachs space-time. For bulk viscous fluid, both exponential and power-law solutions have been stud- ied and some assumptions ...

  9. Anisotropic cosmological models and generalized scalar tensor theory

    Indian Academy of Sciences (India)

    In this paper generalized scalar tensor theory has been considered in the background of anisotropic cosmological models, namely, axially symmetric Bianchi-I, Bianchi-III and Kortowski–Sachs space-time. For bulk viscous fluid, both exponential and power-law solutions have been studied and some assumptions among the ...

  10. Transmittivity and wavefunctions in one-dimensional generalized Aubry models

    International Nuclear Information System (INIS)

    Basu, C.; Mookerjee, A.; Sen, A.K.; Thakur, P.K.

    1990-07-01

    We use the vector recursion method of Haydock to obtain the transmittance of a class of generalized Aubry models in one-dimension. We also study the phase change of the wavefunctions as they travel through the chain and also the behaviour of the conductance with changes in size. (author). 10 refs, 9 figs

  11. Characterizing QALYs under a General Rank Dependent Utility Model

    NARCIS (Netherlands)

    H. Bleichrodt (Han); J. Quiggin (John)

    1997-01-01

    textabstractThis paper provides a characterization of QALYs, the most important outcome measure in medical decision making, in the context of a general rank dependent utility model. We show that both for chronic and for nonchronic health states the characterization of QALYs depends on intuitive

  12. Model-free adaptive sliding mode controller design for generalized ...

    Indian Academy of Sciences (India)

    L M WANG

    2017-08-16

    Aug 16, 2017 ... Abstract. A novel model-free adaptive sliding mode strategy is proposed for a generalized projective synchronization (GPS) between two entirely unknown fractional-order chaotic systems subject to the external disturbances. To solve the difficulties from the little knowledge about the master–slave system ...

  13. Simplicial models for trace spaces II: General higher dimensional automata

    DEFF Research Database (Denmark)

    Raussen, Martin

    Higher Dimensional Automata (HDA) are topological models for the study of concurrency phenomena. The state space for an HDA is given as a pre-cubical complex in which a set of directed paths (d-paths) is singled out. The aim of this paper is to describe a general method that determines the space...

  14. An applied general equilibrium model for Dutch agribusiness policy analysis

    NARCIS (Netherlands)

    Peerlings, J.

    1993-01-01

    The purpose of this thesis was to develop a basic static applied general equilibrium (AGE) model to analyse the effects of agricultural policy changes on Dutch agribusiness. In particular the effects on inter-industry transactions, factor demand, income, and trade are of

  15. Confidence Intervals for Assessing Heterogeneity in Generalized Linear Mixed Models

    Science.gov (United States)

    Wagler, Amy E.

    2014-01-01

    Generalized linear mixed models are frequently applied to data with clustered categorical outcomes. The effect of clustering on the response is often difficult to practically assess partly because it is reported on a scale on which comparisons with regression parameters are difficult to make. This article proposes confidence intervals for…

  16. Bianchi type-V string cosmological models in general relativity

    Indian Academy of Sciences (India)

    Abstract. Bianchi type-V string cosmological models in general relativity are investigated. To get the exact solution of Einstein's field equations, we have taken some scale transformations used by Camci et al [Astrophys. Space Sci. 275, 391 (2001)]. It is shown that Einstein's field equations are solvable for any arbitrary ...

  17. A generalized quarter car modelling approach with frame flexibility ...

    Indian Academy of Sciences (India)

    ... mass distribution and damping. Here we propose a generalized quarter-car modelling approach, incorporating both the frame as well as other-wheel ground contacts. Our approach is linear, uses Laplace transforms, involves vertical motions of key points of interest and has intermediate complexity with improved realism.

  18. On the general procedure for modelling complex ecological systems

    International Nuclear Information System (INIS)

    He Shanyu.

    1987-12-01

    In this paper, the principle of a general procedure for modelling complex ecological systems, i.e. the Adaptive Superposition Procedure (ASP) is shortly stated. The result of application of ASP in a national project for ecological regionalization is also described. (author). 3 refs

  19. Bianchi type-V string cosmological models in general relativity

    Indian Academy of Sciences (India)

    Bianchi type-V string cosmological models in general relativity are investigated. To get the exact solution of Einstein's field equations, we have taken some scale transformations used by Camci et al [Astrophys. Space Sci. 275, 391 (2001)]. It is shown that Einstein's field equations are solvable for any arbitrary cosmic scale ...

  20. Uncertainty in a monthly water balance model using the generalized ...

    Indian Academy of Sciences (India)

    Uncertainty in a monthly water balance model using the generalized likelihood uncertainty estimation methodology. Diego Rivera1,∗. , Yessica Rivas. 2 and Alex Godoy. 3. 1. Laboratory of Comparative Policy in Water Resources Management, University of Concepcion,. CONICYT/FONDAP 15130015, Concepcion, Chile. 2.

  1. On generalized Yang-Mills theories and extensions of the standard model in Clifford (tensorial) spaces

    International Nuclear Information System (INIS)

    Castro, Carlos

    2006-01-01

    We construct the Clifford-space tensorial-gauge fields generalizations of Yang-Mills theories and the Standard Model that allows to predict the existence of new particles (bosons, fermions) and tensor-gauge fields of higher-spins in the 10 Tev regime. We proceed with a detailed discussion of the unique D 4 - D 5 - E 6 - E 7 - E 8 model of Smith based on the underlying Clifford algebraic structures in D = 8, and which furnishes all the properties of the Standard Model and Gravity in four-dimensions, at low energies. A generalization and extension of Smith's model to the full Clifford-space is presented when we write explicitly all the terms of the extended Clifford-space Lagrangian. We conclude by explaining the relevance of multiple-foldings of D = 8 dimensions related to the modulo 8 periodicity of the real Cliford algebras and display the interplay among Clifford, Division, Jordan, and Exceptional algebras, within the context of D = 26, 27, 28 dimensions, corresponding to bosonic string, M and F theory, respectively, advanced earlier by Smith. To finalize we describe explicitly how the E 8 x E 8 Yang-Mills theory can be obtained from a Gauge Theory based on the Clifford (16) group

  2. Solitons and protein folding: An In Silico experiment

    Energy Technology Data Exchange (ETDEWEB)

    Ilieva, N., E-mail: nevena.ilieva@parallel.bas.bg [Institute of Information and Communication Technologies, Bulgarian Aacademy of Sciences, Sofia (Bulgaria); Dai, J., E-mail: daijing491@gmail.com [School of Physics, Beijing Institute of Technology, Beijing (China); Sieradzan, A., E-mail: adams86@wp.pl [Faculty of Chemistry, University of Gdańsk, Gdańsk (Poland); Niemi, A., E-mail: Antti.Niemi@physics.uu.se [Department of Physics and Astronomy, Uppsala University, Uppsala (Sweden); LMPT–CNRS, Université de Tours, Tours (France)

    2015-10-28

    Protein folding [1] is the process of formation of a functional 3D structure from a random coil — the shape in which amino-acid chains leave the ribosome. Anfinsen’s dogma states that the native 3D shape of a protein is completely determined by protein’s amino acid sequence. Despite the progress in understanding the process rate and the success in folding prediction for some small proteins, with presently available physics-based methods it is not yet possible to reliably deduce the shape of a biologically active protein from its amino acid sequence. The protein-folding problem endures as one of the most important unresolved problems in science; it addresses the origin of life itself. Furthermore, a wrong fold is a common cause for a protein to lose its function or even endanger the living organism. Soliton solutions of a generalized discrete non-linear Schrödinger equation (GDNLSE) obtained from the energy function in terms of bond and torsion angles κ and τ provide a constructive theoretical framework for describing protein folds and folding patterns [2]. Here we study the dynamics of this process by means of molecular-dynamics simulations. The soliton manifestation is the pattern helix–loop–helix in the secondary structure of the protein, which explains the importance of understanding loop formation in helical proteins. We performed in silico experiments for unfolding one subunit of the core structure of gp41 from the HIV envelope glycoprotein (PDB ID: 1AIK [3]) by molecular-dynamics simulations with the MD package GROMACS. We analyzed 80 ns trajectories, obtained with one united-atom and two different all-atom force fields, to justify the side-chain orientation quantification scheme adopted in the studies and to eliminate force-field based artifacts. Our results are compatible with the soliton model of protein folding and provide first insight into soliton-formation dynamics.

  3. Analysis of snow feedbacks in 14 general circulation models

    Science.gov (United States)

    Randall, D. A.; Cess, R. D.; Blanchet, J. P.; Chalita, S.; Colman, R.; Dazlich, D. A.; Del Genio, A. D.; Keup, E.; Lacis, A.; Le Treut, H.; Liang, X.-Z.; McAvaney, B. J.; Mahfouf, J. F.; Meleshko, V. P.; Morcrette, J.-J.; Norris, P. M.; Potter, G. L.; Rikus, L.; Roeckner, E.; Royer, J. F.; Schlese, U.; Sheinin, D. A.; Sokolov, A. P.; Taylor, K. E.; Wetherald, R. T.; Yagai, I.; Zhang, M.-H.

    1994-10-01

    Snow feedbacks produced by 14 atmospheric general circulation models have been analyzed through idealized numerical experiments. Included in the analysis is an investigation of the surface energy budgets of the models. Negative or weak positive snow feedbacks occurred in some of the models, while others produced strong positive snow feedbacks. These feedbacks are due not only to melting snow, but also to increases in boundary temperature, changes in air temperature, changes in water vapor, and changes in cloudiness. As a result, the net response of each model is quite complex. We analyze in detail the responses of one model with a strong positive snow feedback and another with a weak negative snow feedback. Some of the models include a temperature dependence of the snow albedo, and this has significantly affected the results.

  4. Generalized Chaplygin gas model, supernovae, and cosmic topology

    International Nuclear Information System (INIS)

    Bento, M.C.; Bertolami, O.; Silva, P.T.; Reboucas, M.J.

    2006-01-01

    In this work we study to which extent the knowledge of spatial topology may place constraints on the parameters of the generalized Chaplygin gas (GCG) model for unification of dark energy and dark matter. By using both the Poincare dodecahedral and binary octahedral spaces as the observable spatial topologies, we examine the current type Ia supernovae (SNe Ia) constraints on the GCG model parameters. We show that the knowledge of spatial topology does provide additional constraints on the A s parameter of the GCG model but does not lift the degeneracy of the α parameter

  5. Generalized Roe's numerical scheme for a two-fluid model

    International Nuclear Information System (INIS)

    Toumi, I.; Raymond, P.

    1993-01-01

    This paper is devoted to a mathematical and numerical study of a six equation two-fluid model. We will prove that the model is strictly hyperbolic due to the inclusion of the virtual mass force term in the phasic momentum equations. The two-fluid model is naturally written under a nonconservative form. To solve the nonlinear Riemann problem for this nonconservative hyperbolic system, a generalized Roe's approximate Riemann solver, is used, based on a linearization of the nonconservative terms. A Godunov type numerical scheme is built, using this approximate Riemann solver. 10 refs., 5 figs,

  6. Simulation Modeling Method and Experimental Investigation on the Uniflow Scavenging System of an Opposed-Piston Folded-Cranktrain Diesel Engine

    Directory of Open Access Journals (Sweden)

    Fukang Ma

    2017-05-01

    Full Text Available The scavenging process for opposed-piston folded-cranktrain (OPFC diesel engines can be described by the time evolution of the in-cylinder and exhaust chamber residual gas rates. The relation curve of in-cylinder and exhaust chamber residual gas rate is called scavenging profile, which is calculated through the changes of in-cylinder and exhaust chamber gas compositions determined by computational fluid dynamics (CFD simulation. The scavenging profile is used to calculate the scavenging process by mono-dimensional (1D simulation. The tracer gas method (TGM is employed to validate the accuracy of the scavenging profile. At the same time, the gas exchange performance under different intake and exhaust state parameters was examined based on the TGM. The results show that the scavenging process from 1D simulation and experiment match well, which means the scavenging model obtained by CFD simulation performs well and validation of its effectiveness by TGM is possible. The difference between intake and exhaust pressure has a significant positive effect on the gas exchange performance and trapped gas mass, but the pressure difference has little effect on the scavenging efficiency and the trapped air mass if the delivery ratio exceeds 1.4.

  7. Folding model analyses of 12C-12C and 16O-16O elastic scattering using the density-dependent LOCV-averaged effective interaction

    Science.gov (United States)

    Rahmat, M.; Modarres, M.

    2018-03-01

    The averaged effective two-body interaction (AEI), which can be generated through the lowest order constrained variational (LOCV) method for symmetric nuclear matter (SNM) with the input [Reid68, Ann. Phys. 50, 411 (1968), 10.1016/0003-4916(68)90126-7] nucleon-nucleon potential, is used as the effective nucleon-nucleon potential in the folding model to describe the heavy-ion (HI) elastic scattering cross sections. The elastic scattering cross sections of 12C-12C and 16O-16O systems are calculated in the above framework. The results are compared with the corresponding calculations coming from the fitting procedures with the input finite range D D M 3 Y 1 -Reid potential and the available experimental data at different incident energies. It is shown that a reasonable description of the elastic 12C-12C and 16O-16O scattering data at the low and medium energies can be obtained by using the above LOCV AEI, without any need to define a parametrized density-dependent function in the effective nucleon-nucleon potential, which is formally considered in the typical D D M 3 Y 1 -Reid interactions.

  8. Holographic entanglement entropy in general holographic superconductor models

    Energy Technology Data Exchange (ETDEWEB)

    Peng, Yan [School of Mathematics and Computer Science, Shaanxi University of Technology,Hanzhong, Shaanxi 723000 (China); Pan, Qiyuan [Institute of Physics and Department of Physics, Hunan Normal University,Changsha, Hunan 410081 (China)

    2014-06-03

    We study the entanglement entropy of general holographic dual models both in AdS soliton and AdS black hole backgrounds with full backreaction. We find that the entanglement entropy is a good probe to explore the properties of the holographic superconductors and provides richer physics in the phase transition. We obtain the effects of the scalar mass, model parameter and backreaction on the entropy, and argue that the jump of the entanglement entropy may be a quite general feature for the first order phase transition. In strong contrast to the insulator/superconductor system, we note that the backreaction coupled with the scalar mass can not be used to trigger the first order phase transition if the model parameter is below its bottom bound in the metal/superconductor system.

  9. Commensurate Priors for Incorporating Historical Information in Clinical Trials Using General and Generalized Linear Models

    Science.gov (United States)

    Hobbs, Brian P.; Sargent, Daniel J.; Carlin, Bradley P.

    2014-01-01

    Assessing between-study variability in the context of conventional random-effects meta-analysis is notoriously difficult when incorporating data from only a small number of historical studies. In order to borrow strength, historical and current data are often assumed to be fully homogeneous, but this can have drastic consequences for power and Type I error if the historical information is biased. In this paper, we propose empirical and fully Bayesian modifications of the commensurate prior model (Hobbs et al., 2011) extending Pocock (1976), and evaluate their frequentist and Bayesian properties for incorporating patient-level historical data using general and generalized linear mixed regression models. Our proposed commensurate prior models lead to preposterior admissible estimators that facilitate alternative bias-variance trade-offs than those offered by pre-existing methodologies for incorporating historical data from a small number of historical studies. We also provide a sample analysis of a colon cancer trial comparing time-to-disease progression using a Weibull regression model. PMID:24795786

  10. Towards a generalized energy prediction model for machine tools.

    Science.gov (United States)

    Bhinge, Raunak; Park, Jinkyoo; Law, Kincho H; Dornfeld, David A; Helu, Moneer; Rachuri, Sudarsan

    2017-04-01

    Energy prediction of machine tools can deliver many advantages to a manufacturing enterprise, ranging from energy-efficient process planning to machine tool monitoring. Physics-based, energy prediction models have been proposed in the past to understand the energy usage pattern of a machine tool. However, uncertainties in both the machine and the operating environment make it difficult to predict the energy consumption of the target machine reliably. Taking advantage of the opportunity to collect extensive, contextual, energy-consumption data, we discuss a data-driven approach to develop an energy prediction model of a machine tool in this paper. First, we present a methodology that can efficiently and effectively collect and process data extracted from a machine tool and its sensors. We then present a data-driven model that can be used to predict the energy consumption of the machine tool for machining a generic part. Specifically, we use Gaussian Process (GP) Regression, a non-parametric machine-learning technique, to develop the prediction model. The energy prediction model is then generalized over multiple process parameters and operations. Finally, we apply this generalized model with a method to assess uncertainty intervals to predict the energy consumed to machine any part using a Mori Seiki NVD1500 machine tool. Furthermore, the same model can be used during process planning to optimize the energy-efficiency of a machining process.

  11. Fold-and-thrust belt evolution influenced by along and across strike thickness variations: new insights from brittle-ductile centrifuge analogue models

    Science.gov (United States)

    Santolaria Otin, Pablo; Harris, Lyal; Casas, Antonio; Soto, Ruth

    2014-05-01

    Using a new centrifuge analogue modelling approach, 38 models were performed to study the influence of along and across strike thickness variations of a ductile-brittle layered sequence on the kinematics and deformation style of fold-and-thrust belts. Four different series, changing the brittle-ductile thickness ratio in models with i) constant thickness, ii) across strike varying thickness, iii) along strike varying thickness and iv) along and across-strike varying thickness, were performed. The brittle sedimentary cover was simulated by "Moon Sand™", regular fine-grained quartz sand coated by polymer and synthetic rubber binders, allowing layers to be placed vertically in the centrifuge (impossible with normal sand). The ductile décollement (evaporites) was simulated by silicone putty (Crazy Aaron Enterprise's Thinking Putty™). Models were run step by step in a high-acceleration centrifuge attaining 900 g, what allows to drastically reduce the experimental time. In addition to surface observation and serial cross-sections at the end of the models, CT scans portray the progressive 3- and 4-dimensional evolution of several models. With constant thickness, the increase of the brittle-ductile ratio results in the decrease of the number of structures where shortening is accommodated and the development of structures does not follow a linear sequence. Across-strike thickness variations trigger the location of deformation towards the wedge front, precluding the emplacement of structures in the hinterland. Along-strike thickness changes result in the lateral variation of the number of structure and a differential displacement of the deformation front. The occurrence of oblique structures is enhanced in wedges with across and along strike thickness variations where, in addition, rotational domains are observed. Comparison with the South Pyrenean Central Unit, in the Southern Pyrenees, characterized by a west- and southward thinning of the pretectonic Mesozoic series

  12. Combining optimal control theory and molecular dynamics for protein folding.

    Science.gov (United States)

    Arkun, Yaman; Gur, Mert

    2012-01-01

    A new method to develop low-energy folding routes for proteins is presented. The novel aspect of the proposed approach is the synergistic use of optimal control theory with Molecular Dynamics (MD). In the first step of the method, optimal control theory is employed to compute the force field and the optimal folding trajectory for the Cα atoms of a Coarse-Grained (CG) protein model. The solution of this CG optimization provides an harmonic approximation of the true potential energy surface around the native state. In the next step CG optimization guides the MD simulation by specifying the optimal target positions for the Cα atoms. In turn, MD simulation provides an all-atom conformation whose Cα positions match closely the reference target positions determined by CG optimization. This is accomplished by Targeted Molecular Dynamics (TMD) which uses a bias potential or harmonic restraint in addition to the usual MD potential. Folding is a dynamical process and as such residues make different contacts during the course of folding. Therefore CG optimization has to be reinitialized and repeated over time to accomodate these important changes. At each sampled folding time, the active contacts among the residues are recalculated based on the all-atom conformation obtained from MD. Using the new set of contacts, the CG potential is updated and the CG optimal trajectory for the Cα atoms is recomputed. This is followed by MD. Implementation of this repetitive CG optimization-MD simulation cycle generates the folding trajectory. Simulations on a model protein Villin demonstrate the utility of the method. Since the method is founded on the general tools of optimal control theory and MD without any restrictions, it is widely applicable to other systems. It can be easily implemented with available MD software packages.

  13. Combining optimal control theory and molecular dynamics for protein folding.

    Directory of Open Access Journals (Sweden)

    Yaman Arkun

    Full Text Available A new method to develop low-energy folding routes for proteins is presented. The novel aspect of the proposed approach is the synergistic use of optimal control theory with Molecular Dynamics (MD. In the first step of the method, optimal control theory is employed to compute the force field and the optimal folding trajectory for the Cα atoms of a Coarse-Grained (CG protein model. The solution of this CG optimization provides an harmonic approximation of the true potential energy surface around the native state. In the next step CG optimization guides the MD simulation by specifying the optimal target positions for the Cα atoms. In turn, MD simulation provides an all-atom conformation whose Cα positions match closely the reference target positions determined by CG optimization. This is accomplished by Targeted Molecular Dynamics (TMD which uses a bias potential or harmonic restraint in addition to the usual MD potential. Folding is a dynamical process and as such residues make different contacts during the course of folding. Therefore CG optimization has to be reinitialized and repeated over time to accomodate these important changes. At each sampled folding time, the active contacts among the residues are recalculated based on the all-atom conformation obtained from MD. Using the new set of contacts, the CG potential is updated and the CG optimal trajectory for the Cα atoms is recomputed. This is followed by MD. Implementation of this repetitive CG optimization-MD simulation cycle generates the folding trajectory. Simulations on a model protein Villin demonstrate the utility of the method. Since the method is founded on the general tools of optimal control theory and MD without any restrictions, it is widely applicable to other systems. It can be easily implemented with available MD software packages.

  14. Generalized Modeling of the Human Lower Limb Assembly

    Science.gov (United States)

    Cofaru, Ioana; Huzu, Iulia

    2014-11-01

    The main reason for creating a generalized assembly of the main bones of the lower human member is to create the premises of realizing a biomechanic assisted study which could be used for the study of the high range of varieties of pathologies that exist at this level. Starting from 3D CAD models of the main bones of the lower human member, which were realized in previous researches, in this study a generalized assembly system was developed, system in which are highlighted both the situation of an healthy subject and the situation of the situation of a subject affected by axial deviations. In order to achieve these purpose reference systems were created, systems that are in accordance with the mechanical axes and the anatomic axes of the lower member, which were later generally assembled in a manner that provides an easy customization option

  15. Quantifying the Sources of Kinetic Frustration in Folding Simulations of Small Proteins

    Science.gov (United States)

    2015-01-01

    Experiments and atomistic simulations of polypeptides have revealed structural intermediates that promote or inhibit conformational transitions to the native state during folding. We invoke a concept of “kinetic frustration” to quantify the prevalence and impact of these behaviors on folding rates within a large set of atomistic simulation data for 10 fast-folding proteins, where each protein’s conformational space is represented as a Markov state model of conformational transitions. Our graph theoretic approach addresses what conformational features correlate with folding inhibition and therefore permits comparison among features within a single protein network and also more generally between proteins. Nonnative contacts and nonnative secondary structure formation can thus be quantitatively implicated in inhibiting folding for several of the tested peptides. PMID:25136267

  16. Attractive Hubbard model with disorder and the generalized Anderson theorem

    International Nuclear Information System (INIS)

    Kuchinskii, E. Z.; Kuleeva, N. A.; Sadovskii, M. V.

    2015-01-01

    Using the generalized DMFT+Σ approach, we study the influence of disorder on single-particle properties of the normal phase and the superconducting transition temperature in the attractive Hubbard model. A wide range of attractive potentials U is studied, from the weak coupling region, where both the instability of the normal phase and superconductivity are well described by the BCS model, to the strong-coupling region, where the superconducting transition is due to Bose-Einstein condensation (BEC) of compact Cooper pairs, formed at temperatures much higher than the superconducting transition temperature. We study two typical models of the conduction band with semi-elliptic and flat densities of states, respectively appropriate for three-dimensional and two-dimensional systems. For the semi-elliptic density of states, the disorder influence on all single-particle properties (e.g., density of states) is universal for an arbitrary strength of electronic correlations and disorder and is due to only the general disorder widening of the conduction band. In the case of a flat density of states, universality is absent in the general case, but still the disorder influence is mainly due to band widening, and the universal behavior is restored for large enough disorder. Using the combination of DMFT+Σ and Nozieres-Schmitt-Rink approximations, we study the disorder influence on the superconducting transition temperature T c for a range of characteristic values of U and disorder, including the BCS-BEC crossover region and the limit of strong-coupling. Disorder can either suppress T c (in the weak-coupling region) or significantly increase T c (in the strong-coupling region). However, in all cases, the generalized Anderson theorem is valid and all changes of the superconducting critical temperature are essentially due to only the general disorder widening of the conduction band

  17. Penalized Estimation in Large-Scale Generalized Linear Array Models

    DEFF Research Database (Denmark)

    Lund, Adam; Vincent, Martin; Hansen, Niels Richard

    2017-01-01

    Large-scale generalized linear array models (GLAMs) can be challenging to fit. Computation and storage of its tensor product design matrix can be impossible due to time and memory constraints, and previously considered design matrix free algorithms do not scale well with the dimension of the para......Large-scale generalized linear array models (GLAMs) can be challenging to fit. Computation and storage of its tensor product design matrix can be impossible due to time and memory constraints, and previously considered design matrix free algorithms do not scale well with the dimension...... of the parameter vector. A new design matrix free algorithm is proposed for computing the penalized maximum likelihood estimate for GLAMs, which, in particular, handles nondifferentiable penalty functions. The proposed algorithm is implemented and available via the R package glamlasso. It combines several ideas...

  18. A Unified Bayesian Inference Framework for Generalized Linear Models

    Science.gov (United States)

    Meng, Xiangming; Wu, Sheng; Zhu, Jiang

    2018-03-01

    In this letter, we present a unified Bayesian inference framework for generalized linear models (GLM) which iteratively reduces the GLM problem to a sequence of standard linear model (SLM) problems. This framework provides new perspectives on some established GLM algorithms derived from SLM ones and also suggests novel extensions for some other SLM algorithms. Specific instances elucidated under such framework are the GLM versions of approximate message passing (AMP), vector AMP (VAMP), and sparse Bayesian learning (SBL). It is proved that the resultant GLM version of AMP is equivalent to the well-known generalized approximate message passing (GAMP). Numerical results for 1-bit quantized compressed sensing (CS) demonstrate the effectiveness of this unified framework.

  19. A Non-Gaussian Spatial Generalized Linear Latent Variable Model

    KAUST Repository

    Irincheeva, Irina

    2012-08-03

    We consider a spatial generalized linear latent variable model with and without normality distributional assumption on the latent variables. When the latent variables are assumed to be multivariate normal, we apply a Laplace approximation. To relax the assumption of marginal normality in favor of a mixture of normals, we construct a multivariate density with Gaussian spatial dependence and given multivariate margins. We use the pairwise likelihood to estimate the corresponding spatial generalized linear latent variable model. The properties of the resulting estimators are explored by simulations. In the analysis of an air pollution data set the proposed methodology uncovers weather conditions to be a more important source of variability than air pollution in explaining all the causes of non-accidental mortality excluding accidents. © 2012 International Biometric Society.

  20. Bodies Folded in Migrant Crypts

    DEFF Research Database (Denmark)

    Galis, Vasilis; Tzokas, Spyros; Tympas, Aristotle

    2016-01-01

    , and to performing mobility in general. Dis/ability and migration have not been associated in the literature. We adopt an analytical symmetry between humans and non-humans, in this case between bodies and crypts. By suggesting an infected, ambivalent, and hybrid approach to the human subject, the body......This article considers media narratives that suggest that hiding in trucks, buses, and other vehicles to cross borders has, in fact, been a common practice in the context of migration to, and within, Europe. We aim to problematize how the tension between the materiality of bordering practices...... and human migrants generates a dis/abled subject. In this context, dis/ability may be a cause or consequence of migration, both in physical/material (the folding of bodies in the crypt) and cultural/semiotic terms, and may become a barrier to accessing protection, to entering and/or crossing a country...

  1. Treatment of cloud radiative effects in general circulation models

    Energy Technology Data Exchange (ETDEWEB)

    Wang, W.C.; Dudek, M.P.; Liang, X.Z.; Ding, M. [State Univ. of New York, Albany, NY (United States)] [and others

    1996-04-01

    We participate in the Atmospheric Radiation Measurement (ARM) program with two objectives: (1) to improve the general circulation model (GCM) cloud/radiation treatment with a focus on cloud verticle overlapping and layer cloud optical properties, and (2) to study the effects of cloud/radiation-climate interaction on GCM climate simulations. This report summarizes the project progress since the Fourth ARM Science Team meeting February 28-March 4, 1994, in Charleston, South Carolina.

  2. Generalized isothermal models with strange equation of state

    Indian Academy of Sciences (India)

    intention to study the Einstein–Maxwell system with a linear equation of state with ... It is our intention to model the interior of a dense realistic star with a general ... The definition m(r) = 1. 2. ∫ r. 0 ω2ρ(ω)dω. (14) represents the mass contained within a radius r which is a useful physical quantity. The mass function (14) has ...

  3. Classification images and bubbles images in the generalized linear model.

    Science.gov (United States)

    Murray, Richard F

    2012-07-09

    Classification images and bubbles images are psychophysical tools that use stimulus noise to investigate what features people use to make perceptual decisions. Previous work has shown that classification images can be estimated using the generalized linear model (GLM), and here I show that this is true for bubbles images as well. Expressing the two approaches in terms of a single statistical model clarifies their relationship to one another, makes it possible to measure classification images and bubbles images simultaneously, and allows improvements developed for one method to be used with the other.

  4. Generalized model for Memristor-based Wien family oscillators

    KAUST Repository

    Talukdar, Abdul Hafiz Ibne

    2012-07-23

    In this paper, we report the unconventional characteristics of Memristor in Wien oscillators. Generalized mathematical models are developed to analyze four members of the Wien family using Memristors. Sustained oscillation is reported for all types though oscillating resistance and time dependent poles are present. We have also proposed an analytical model to estimate the desired amplitude of oscillation before the oscillation starts. These Memristor-based oscillation results, presented for the first time, are in good agreement with simulation results. © 2011 Elsevier Ltd.

  5. A generalization of the bond fluctuation model to viscoelastic environments

    International Nuclear Information System (INIS)

    Fritsch, Christian C

    2014-01-01

    A lattice-based simulation method for polymer diffusion in a viscoelastic medium is presented. This method combines the eight-site bond fluctuation model with an algorithm for the simulation of fractional Brownian motion on the lattice. The method applies to unentangled self-avoiding chains and is probed for anomalous diffusion exponents α between 0.7 and 1.0. The simulation results are in very good agreement with the predictions of the generalized Rouse model of a self-avoiding chain polymer in a viscoelastic medium. (paper)

  6. Structural dynamic analysis with generalized damping models analysis

    CERN Document Server

    Adhikari , Sondipon

    2013-01-01

    Since Lord Rayleigh introduced the idea of viscous damping in his classic work ""The Theory of Sound"" in 1877, it has become standard practice to use this approach in dynamics, covering a wide range of applications from aerospace to civil engineering. However, in the majority of practical cases this approach is adopted more for mathematical convenience than for modeling the physics of vibration damping. Over the past decade, extensive research has been undertaken on more general ""non-viscous"" damping models and vibration of non-viscously damped systems. This book, along with a related book

  7. Energy spectra of odd nuclei in the generalized model

    Directory of Open Access Journals (Sweden)

    I. O. Korzh

    2015-04-01

    Full Text Available Based on the generalized nuclear model, energy spectra of the odd nuclei of such elements as 25Mg, 41K, and 65Cu are determined, and the structure of wave functions of these nuclei in the excited and normal states is studied. High quality in determining the energy spectra is possible due to the accurate calculations of all elements of the energy matrix. It is demonstrated that the structure of the wave functions so determined provides the possibility to more accurately select the nuclear model and the method for calculating the nucleon cross-sections of the inelastic scattering of nucleons by odd nuclei.

  8. Regularization Paths for Generalized Linear Models via Coordinate Descent

    Directory of Open Access Journals (Sweden)

    Jerome Friedman

    2010-02-01

    Full Text Available We develop fast algorithms for estimation of generalized linear models with convex penalties. The models include linear regression, two-class logistic regression, and multi- nomial regression problems while the penalties include ℓ1 (the lasso, ℓ2 (ridge regression and mixtures of the two (the elastic net. The algorithms use cyclical coordinate descent, computed along a regularization path. The methods can handle large problems and can also deal efficiently with sparse features. In comparative timings we find that the new algorithms are considerably faster than competing methods.

  9. Pairing correlations in a generalized Hubbard model for the cuprates

    Science.gov (United States)

    Arrachea, Liliana; Aligia, A. A.

    2000-04-01

    Using numerical diagonalization of a 4×4 cluster, we calculate on-site s, extended-s, and dx2-y2 pairing correlation functions (PCF's) in an effective generalized Hubbard model for the cuprates, with nearest-neighbor correlated hopping and next-nearest-neighbor hopping t'. The vertex contributions to the PCF's are significantly enhanced, relative to the t-t'-U model. The behavior of the PCF's and their vertex contributions, and signatures of anomalous flux quantization, indicate superconductivity in the d-wave channel for moderate doping and in the s-wave channel for high doping and small U.

  10. dx2-y2 superconductivity in a generalized Hubbard model

    Science.gov (United States)

    Arrachea, Liliana; Aligia, A. A.

    1999-01-01

    We consider an extended Hubbard model with nearest-neighbor correlated hopping and next-nearest-neighbor hopping t' obtained as an effective model for cuprate superconductors. Using a generalized Hartree-Fock BCS approximation, we find that for high enough t' and doping, antiferromagnetism is destroyed and the system exhibits d-wave superconductivity. Near optimal doping we consider the effect of antiferromagnetic spin fluctuations on the normal self-energy using a phenomenological susceptibility. The resulting superconducting critical temperature as a function of doping is in good agreement with experiment.

  11. Pairing Correlations in a Generalized Hubbard Model for the Cuprates

    OpenAIRE

    Arrachea, L.; Aligia, A.

    1999-01-01

    Using numerical diagonalization of a 4x4 cluster, we calculate on-site s, extended s and d pairing correlation functions (PCF) in an effective generalized Hubbard model for the cuprates, with nearest-neighbor correlated hopping and next nearest-neighbor hopping t'. The vertex contributions (VC) to the PCF are significantly enhanced, relative to the t-t'-U model. The behavior of the PCF and their VC, and signatures of anomalous flux quantization, indicate superconductivity in the d-wave channe...

  12. The linear model and hypothesis a general unifying theory

    CERN Document Server

    Seber, George

    2015-01-01

    This book provides a concise and integrated overview of hypothesis testing in four important subject areas, namely linear and nonlinear models, multivariate analysis, and large sample theory. The approach used is a geometrical one based on the concept of projections and their associated idempotent matrices, thus largely avoiding the need to involve matrix ranks. It is shown that all the hypotheses encountered are either linear or asymptotically linear, and that all the underlying models used are either exactly or asymptotically linear normal models. This equivalence can be used, for example, to extend the concept of orthogonality in the analysis of variance to other models, and to show that the asymptotic equivalence of the likelihood ratio, Wald, and Score (Lagrange Multiplier) hypothesis tests generally applies.

  13. Contextual interactions in a generalized energy model of complex cells.

    Science.gov (United States)

    Dellen, Babette K; Clark, John W; Wessel, Ralf

    2009-01-01

    We propose a generalized energy model of complex cells to describe modulatory contextual influences on the responses of neurons in the primary visual cortex (V1). Many orientation-selective cells in V1 respond to contrast of orientation and motion of stimuli exciting the classical receptive field (CRF) and the non-CRF, or surround. In the proposed model, a central spatiotemporal filter, defining the CRF, is nonlinearly combined with a spatiotemporal filter extending into the non-CRF. These filters are assumed to describe simple-cell responses, while the nonlinear combination of their responses describes the responses of complex cells. This mathematical operation accounts for the inherent nonlinearity of complex cells, such as phase independence and frequency doubling, and for nonlinear interactions between stimuli in the CRF and surround of the cell, including sensitivity to feature contrast. If only the CRF of the generalized complex cell is stimulated by a drifting grating, the model reduces to the standard energy model. The theoretical predictions of the model are supported by computer simulations and compared with experimental data from V1.

  14. Returning to the fold

    Science.gov (United States)

    2016-03-01

    This month marks ten years since the general principles of DNA origami were established, a technique that changed the field of DNA nanotechnology and that promises new physical and biomedical applications.

  15. A generalized mechanical model for suture interfaces of arbitrary geometry

    Science.gov (United States)

    Li, Yaning; Ortiz, Christine; Boyce, Mary C.

    2013-04-01

    Suture interfaces with a triangular wave form commonly found in nature have recently been shown to exhibit exceptional mechanical behavior, where geometric parameters such as amplitude, frequency, and hierarchy can be used to nonlinearly tailor and amplify mechanical properties. In this study, using the principle of complementary virtual work, we formulate a generalized, composite mechanical model for arbitrarily-shaped interdigitating suture interfaces in order to more broadly investigate the influence of wave-form geometry on load transmission, deformation mechanisms, anisotropy, and stiffness, strength, and toughness of the suture interface for tensile and shear loading conditions. The application of this suture interface model is exemplified for the case of the general trapezoidal wave-form. Expressions for the in-plane stiffness, strength and fracture toughness and failure mechanisms are derived as nonlinear functions of shape factor β (which characterizes the general trapezoidal shape as triangular, trapezoidal, rectangular or anti-trapezoidal), the wavelength/amplitude ratio, the interface width/wavelength ratio, and the stiffness and strength ratios of the skeletal/interfacial phases. These results provide guidelines for choosing and tailoring interface geometry to optimize the mechanical performance in resisting different loads. The presented model provides insights into the relation between the mechanical function and the morphological diversity of suture interface geometries observed in natural systems.

  16. Border Collision Bifurcations in a Generalized Model of Population Dynamics

    Directory of Open Access Journals (Sweden)

    Lilia M. Ladino

    2016-01-01

    Full Text Available We analyze the dynamics of a generalized discrete time population model of a two-stage species with recruitment and capture. This generalization, which is inspired by other approaches and real data that one can find in literature, consists in considering no restriction for the value of the two key parameters appearing in the model, that is, the natural death rate and the mortality rate due to fishing activity. In the more general case the feasibility of the system has been preserved by posing opportune formulas for the piecewise map defining the model. The resulting two-dimensional nonlinear map is not smooth, though continuous, as its definition changes as any border is crossed in the phase plane. Hence, techniques from the mathematical theory of piecewise smooth dynamical systems must be applied to show that, due to the existence of borders, abrupt changes in the dynamic behavior of population sizes and multistability emerge. The main novelty of the present contribution with respect to the previous ones is that, while using real data, richer dynamics are produced, such as fluctuations and multistability. Such new evidences are of great interest in biology since new strategies to preserve the survival of the species can be suggested.

  17. Building multiclass classifiers for remote homology detection and fold recognition

    Directory of Open Access Journals (Sweden)

    Karypis George

    2006-10-01

    Full Text Available Abstract Background Protein remote homology detection and fold recognition are central problems in computational biology. Supervised learning algorithms based on support vector machines are currently one of the most effective methods for solving these problems. These methods are primarily used to solve binary classification problems and they have not been extensively used to solve the more general multiclass remote homology prediction and fold recognition problems. Results We present a comprehensive evaluation of a number of methods for building SVM-based multiclass classification schemes in the context of the SCOP protein classification. These methods include schemes that directly build an SVM-based multiclass model, schemes that employ a second-level learning approach to combine the predictions generated by a set of binary SVM-based classifiers, and schemes that build and combine binary classifiers for various levels of the SCOP hierarchy beyond those defining the target classes. Conclusion Analyzing the performance achieved by the different approaches on four different datasets we show that most of the proposed multiclass SVM-based classification approaches are quite effective in solving the remote homology prediction and fold recognition problems and that the schemes that use predictions from binary models constructed for ancestral categories within the SCOP hierarchy tend to not only lead to lower error rates but also reduce the number of errors in which a superfamily is assigned to an entirely different fold and a fold is predicted as being from a different SCOP class. Our results also show that the limited size of the training data makes it hard to learn complex second-level models, and that models of moderate complexity lead to consistently better results.

  18. A general mixture model for sediment laden flows

    Science.gov (United States)

    Liang, Lixin; Yu, Xiping; Bombardelli, Fabián

    2017-09-01

    A mixture model for general description of sediment-laden flows is developed based on an Eulerian-Eulerian two-phase flow theory, with the aim at gaining computational speed in the prediction, but preserving the accuracy of the complete two-fluid model. The basic equations of the model include the mass and momentum conservation equations for the sediment-water mixture, and the mass conservation equation for sediment. However, a newly-obtained expression for the slip velocity between phases allows for the computation of the sediment motion, without the need of solving the momentum equation for sediment. The turbulent motion is represented for both the fluid and the particulate phases. A modified k-ε model is used to describe the fluid turbulence while an algebraic model is adopted for turbulent motion of particles. A two-dimensional finite difference method based on the SMAC scheme was used to numerically solve the mathematical model. The model is validated through simulations of fluid and suspended sediment motion in steady open-channel flows, both in equilibrium and non-equilibrium states, as well as in oscillatory flows. The computed sediment concentrations, horizontal velocity and turbulent kinetic energy of the mixture are all shown to be in good agreement with available experimental data, and importantly, this is done at a fraction of the computational efforts required by the complete two-fluid model.

  19. A general modeling framework for describing spatially structured population dynamics

    Science.gov (United States)

    Sample, Christine; Fryxell, John; Bieri, Joanna; Federico, Paula; Earl, Julia; Wiederholt, Ruscena; Mattsson, Brady; Flockhart, Tyler; Nicol, Sam; Diffendorfer, James E.; Thogmartin, Wayne E.; Erickson, Richard A.; Norris, D. Ryan

    2017-01-01

    Variation in movement across time and space fundamentally shapes the abundance and distribution of populations. Although a variety of approaches model structured population dynamics, they are limited to specific types of spatially structured populations and lack a unifying framework. Here, we propose a unified network-based framework sufficiently novel in its flexibility to capture a wide variety of spatiotemporal processes including metapopulations and a range of migratory patterns. It can accommodate different kinds of age structures, forms of population growth, dispersal, nomadism and migration, and alternative life-history strategies. Our objective was to link three general elements common to all spatially structured populations (space, time and movement) under a single mathematical framework. To do this, we adopt a network modeling approach. The spatial structure of a population is represented by a weighted and directed network. Each node and each edge has a set of attributes which vary through time. The dynamics of our network-based population is modeled with discrete time steps. Using both theoretical and real-world examples, we show how common elements recur across species with disparate movement strategies and how they can be combined under a unified mathematical framework. We illustrate how metapopulations, various migratory patterns, and nomadism can be represented with this modeling approach. We also apply our network-based framework to four organisms spanning a wide range of life histories, movement patterns, and carrying capacities. General computer code to implement our framework is provided, which can be applied to almost any spatially structured population. This framework contributes to our theoretical understanding of population dynamics and has practical management applications, including understanding the impact of perturbations on population size, distribution, and movement patterns. By working within a common framework, there is less chance

  20. A general modeling framework for describing spatially structured population dynamics.

    Science.gov (United States)

    Sample, Christine; Fryxell, John M; Bieri, Joanna A; Federico, Paula; Earl, Julia E; Wiederholt, Ruscena; Mattsson, Brady J; Flockhart, D T Tyler; Nicol, Sam; Diffendorfer, Jay E; Thogmartin, Wayne E; Erickson, Richard A; Norris, D Ryan

    2018-01-01

    Variation in movement across time and space fundamentally shapes the abundance and distribution of populations. Although a variety of approaches model structured population dynamics, they are limited to specific types of spatially structured populations and lack a unifying framework. Here, we propose a unified network-based framework sufficiently novel in its flexibility to capture a wide variety of spatiotemporal processes including metapopulations and a range of migratory patterns. It can accommodate different kinds of age structures, forms of population growth, dispersal, nomadism and migration, and alternative life-history strategies. Our objective was to link three general elements common to all spatially structured populations (space, time and movement) under a single mathematical framework. To do this, we adopt a network modeling approach. The spatial structure of a population is represented by a weighted and directed network. Each node and each edge has a set of attributes which vary through time. The dynamics of our network-based population is modeled with discrete time steps. Using both theoretical and real-world examples, we show how common elements recur across species with disparate movement strategies and how they can be combined under a unified mathematical framework. We illustrate how metapopulations, various migratory patterns, and nomadism can be represented with this modeling approach. We also apply our network-based framework to four organisms spanning a wide range of life histories, movement patterns, and carrying capacities. General computer code to implement our framework is provided, which can be applied to almost any spatially structured population. This framework contributes to our theoretical understanding of population dynamics and has practical management applications, including understanding the impact of perturbations on population size, distribution, and movement patterns. By working within a common framework, there is less chance

  1. Fault-related-folding structures and reflection seismic sections. Study by seismic modeling and balanced cross section; Danso ga kaizaisuru shukyoku kozo no keitai to jishin tansa danmen. 2. Seismic modeling oyobi balanced cross section ni yoru study

    Energy Technology Data Exchange (ETDEWEB)

    Tamagawa, T.; Matsuoka, T. [Japan Petroleum Exploration Corp., Tokyo (Japan); Tsukui, R. [Japan National Oil Corp., Tokyo (Japan). Technology Research Center

    1997-05-27

    It occasionally happens that there exists a part where reflection near the thrust is not clearly observed in a thrust zone seismic survey cross section. For the effective interpretation of such an occurrence, the use of geological structures as well as the reflected pattern is effective. When the velocity structures for a fold structure having a listric fault caused anticline (unidirectionally inclined with a backlimb, without a forelimb) and for a fault propagation fold are involved, a wrong interpretation may be made since they look alike in reflection wave pattern despite their difference in geological structure. In the concept of balanced cross section, a check is performed, when the stratum after deformation is recovered to the time of deposition, as to whether the geologic stratum area is conserved without excess or shortage. An excess or shortage occurs if there is an error in the model, and this shows that the fault surface or fold structure is not correctly reflected. Positive application of geological knowledge is required in the processing and interpreting of data from a seismic survey. 6 refs., 6 figs.

  2. General

    Indian Academy of Sciences (India)

    Page S20: NMR compound 4i. Page S22: NMR compound 4j. General: Chemicals were purchased from Fluka, Merck and Aldrich Chemical Companies. All the products were characterized by comparison of their IR, 1H NMR and 13C NMR spectroscopic data and their melting points with reported values. General procedure ...

  3. Fracture zones constrained by neutral surfaces in a fault-related fold: Insights from the Kelasu tectonic zone, Kuqa Depression

    Science.gov (United States)

    Sun, Shuai; Hou, Guiting; Zheng, Chunfang

    2017-11-01

    Stress variation associated with folding is one of the controlling factors in the development of tectonic fractures, however, little attention has been paid to the influence of neutral surfaces during folding on fracture distribution in a fault-related fold. In this study, we take the Cretaceous Bashijiqike Formation in the Kuqa Depression as an example and analyze the distribution of tectonic fractures in fault-related folds by core observation and logging data analysis. Three fracture zones are identified in a fault-related fold: a tensile zone, a transition zone and a compressive zone, which may be constrained by two neutral surfaces of fold. Well correlation reveals that the tensile zone and the transition zone reach the maximum thickness at the fold hinge and get thinner in the fold limbs. A 2D viscoelastic stress field model of a fault-related fold was constructed to further investigate the mechanism of fracturing. Statistical and numerical analysis reveal that the tensile zone and the transition zone become thicker with decreasing interlimb angle. Stress variation associated with folding is the first level of control over the general pattern of fracture distribution while faulting is a secondary control over the development of local fractures in a fault-related fold.

  4. Generalized in vitro-in vivo relationship (IVIVR model based on artificial neural networks

    Directory of Open Access Journals (Sweden)

    Mendyk A

    2013-03-01

    Full Text Available Aleksander Mendyk,1 Pawel Tuszynski,1 Sebastian Polak,2 Renata Jachowicz1 1Department of Pharmaceutical Technology and Biopharmaceutics, 2Department of Social Pharmacy, Faculty of Pharmacy, Jagiellonian University Medical College, Kraków, Poland Background: The aim of this study was to develop a generalized in vitro-in vivo relationship (IVIVR model based on in vitro dissolution profiles together with quantitative and qualitative composition of dosage formulations as covariates. Such a model would be of substantial aid in the early stages of development of a pharmaceutical formulation, when no in vivo results are yet available and it is impossible to create a classical in vitro-in vivo correlation (IVIVC/IVIVR. Methods: Chemoinformatics software was used to compute the molecular descriptors of drug substances (ie, active pharmaceutical ingredients and excipients. The data were collected from the literature. Artificial neural networks were used as the modeling tool. The training process was carried out using the 10-fold cross-validation technique. Results: The database contained 93 formulations with 307 inputs initially, and was later limited to 28 in a course of sensitivity analysis. The four best models were introduced into the artificial neural network ensemble. Complete in vivo profiles were predicted accurately for 37.6% of the formulations. Conclusion: It has been shown that artificial neural networks can be an effective predictive tool for constructing IVIVR in an integrated generalized model for various formulations. Because IVIVC/IVIVR is classically conducted for 2–4 formulations and with a single active pharmaceutical ingredient, the approach described here is unique in that it incorporates various active pharmaceutical ingredients and dosage forms into a single model. Thus, preliminary IVIVC/IVIVR can be available without in vivo data, which is impossible using current IVIVC/IVIVR procedures. Keywords: artificial neural networks

  5. Generalized in vitro-in vivo relationship (IVIVR) model based on artificial neural networks.

    Science.gov (United States)

    Mendyk, Aleksander; Tuszyński, Paweł K; Polak, Sebastian; Jachowicz, Renata

    2013-01-01

    The aim of this study was to develop a generalized in vitro-in vivo relationship (IVIVR) model based on in vitro dissolution profiles together with quantitative and qualitative composition of dosage formulations as covariates. Such a model would be of substantial aid in the early stages of development of a pharmaceutical formulation, when no in vivo results are yet available and it is impossible to create a classical in vitro-in vivo correlation (IVIVC)/IVIVR. Chemoinformatics software was used to compute the molecular descriptors of drug substances (ie, active pharmaceutical ingredients) and excipients. The data were collected from the literature. Artificial neural networks were used as the modeling tool. The training process was carried out using the 10-fold cross-validation technique. The database contained 93 formulations with 307 inputs initially, and was later limited to 28 in a course of sensitivity analysis. The four best models were introduced into the artificial neural network ensemble. Complete in vivo profiles were predicted accurately for 37.6% of the formulations. It has been shown that artificial neural networks can be an effective predictive tool for constructing IVIVR in an integrated generalized model for various formulations. Because IVIVC/IVIVR is classically conducted for 2-4 formulations and with a single active pharmaceutical ingredient, the approach described here is unique in that it incorporates various active pharmaceutical ingredients and dosage forms into a single model. Thus, preliminary IVIVC/IVIVR can be available without in vivo data, which is impossible using current IVIVC/IVIVR procedures.

  6. Reshocks, rarefactions, and the generalized Layzer model for hydrodynamic instabilities

    Energy Technology Data Exchange (ETDEWEB)

    Mikaelian, K O

    2008-06-10

    We report numerical simulations and analytic modeling of shock tube experiments on Rayleigh-Taylor and Richtmyer-Meshkov instabilities. We examine single interfaces of the type A/B where the incident shock is initiated in A and the transmitted shock proceeds into B. Examples are He/air and air/He. In addition, we study finite-thickness or double-interface A/B/A configurations like air/SF{sub 6}/air gas-curtain experiments. We first consider conventional shock tubes that have a 'fixed' boundary: A solid endwall which reflects the transmitted shock and reshocks the interface(s). Then we focus on new experiments with a 'free' boundary--a membrane disrupted mechanically or by the transmitted shock, sending back a rarefaction towards the interface(s). Complex acceleration histories are achieved, relevant for Inertial Confinement Fusion implosions. We compare our simulation results with a generalized Layzer model for two fluids with time-dependent densities, and derive a new freeze-out condition whereby accelerating and compressive forces cancel each other out. Except for the recently reported failures of the Layzer model, the generalized Layzer model and hydrocode simulations for reshocks and rarefactions agree well with each other, and remain to be verified experimentally.

  7. Consensus-based training and assessment model for general surgery.

    Science.gov (United States)

    Szasz, P; Louridas, M; de Montbrun, S; Harris, K A; Grantcharov, T P

    2016-05-01

    Surgical education is becoming competency-based with the implementation of in-training milestones. Training guidelines should reflect these changes and determine the specific procedures for such milestone assessments. This study aimed to develop a consensus view regarding operative procedures and tasks considered appropriate for junior and senior trainees, and the procedures that can be used as technical milestone assessments for trainee progression in general surgery. A Delphi process was followed where questionnaires were distributed to all 17 Canadian general surgery programme directors. Items were ranked on a 5-point Likert scale, with consensus defined as Cronbach's α of at least 0·70. Items rated 4 or above on the 5-point Likert scale by 80 per cent of the programme directors were included in the models. Two Delphi rounds were completed, with 14 programme directors taking part in round one and 11 in round two. The overall consensus was high (Cronbach's α = 0·98). The training model included 101 unique procedures and tasks, 24 specific to junior trainees, 68 specific to senior trainees, and nine appropriate to all. The assessment model included four procedures. A system of operative procedures and tasks for junior- and senior-level trainees has been developed along with an assessment model for trainee progression. These can be used as milestones in competency-based assessments. © 2016 BJS Society Ltd Published by John Wiley & Sons Ltd.

  8. Generalized linear mixed model for segregation distortion analysis.

    Science.gov (United States)

    Zhan, Haimao; Xu, Shizhong

    2011-11-11

    Segregation distortion is a phenomenon that the observed genotypic frequencies of a locus fall outside the expected Mendelian segregation ratio. The main cause of segregation distortion is viability selection on linked marker loci. These viability selection loci can be mapped using genome-wide marker information. We developed a generalized linear mixed model (GLMM) under the liability model to jointly map all viability selection loci of the genome. Using a hierarchical generalized linear mixed model, we can handle the number of loci several times larger than the sample size. We used a dataset from an F(2) mouse family derived from the cross of two inbred lines to test the model and detected a major segregation distortion locus contributing 75% of the variance of the underlying liability. Replicated simulation experiments confirm that the power of viability locus detection is high and the false positive rate is low. Not only can the method be used to detect segregation distortion loci, but also used for mapping quantitative trait loci of disease traits using case only data in humans and selected populations in plants and animals.

  9. Gyral Folding Pattern Analysis via Surface Profiling

    Science.gov (United States)

    Li, Kaiming; Guo, Lei; Li, Gang; Nie, Jingxin; Faraco, Carlos; Cui, Guangbin; Zhao, Qun; Miller, L. Stephen; Liu, Tianming

    2010-01-01

    Folding is an essential shape characteristic of the human cerebral cortex. Descriptors of cortical folding patterns have been studied for decades. However, many previous studies are either based on local shape descriptors such as curvature, or based on global descriptors such as gyrification index or spherical wavelets. This paper proposes a gyrus-scale folding pattern analysis technique via cortical surface profiling. Firstly, we sample the cortical surface into 2D profiles and model them using a power function. This step provides both the flexibility of representing arbitrary shape by profiling and the compactness of representing shape by parametric modeling. Secondly, based on the estimated model parameters, we extract affine-invariant features on the cortical surface, and apply the affinity propagation clustering algorithm to parcellate the cortex into cortical regions with strict hierarchy and smooth transitions among them. Finally, a second-round surface profiling is performed on the parcellated cortical surface, and the number of hinges is detected to describe the gyral folding pattern. We have applied the surface profiling method to two normal brain datasets and a Schizophrenia patient dataset. The experimental results demonstrate that the proposed method can accurately classify human gyri into 2-hinge, 3-hinge and 4-hinge patterns. The distribution of these folding patterns on brain lobes and the relationship between fiber density and gyral folding patterns are further investigated. Results from the Schizophrenia dataset are consistent with commonly found abnormality in former studies by others, which demonstrates the potential clinical applications of the proposed technique. PMID:20472071

  10. Profile local linear estimation of generalized semiparametric regression model for longitudinal data.

    Science.gov (United States)

    Sun, Yanqing; Sun, Liuquan; Zhou, Jie

    2013-07-01

    This paper studies the generalized semiparametric regression model for longitudinal data where the covariate effects are constant for some and time-varying for others. Different link functions can be used to allow more flexible modelling of longitudinal data. The nonparametric components of the model are estimated using a local linear estimating equation and the parametric components are estimated through a profile estimating function. The method automatically adjusts for heterogeneity of sampling times, allowing the sampling strategy to depend on the past sampling history as well as possibly time-dependent covariates without specifically model such dependence. A [Formula: see text]-fold cross-validation bandwidth selection is proposed as a working tool for locating an appropriate bandwidth. A criteria for selecting the link function is proposed to provide better fit of the data. Large sample properties of the proposed estimators are investigated. Large sample pointwise and simultaneous confidence intervals for the regression coefficients are constructed. Formal hypothesis testing procedures are proposed to check for the covariate effects and whether the effects are time-varying. A simulation study is conducted to examine the finite sample performances of the proposed estimation and hypothesis testing procedures. The methods are illustrated with a data example.

  11. A generalized and parameterized interference model for cognitive radio networks

    KAUST Repository

    Mahmood, Nurul Huda

    2011-06-01

    For meaningful co-existence of cognitive radios with primary system, it is imperative that the cognitive radio system is aware of how much interference it generates at the primary receivers. This can be done through statistical modeling of the interference as perceived at the primary receivers. In this work, we propose a generalized model for the interference generated by a cognitive radio network, in the presence of small and large scale fading, at a primary receiver located at the origin. We then demonstrate how this model can be used to estimate the impact of cognitive radio transmission on the primary receiver in terms of different outage probabilities. Finally, our analytical findings are validated through some selected computer-based simulations. © 2011 IEEE.

  12. Three General Theoretical Models in Sociology: An Articulated ?(Disunity?

    Directory of Open Access Journals (Sweden)

    Thaís García-Pereiro

    2015-01-01

    Full Text Available After merely a brief, comparative reconstruction of the three most general theoretical models underlying contemporary Sociology (atomic, systemic, and fluid it becomes necessary to review the question about the unity or plurality of Sociology, which is the main objective of this paper. To do so, the basic terms of the question are firstly updated by following the hegemonic trends in current studies of science. Secondly the convergences and divergences among the three models discussed are shown. Following some additional discussion, the conclusion is reached that contemporary Sociology is not unitary, and need not be so. It is plural, but its plurality is limited and articulated by those very models. It may therefore be portrayed as integrated and commensurable, to the extent that a partial and unstable (disunity may be said to exist in Sociology, which is not too far off from what happens in the natural sciences.

  13. Analysis of Robust Quasi-deviances for Generalized Linear Models

    Directory of Open Access Journals (Sweden)

    Eva Cantoni

    2004-04-01

    Full Text Available Generalized linear models (McCullagh and Nelder 1989 are a popular technique for modeling a large variety of continuous and discrete data. They assume that the response variables Yi , for i = 1, . . . , n, come from a distribution belonging to the exponential family, such that E[Yi ] = ?i and V[Yi ] = V (?i , and that ?i = g(?i = xiT?, where ? ? IR p is the vector of parameters, xi ? IR p, and g(. is the link function. The non-robustness of the maximum likelihood and the maximum quasi-likelihood estimators has been studied extensively in the literature. For model selection, the classical analysis-of-deviance approach shares the same bad robustness properties. To cope with this, Cantoni and Ronchetti (2001 propose a robust approach based on robust quasi-deviance functions for estimation and variable selection. We refer to that paper for a deeper discussion and the review of the literature.

  14. Generalized Information Matrix Tests for Detecting Model Misspecification

    Directory of Open Access Journals (Sweden)

    Richard M. Golden

    2016-11-01

    Full Text Available Generalized Information Matrix Tests (GIMTs have recently been used for detecting the presence of misspecification in regression models in both randomized controlled trials and observational studies. In this paper, a unified GIMT framework is developed for the purpose of identifying, classifying, and deriving novel model misspecification tests for finite-dimensional smooth probability models. These GIMTs include previously published as well as newly developed information matrix tests. To illustrate the application of the GIMT framework, we derived and assessed the performance of new GIMTs for binary logistic regression. Although all GIMTs exhibited good level and power performance for the larger sample sizes, GIMT statistics with fewer degrees of freedom and derived using log-likelihood third derivatives exhibited improved level and power performance.

  15. Generalized transport model for phase transition with memory

    International Nuclear Information System (INIS)

    Chen, Chi; Ciucci, Francesco

    2013-01-01

    A general model for phenomenological transport in phase transition is derived, which extends Jäckle and Frisch model of phase transition with memory and the Cahn–Hilliard model. In addition to including interfacial energy to account for the presence of interfaces, we introduce viscosity and relaxation contributions, which result from incorporating memory effect into the driving potential. Our simulation results show that even without interfacial energy term, the viscous term can lead to transient diffuse interfaces. From the phase transition induced hysteresis, we discover different energy dissipation mechanism for the interfacial energy and the viscosity effect. In addition, by combining viscosity and interfacial energy, we find that if the former dominates, then the concentration difference across the phase boundary is reduced; conversely, if the interfacial energy is greater then this difference is enlarged.

  16. Topics in conformal invariance and generalized sigma models

    International Nuclear Information System (INIS)

    Bernardo, L.M.; Lawrence Berkeley National Lab., CA

    1997-05-01

    This thesis consists of two different parts, having in common the fact that in both, conformal invariance plays a central role. In the first part, the author derives conditions for conformal invariance, in the large N limit, and for the existence of an infinite number of commuting classical conserved quantities, in the Generalized Thirring Model. The treatment uses the bosonized version of the model. Two different approaches are used to derive conditions for conformal invariance: the background field method and the Hamiltonian method based on an operator algebra, and the agreement between them is established. The author constructs two infinite sets of non-local conserved charges, by specifying either periodic or open boundary conditions, and he finds the Poisson Bracket algebra satisfied by them. A free field representation of the algebra satisfied by the relevant dynamical variables of the model is also presented, and the structure of the stress tensor in terms of free fields (and free currents) is studied in detail. In the second part, the author proposes a new approach for deriving the string field equations from a general sigma model on the world sheet. This approach leads to an equation which combines some of the attractive features of both the renormalization group method and the covariant beta function treatment of the massless excitations. It has the advantage of being covariant under a very general set of both local and non-local transformations in the field space. The author applies it to the tachyon, massless and first massive level, and shows that the resulting field equations reproduce the correct spectrum of a left-right symmetric closed bosonic string

  17. A generalized formulation of the dynamic Smagorinsky model

    Directory of Open Access Journals (Sweden)

    Urs Schaefer-Rolffs

    2017-04-01

    Full Text Available A generalized formulation of the Dynamic Smagorinsky Model (DSM is proposed as a versatile turbulent momentum diffusion scheme for Large-Eddy Simulations. The difference to previous versions of the DSM is a modified test filter range that can be chosen independently from the resolution scale to separate the impact of the test filter on the simulated flow from the impact of the resolution. The generalized DSM (gDSM in a two-dimensional version is validated in a verification study as a horizontal momentum diffusion scheme with the Kühlungsborn Mechanistic General Circulation Model at high resolution (wavenumber 330 without hyperdiffusion. Three-day averaged results applying three different test filters in the macro-turbulent inertial range are presented and compared with analogous simulations where the standard DSM is used instead. The comparison of the different filters results in all cases in similar globally averaged Smagorinsky parameters cS≃0.35$c_S\\simeq0.35$ and horizontal kinetic energy spectra. Hence, the basic assumption of scale invariance underlying the application of the gDSM to parameterize atmospheric turbulence is justified. In addition, the smallest resolved scales contain less energy when the gDSM is applied, thus increasing the stability of the simulation.

  18. Applications of Skew Models Using Generalized Logistic Distribution

    Directory of Open Access Journals (Sweden)

    Pushpa Narayan Rathie

    2016-04-01

    Full Text Available We use the skew distribution generation procedure proposed by Azzalini [Scand. J. Stat., 1985, 12, 171–178] to create three new probability distribution functions. These models make use of normal, student-t and generalized logistic distribution, see Rathie and Swamee [Technical Research Report No. 07/2006. Department of Statistics, University of Brasilia: Brasilia, Brazil, 2006]. Expressions for the moments about origin are derived. Graphical illustrations are also provided. The distributions derived in this paper can be seen as generalizations of the distributions given by Nadarajah and Kotz [Acta Appl. Math., 2006, 91, 1–37]. Applications with unimodal and bimodal data are given to illustrate the applicability of the results derived in this paper. The applications include the analysis of the following data sets: (a spending on public education in various countries in 2003; (b total expenditure on health in 2009 in various countries and (c waiting time between eruptions of the Old Faithful Geyser in the Yellow Stone National Park, Wyoming, USA. We compare the fit of the distributions introduced in this paper with the distributions given by Nadarajah and Kotz [Acta Appl. Math., 2006, 91, 1–37]. The results show that our distributions, in general, fit better the data sets. The general R codes for fitting the distributions introduced in this paper are given in Appendix A.

  19. Identifying model error in metabolic flux analysis - a generalized least squares approach.

    Science.gov (United States)

    Sokolenko, Stanislav; Quattrociocchi, Marco; Aucoin, Marc G

    2016-09-13

    The estimation of intracellular flux through traditional metabolic flux analysis (MFA) using an overdetermined system of equations is a well established practice in metabolic engineering. Despite the continued evolution of the methodology since its introduction, there has been little focus on validation and identification of poor model fit outside of identifying "gross measurement error". The growing complexity of metabolic models, which are increasingly generated from genome-level data, has necessitated robust validation that can directly assess model fit. In this work, MFA calculation is framed as a generalized least squares (GLS) problem, highlighting the applicability of the common t-test for model validation. To differentiate between measurement and model error, we simulate ideal flux profiles directly from the model, perturb them with estimated measurement error, and compare their validation to real data. Application of this strategy to an established Chinese Hamster Ovary (CHO) cell model shows how fluxes validated by traditional means may be largely non-significant due to a lack of model fit. With further simulation, we explore how t-test significance relates to calculation error and show that fluxes found to be non-significant have 2-4 fold larger error (if measurement uncertainty is in the 5-10 % range). The proposed validation method goes beyond traditional detection of "gross measurement error" to identify lack of fit between model and data. Although the focus of this work is on t-test validation and traditional MFA, the presented framework is readily applicable to other regression analysis methods and MFA formulations.

  20. General Business Model Patterns for Local Energy Management Concepts

    International Nuclear Information System (INIS)

    Facchinetti, Emanuele; Sulzer, Sabine

    2016-01-01

    The transition toward a more sustainable global energy system, significantly relying on renewable energies and decentralized energy systems, requires a deep reorganization of the energy sector. The way how energy services are generated, delivered, and traded is expected to be very different in the coming years. Business model innovation is recognized as a key driver for the successful implementation of the energy turnaround. This work contributes to this topic by introducing a heuristic methodology easing the identification of general business model patterns best suited for Local Energy Management concepts such as Energy Hubs. A conceptual framework characterizing the Local Energy Management business model solution space is developed. Three reference business model patterns providing orientation across the defined solution space are identified, analyzed, and compared. Through a market review, a number of successfully implemented innovative business models have been analyzed and allocated within the defined solution space. The outcomes of this work offer to potential stakeholders a starting point and guidelines for the business model innovation process, as well as insights for policy makers on challenges and opportunities related to Local Energy Management concepts.

  1. General business model patterns for Local Energy Management concepts

    Directory of Open Access Journals (Sweden)

    Emanuele eFacchinetti

    2016-03-01

    Full Text Available The transition towards a more sustainable global energy system, significantly relying on renewable energies and decentralized energy systems, requires a deep reorganization of the energy sector. The way how energy services are generated, delivered and traded is expected to be very different in the coming years. Business model innovation is recognized as a key driver for the successful implementation of the energy turnaround. This work contributes to this topic by introducing a heuristic methodology easing the identification of general business model patterns best suited for Local Energy Management concepts such as Energy Hubs. A conceptual framework characterizing the Local Energy Management business model solution space is developed. Three reference business model patterns providing orientation across the defined solution space are identified, analyzed and compared. Through a market review a number of successfully implemented innovative business models have been analyzed and allocated within the defined solution space. The outcomes of this work offer to potential stakeholders a starting point and guidelines for the business model innovation process, as well as insights for policy makers on challenges and opportunities related to Local Energy Management concepts.

  2. A generalized logarithmic image processing model based on the gigavision sensor model.

    Science.gov (United States)

    Deng, Guang

    2012-03-01

    The logarithmic image processing (LIP) model is a mathematical theory providing generalized linear operations for image processing. The gigavision sensor (GVS) is a new imaging device that can be described by a statistical model. In this paper, by studying these two seemingly unrelated models, we develop a generalized LIP (GLIP) model. With the LIP model being its special case, the GLIP model not only provides new insights into the LIP model but also defines new image representations and operations for solving general image processing problems that are not necessarily related to the GVS. A new parametric LIP model is also developed. To illustrate the application of the new scalar multiplication operation, we propose an energy-preserving algorithm for tone mapping, which is a necessary step in image dehazing. By comparing with results using two state-of-the-art algorithms, we show that the new scalar multiplication operation is an effective tool for tone mapping.

  3. Generalized Magnetic Field Effects in Burgers' Nanofluid Model.

    Directory of Open Access Journals (Sweden)

    M M Rashidi

    Full Text Available Analysis has been conducted to present the generalized magnetic field effects on the flow of a Burgers' nanofluid over an inclined wall. Mathematical modelling for hydro-magnetics reveals that the term "[Formula: see text]" is for the Newtonian model whereas the generalized magnetic field term (as mentioned in Eq 4 is for the Burgers' model which is incorporated in the current analysis to get the real insight of the problem for hydro-magnetics. Brownian motion and thermophoresis phenomenon are presented to analyze the nanofluidics for the non-Newtonian fluid. Mathematical analysis is completed in the presence of non-uniform heat generation/absorption. The constructed set of partial differential system is converted into coupled nonlinear ordinary differential system by employing the suitable transformations. Homotopy approach is employed to construct the analytical solutions which are shown graphically for sundr5y parameters including Deborah numbers, magnetic field, thermophoresis, Brownian motion and non-uniform heat generation/absorption. A comparative study is also presented showing the comparison of present results with an already published data.

  4. Generalized martingale model of the uncertainty evolution of streamflow forecasts

    Science.gov (United States)

    Zhao, Tongtiegang; Zhao, Jianshi; Yang, Dawen; Wang, Hao

    2013-07-01

    Streamflow forecasts are dynamically updated in real-time, thus facilitating a process of forecast uncertainty evolution. Forecast uncertainty generally decreases over time and as more hydrologic information becomes available. The process of forecasting and uncertainty updating can be described by the martingale model of forecast evolution (MMFE), which formulates the total forecast uncertainty of a streamflow in one future period as the sum of forecast improvements in the intermediate periods. This study tests the assumptions, i.e., unbiasedness, Gaussianity, temporal independence, and stationarity, of MMFE using real-world streamflow forecast data. The results show that (1) real-world forecasts can be biased and tend to underestimate the actual streamflow, and (2) real-world forecast uncertainty is non-Gaussian and heavy-tailed. Based on these statistical tests, this study proposes a generalized martingale model GMMFE for the simulation of biased and non-Gaussian forecast uncertainties. The new model combines the normal quantile transform (NQT) with MMFE to formulate the uncertainty evolution of real-world streamflow forecasts. Reservoir operations based on a synthetic forecast by GMMFE illustrates that applications of streamflow forecasting facilitate utility improvements and that special attention should be focused on the statistical distribution of forecast uncertainty.

  5. Introducing Charge Hydration Asymmetry into the Generalized Born Model.

    Science.gov (United States)

    Mukhopadhyay, Abhishek; Aguilar, Boris H; Tolokh, Igor S; Onufriev, Alexey V

    2014-04-08

    The effect of charge hydration asymmetry (CHA)-non-invariance of solvation free energy upon solute charge inversion-is missing from the standard linear response continuum electrostatics. The proposed charge hydration asymmetric-generalized Born (CHA-GB) approximation introduces this effect into the popular generalized Born (GB) model. The CHA is added to the GB equation via an analytical correction that quantifies the specific propensity of CHA of a given water model; the latter is determined by the charge distribution within the water model. Significant variations in CHA seen in explicit water (TIP3P, TIP4P-Ew, and TIP5P-E) free energy calculations on charge-inverted "molecular bracelets" are closely reproduced by CHA-GB, with the accuracy similar to models such as SEA and 3D-RISM that go beyond the linear response. Compared against reference explicit (TIP3P) electrostatic solvation free energies, CHA-GB shows about a 40% improvement in accuracy over the canonical GB, tested on a diverse set of 248 rigid small neutral molecules (root mean square error, rmse = 0.88 kcal/mol for CHA-GB vs 1.24 kcal/mol for GB) and 48 conformations of amino acid analogs (rmse = 0.81 kcal/mol vs 1.26 kcal/mol). CHA-GB employs a novel definition of the dielectric boundary that does not subsume the CHA effects into the intrinsic atomic radii. The strategy leads to finding a new set of intrinsic atomic radii optimized for CHA-GB; these radii show physically meaningful variation with the atom type, in contrast to the radii set optimized for GB. Compared to several popular radii sets used with the original GB model, the new radii set shows better transferability between different classes of molecules.

  6. A general relativistic hydrostatic model for a galaxy

    International Nuclear Information System (INIS)

    Hojman, R.; Pena, L.; Zamorano, N.

    1991-08-01

    The existence of huge amounts of mass laying at the center of some galaxies has been inferred by data gathered at different wavelengths. It seems reasonable then, to incorporate general relativity in the study of these objects. A general relativistic hydrostatic model for a galaxy is studied. We assume that the galaxy is dominated by the dark mass except at the nucleus, where the luminous matter prevails. It considers four different concentric spherically symmetric regions, properly matched and with a specific equation of state for each of them. It yields a slowly raising orbital velocity for a test particle moving in the background gravitational field of the dark matter region. In this sense we think of this model as representing a spiral galaxy. The dependence of the mass on the radius in cluster and field spiral galaxies published recently, can be used to fix the size of the inner luminous core. A vanishing pressure at the edge of the galaxy and the assumption of hydrostatic equilibrium everywhere generates a jump in the density and the orbital velocity at the shell enclosing the galaxy. This is a prediction of this model. The ratio between the size core and the shells introduced here are proportional to their densities. In this sense the model is scale invariant. It can be used to reproduce a galaxy or the central region of a galaxy. We have also compared our results with those obtained with the Newtonian isothermal sphere. The luminosity is not included in our model as an extra variable in the determination of the orbital velocity. (author). 29 refs, 10 figs

  7. 3D fold growth rates in transpressional tectonic settings

    Science.gov (United States)

    Frehner, Marcel

    2015-04-01

    Geological folds are inherently three-dimensional (3D) structures; hence, they also grow in 3D. In this study, fold growth in all three dimensions is quantified numerically using a finite-element algorithm for simulating deformation of Newtonian media in 3D. The presented study is an extension and generalization of the work presented in Frehner (2014), which only considered unidirectional layer-parallel compression. In contrast, the full range from strike slip settings (i.e., simple shear) to unidirectional layer-parallel compression is considered here by varying the convergence angle of the boundary conditions; hence the results are applicable to general transpressional tectonic settings. Only upright symmetrical single-layer fold structures are considered. The horizontal higher-viscous layer exhibits an initial point-like perturbation. Due to the mixed pure- and simple shear boundary conditions a mechanical buckling instability grows from this perturbation in all three dimensions, described by: Fold amplification (vertical growth): Fold amplification describes the growth from a fold shape with low limb-dip angle to a shape with higher limb-dip angle. Fold elongation (growth parallel to fold axis): Fold elongation describes the growth from a dome-shaped (3D) structure to a more cylindrical fold (2D). Sequential fold growth (growth perpendicular to fold axial plane): Sequential fold growth describes the growth of secondary (and further) folds adjacent to the initial isolated fold. The term 'lateral fold growth' is used as an umbrella term for both fold elongation and sequential fold growth. In addition, the orientation of the fold axis is tracked as a function of the convergence angle. Even though the absolute values of all three growth rates are markedly reduced with increasing simple-shear component at the boundaries, the general pattern of the quantified fold growth under the studied general-shear boundary conditions is surprisingly similar to the end

  8. A generalized methodology to characterize composite materials for pyrolysis models

    Science.gov (United States)

    McKinnon, Mark B.

    The predictive capabilities of computational fire models have improved in recent years such that models have become an integral part of many research efforts. Models improve the understanding of the fire risk of materials and may decrease the number of expensive experiments required to assess the fire hazard of a specific material or designed space. A critical component of a predictive fire model is the pyrolysis sub-model that provides a mathematical representation of the rate of gaseous fuel production from condensed phase fuels given a heat flux incident to the material surface. The modern, comprehensive pyrolysis sub-models that are common today require the definition of many model parameters to accurately represent the physical description of materials that are ubiquitous in the built environment. Coupled with the increase in the number of parameters required to accurately represent the pyrolysis of materials is the increasing prevalence in the built environment of engineered composite materials that have never been measured or modeled. The motivation behind this project is to develop a systematic, generalized methodology to determine the requisite parameters to generate pyrolysis models with predictive capabilities for layered composite materials that are common in industrial and commercial applications. This methodology has been applied to four common composites in this work that exhibit a range of material structures and component materials. The methodology utilizes a multi-scale experimental approach in which each test is designed to isolate and determine a specific subset of the parameters required to define a material in the model. Data collected in simultaneous thermogravimetry and differential scanning calorimetry experiments were analyzed to determine the reaction kinetics, thermodynamic properties, and energetics of decomposition for each component of the composite. Data collected in microscale combustion calorimetry experiments were analyzed to

  9. A GENERALIZATION OF TRADITIONAL KANO MODEL FOR CUSTOMER REQUIREMENTS ANALYSIS

    Directory of Open Access Journals (Sweden)

    Renáta Turisová

    2015-07-01

    Full Text Available Purpose: The theory of attractiveness determines the relationship between the technically achieved and customer perceived quality of product attributes. The most frequently used approach in the theory of attractiveness is the implementation of Kano‘s model. There exist a lot of generalizations of that model which take into consideration various aspects and approaches focused on understanding the customer preferences and identification of his priorities for a selling  product. The aim of this article is to outline another possible generalization of Kano‘s model.Methodology/Approach: The traditional Kano’s model captures the nonlinear relationship between reached attributes of quality and customer requirements. The individual attributes of quality are divided into three main categories: must-be, one-dimensional, attractive quality and into two side categories: indifferent and reverse quality. The well selling product has to contain the must-be attribute. It should contain as many one-dimensional attributes as possible. If there are also supplementary attractive attributes, it means that attractiveness of the entire product, from the viewpoint of the customer, nonlinearly sharply rises what has a direct positive impact on a decision of potential customer when purchasing the product. In this article, we show that inclusion of individual quality attributes of a product to the mentioned categories depends, among other things, also on costs on life cycle of the product, respectively on a price of the product on the market.Findings: In practice, we are often encountering the inclusion of products into different price categories: lower, middle and upper class. For a certain type of products the category is either directly declared by a producer (especially in automotive industry, or is determined by a customer by means of assessment of available market prices. To each of those groups of a products different customer expectations can be assigned

  10. Generalized Laplacian eigenmaps for modeling and tracking human motions.

    Science.gov (United States)

    Martinez-del-Rincon, Jesus; Lewandowski, Michal; Nebel, Jean-Christophe; Makris, Dimitrios

    2014-09-01

    This paper presents generalized Laplacian eigenmaps, a novel dimensionality reduction approach designed to address stylistic variations in time series. It generates compact and coherent continuous spaces whose geometry is data-driven. This paper also introduces graph-based particle filter, a novel methodology conceived for efficient tracking in low dimensional space derived from a spectral dimensionality reduction method. Its strengths are a propagation scheme, which facilitates the prediction in time and style, and a noise model coherent with the manifold, which prevents divergence, and increases robustness. Experiments show that a combination of both techniques achieves state-of-the-art performance for human pose tracking in underconstrained scenarios.

  11. Estimation and variable selection for generalized additive partial linear models

    KAUST Repository

    Wang, Li

    2011-08-01

    We study generalized additive partial linear models, proposing the use of polynomial spline smoothing for estimation of nonparametric functions, and deriving quasi-likelihood based estimators for the linear parameters. We establish asymptotic normality for the estimators of the parametric components. The procedure avoids solving large systems of equations as in kernel-based procedures and thus results in gains in computational simplicity. We further develop a class of variable selection procedures for the linear parameters by employing a nonconcave penalized quasi-likelihood, which is shown to have an asymptotic oracle property. Monte Carlo simulations and an empirical example are presented for illustration. © Institute of Mathematical Statistics, 2011.

  12. Computable general equilibrium model fiscal year 2013 capability development report

    Energy Technology Data Exchange (ETDEWEB)

    Edwards, Brian Keith [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Rivera, Michael Kelly [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Boero, Riccardo [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2016-05-17

    This report documents progress made on continued developments of the National Infrastructure Simulation and Analysis Center (NISAC) Computable General Equilibrium Model (NCGEM), developed in fiscal year 2012. In fiscal year 2013, NISAC the treatment of the labor market and tests performed with the model to examine the properties of the solutions computed by the model. To examine these, developers conducted a series of 20 simulations for 20 U.S. States. Each of these simulations compared an economic baseline simulation with an alternative simulation that assumed a 20-percent reduction in overall factor productivity in the manufacturing industries of each State. Differences in the simulation results between the baseline and alternative simulations capture the economic impact of the reduction in factor productivity. While not every State is affected in precisely the same way, the reduction in manufacturing industry productivity negatively affects the manufacturing industries in each State to an extent proportional to the reduction in overall factor productivity. Moreover, overall economic activity decreases when manufacturing sector productivity is reduced. Developers ran two additional simulations: (1) a version of the model for the State of Michigan, with manufacturing divided into two sub-industries (automobile and other vehicle manufacturing as one sub-industry and the rest of manufacturing as the other subindustry); and (2) a version of the model for the United States, divided into 30 industries. NISAC conducted these simulations to illustrate the flexibility of industry definitions in NCGEM and to examine the simulation properties of in more detail.

  13. Scaling of Precipitation Extremes Modelled by Generalized Pareto Distribution

    Science.gov (United States)

    Rajulapati, C. R.; Mujumdar, P. P.

    2017-12-01

    Precipitation extremes are often modelled with data from annual maximum series or peaks over threshold series. The Generalized Pareto Distribution (GPD) is commonly used to fit the peaks over threshold series. Scaling of precipitation extremes from larger time scales to smaller time scales when the extremes are modelled with the GPD is burdened with difficulties arising from varying thresholds for different durations. In this study, the scale invariance theory is used to develop a disaggregation model for precipitation extremes exceeding specified thresholds. A scaling relationship is developed for a range of thresholds obtained from a set of quantiles of non-zero precipitation of different durations. The GPD parameters and exceedance rate parameters are modelled by the Bayesian approach and the uncertainty in scaling exponent is quantified. A quantile based modification in the scaling relationship is proposed for obtaining the varying thresholds and exceedance rate parameters for shorter durations. The disaggregation model is applied to precipitation datasets of Berlin City, Germany and Bangalore City, India. From both the applications, it is observed that the uncertainty in the scaling exponent has a considerable effect on uncertainty in scaled parameters and return levels of shorter durations.

  14. NLO electroweak corrections in general scalar singlet models

    Science.gov (United States)

    Costa, Raul; Sampaio, Marco O. P.; Santos, Rui

    2017-07-01

    If no new physics signals are found, in the coming years, at the Large Hadron Collider Run-2, an increase in precision of the Higgs couplings measurements will shift the discussion to the effects of higher order corrections. In Beyond the Standard Model (BSM) theories this may become the only tool to probe new physics. Extensions of the Standard Model (SM) with several scalar singlets may address several of its problems, namely to explain dark matter, the matter-antimatter asymmetry, or to improve the stability of the SM up to the Planck scale. In this work we propose a general framework to calculate one loop-corrections to the propagators and to the scalar field vacuum expectation values of BSM models with an arbitrary number of scalar singlets. We then apply our method to a real and to a complex scalar singlet models. We assess the importance of the one-loop radiative corrections first by computing them for a tree level mixing sum constraint, and then for the main Higgs production process gg → H. We conclude that, for the currently allowed parameter space of these models, the corrections can be at most a few percent. Notably, a non-zero correction can survive when dark matter is present, in the SM-like limit of the Higgs couplings to other SM particles.

  15. Detection of Fraudulent Transactions Through a Generalized Mixed Linear Models

    Directory of Open Access Journals (Sweden)

    Jackelyne Gómez–Restrepo

    2012-12-01

    Full Text Available The detection of bank frauds is a topic which many financial sector companieshave invested time and resources into. However, finding patterns inthe methodologies used to commit fraud in banks is a job that primarily involvesintimate knowledge of customer behavior, with the idea of isolatingthose transactions which do not correspond to what the client usually does.Thus, the solutions proposed in literature tend to focus on identifying outliersor groups, but fail to analyse each client or forecast fraud. This paperevaluates the implementation of a generalized linear model to detect fraud.With this model, unlike conventional methods, we consider the heterogeneityof customers. We not only generate a global model, but also a model for eachcustomer which describes the behavior of each one according to their transactionalhistory and previously detected fraudulent transactions. In particular,a mixed logistic model is used to estimate the probability that a transactionis fraudulent, using information that has been taken by the banking systemsin different moments of time.

  16. GENERALIZATION TECHNIQUE FOR 2D+SCALE DHE DATA MODEL

    Directory of Open Access Journals (Sweden)

    H. Karim

    2016-10-01

    Full Text Available Different users or applications need different scale model especially in computer application such as game visualization and GIS modelling. Some issues has been raised on fulfilling GIS requirement of retaining the details while minimizing the redundancy of the scale datasets. Previous researchers suggested and attempted to add another dimension such as scale or/and time into a 3D model, but the implementation of scale dimension faces some problems due to the limitations and availability of data structures and data models. Nowadays, various data structures and data models have been proposed to support variety of applications and dimensionality but lack research works has been conducted in terms of supporting scale dimension. Generally, the Dual Half Edge (DHE data structure was designed to work with any perfect 3D spatial object such as buildings. In this paper, we attempt to expand the capability of the DHE data structure toward integration with scale dimension. The description of the concept and implementation of generating 3D-scale (2D spatial + scale dimension for the DHE data structure forms the major discussion of this paper. We strongly believed some advantages such as local modification and topological element (navigation, query and semantic information in scale dimension could be used for the future 3D-scale applications.

  17. Generalized constraint neural network regression model subject to linear priors.

    Science.gov (United States)

    Qu, Ya-Jun; Hu, Bao-Gang

    2011-12-01

    This paper is reports an extension of our previous investigations on adding transparency to neural networks. We focus on a class of linear priors (LPs), such as symmetry, ranking list, boundary, monotonicity, etc., which represent either linear-equality or linear-inequality priors. A generalized constraint neural network-LPs (GCNN-LPs) model is studied. Unlike other existing modeling approaches, the GCNN-LP model exhibits its advantages. First, any LP is embedded by an explicitly structural mode, which may add a higher degree of transparency than using a pure algorithm mode. Second, a direct elimination and least squares approach is adopted to study the model, which produces better performances in both accuracy and computational cost over the Lagrange multiplier techniques in experiments. Specific attention is paid to both "hard (strictly satisfied)" and "soft (weakly satisfied)" constraints for regression problems. Numerical investigations are made on synthetic examples as well as on the real-world datasets. Simulation results demonstrate the effectiveness of the proposed modeling approach in comparison with other existing approaches.

  18. Evolutionary optimization of protein folding.

    Directory of Open Access Journals (Sweden)

    Cédric Debès

    Full Text Available Nature has shaped the make up of proteins since their appearance, [Formula: see text]3.8 billion years ago. However, the fundamental drivers of structural change responsible for the extraordinary diversity of proteins have yet to be elucidated. Here we explore if protein evolution affects folding speed. We estimated folding times for the present-day catalog of protein domains directly from their size-modified contact order. These values were mapped onto an evolutionary timeline of domain appearance derived from a phylogenomic analysis of protein domains in 989 fully-sequenced genomes. Our results show a clear overall increase of folding speed during evolution, with known ultra-fast downhill folders appearing rather late in the timeline. Remarkably, folding optimization depends on secondary structure. While alpha-folds showed a tendency to fold faster throughout evolution, beta-folds exhibited a trend of folding time increase during the last [Formula: see text]1.5 billion years that began during the "big bang" of domain combinations. As a consequence, these domain structures are on average slow folders today. Our results suggest that fast and efficient folding of domains shaped the universe of protein structure. This finding supports the hypothesis that optimization of the kinetic and thermodynamic accessibility of the native fold reduces protein aggregation propensities that hamper cellular functions.

  19. Unified understanding of folding and binding mechanisms of globular and intrinsically disordered proteins.

    Science.gov (United States)

    Arai, Munehito

    2018-01-06

    Extensive experimental and theoretical studies have advanced our understanding of the mechanisms of folding and binding of globular proteins, and coupled folding and binding of intrinsically disordered proteins (IDPs). The forces responsible for conformational changes and binding are common in both proteins; however, these mechanisms have been separately discussed. Here, we attempt to integrate the mechanisms of coupled folding and binding of IDPs, folding of small and multi-subdomain proteins, folding of multimeric proteins, and ligand binding of globular proteins in terms of conformational selection and induced-fit mechanisms as well as the nucleation-condensation mechanism that is intermediate between them. Accumulating evidence has shown that both the rate of conformational change and apparent rate of binding between interacting elements can determine reaction mechanisms. Coupled folding and binding of IDPs occurs mainly by induced-fit because of the slow folding in the free form, while ligand binding of globular proteins occurs mainly by conformational selection because of rapid conformational change. Protein folding can be regarded as the binding of intramolecular segments accompanied by secondary structure formation. Multi-subdomain proteins fold mainly by the induced-fit (hydrophobic collapse) mechanism, as the connection of interacting segments enhances the binding (compaction) rate. Fewer hydrophobic residues in small proteins reduce the intramolecular binding rate, resulting in the nucleation-condensation mechanism. Thus, the folding and binding of globular proteins and IDPs obey the same general principle, suggesting that the coarse-grained, statistical mechanical model of protein folding is promising for a unified theoretical description of all mechanisms.

  20. [Treatment of cloud radiative effects in general circulation models

    International Nuclear Information System (INIS)

    Wang, W.C.

    1993-01-01

    This is a renewal proposal for an on-going project of the Department of Energy (DOE)/Atmospheric Radiation Measurement (ARM) Program. The objective of the ARM Program is to improve the treatment of radiation-cloud in GCMs so that reliable predictions of the timing and magnitude of greenhouse gas-induced global warming and regional responses can be made. The ARM Program supports two research areas: (I) The modeling and analysis of data related to the parameterization of clouds and radiation in general circulation models (GCMs); and (II) the development of advanced instrumentation for both mapping the three-dimensional structure of the atmosphere and high accuracy/precision radiometric observations. The present project conducts research in area (I) and focuses on GCM treatment of cloud life cycle, optical properties, and vertical overlapping. The project has two tasks: (1) Development and Refinement of GCM Radiation-Cloud Treatment Using ARM Data; and (2) Validation of GCM Radiation-Cloud Treatment

  1. A stratiform cloud parameterization for General Circulation Models

    International Nuclear Information System (INIS)

    Ghan, S.J.; Leung, L.R.; Chuang, C.C.; Penner, J.E.; McCaa, J.

    1994-01-01

    The crude treatment of clouds in General Circulation Models (GCMs) is widely recognized as a major limitation in the application of these models to predictions of global climate change. The purpose of this project is to develop a paxameterization for stratiform clouds in GCMs that expresses stratiform clouds in terms of bulk microphysical properties and their subgrid variability. In this parameterization, precipitating cloud species are distinguished from non-precipitating species, and the liquid phase is distinguished from the ice phase. The size of the non-precipitating cloud particles (which influences both the cloud radiative properties and the conversion of non-precipitating cloud species to precipitating species) is determined by predicting both the mass and number concentrations of each species

  2. Convex Relaxations for a Generalized Chan-Vese Model

    KAUST Repository

    Bae, Egil

    2013-01-01

    We revisit the Chan-Vese model of image segmentation with a focus on the encoding with several integer-valued labeling functions. We relate several representations with varying amount of complexity and demonstrate the connection to recent relaxations for product sets and to dual maxflow-based formulations. For some special cases, it can be shown that it is possible to guarantee binary minimizers. While this is not true in general, we show how to derive a convex approximation of the combinatorial problem for more than 4 phases. We also provide a method to avoid overcounting of boundaries in the original Chan-Vese model without departing from the efficient product-set representation. Finally, we derive an algorithm to solve the associated discretized problem, and demonstrate that it allows to obtain good approximations for the segmentation problem with various number of regions. © 2013 Springer-Verlag.

  3. A Chemical Containment Model for the General Purpose Work Station

    Science.gov (United States)

    Flippen, Alexis A.; Schmidt, Gregory K.

    1994-01-01

    Contamination control is a critical safety requirement imposed on experiments flying on board the Spacelab. The General Purpose Work Station, a Spacelab support facility used for life sciences space flight experiments, is designed to remove volatile compounds from its internal airpath and thereby minimize contamination of the Spacelab. This is accomplished through the use of a large, multi-stage filter known as the Trace Contaminant Control System. Many experiments planned for the Spacelab require the use of toxic, volatile fixatives in order to preserve specimens prior to postflight analysis. The NASA-Ames Research Center SLS-2 payload, in particular, necessitated the use of several toxic, volatile compounds in order to accomplish the many inflight experiment objectives of this mission. A model was developed based on earlier theories and calculations which provides conservative predictions of the resultant concentrations of these compounds given various spill scenarios. This paper describes the development and application of this model.

  4. Generalized flux states of the t-J model

    International Nuclear Information System (INIS)

    Nori, F.; Abrahams, E.; Zimanyi, G.T.

    1990-01-01

    We investigate certain generalized flux phases arising in a mean-field approach to the t-J model. First, we establish that the energy of noninteracting electrons moving in a uniform magnetic field has an absolute minimum as a function of the flux at exactly one flux quantum per particle. Using this result, we show that if the hard-core nature of the hole bosons is taken into account, then the slave-boson mean-field approximation for the t-J Hamiltonian allows for a solution where both the spinons and the holons experience an average flux of one flux quantum per particle. This enables them to achieve the lowest possible energy within the manifold of spatially uniform flux states. In the case of the continuum model, this is possible only for certain fractional fillings and we speculate that the system may react to this frustration effect by phase separation

  5. Explicit estimating equations for semiparametric generalized linear latent variable models

    KAUST Repository

    Ma, Yanyuan

    2010-07-05

    We study generalized linear latent variable models without requiring a distributional assumption of the latent variables. Using a geometric approach, we derive consistent semiparametric estimators. We demonstrate that these models have a property which is similar to that of a sufficient complete statistic, which enables us to simplify the estimating procedure and explicitly to formulate the semiparametric estimating equations. We further show that the explicit estimators have the usual root n consistency and asymptotic normality. We explain the computational implementation of our method and illustrate the numerical performance of the estimators in finite sample situations via extensive simulation studies. The advantage of our estimators over the existing likelihood approach is also shown via numerical comparison. We employ the method to analyse a real data example from economics. © 2010 Royal Statistical Society.

  6. A stratiform cloud parameterization for general circulation models

    International Nuclear Information System (INIS)

    Ghan, S.J.; Leung, L.R.; Chuang, C.C.; Penner, J.E.; McCaa, J.

    1994-01-01

    The crude treatment of clouds in general circulation models (GCMs) is widely recognized as a major limitation in applying these models to predictions of global climate change. The purpose of this project is to develop in GCMs a stratiform cloud parameterization that expresses clouds in terms of bulk microphysical properties and their subgrid variability. Various clouds variables and their interactions are summarized. Precipitating cloud species are distinguished from non-precipitating species, and the liquid phase is distinguished from the ice phase. The size of the non-precipitating cloud particles (which influences both the cloud radiative properties and the conversion of non-precipitating cloud species to precipitating species) is determined by predicting both the mass and number concentrations of each species

  7. A more general interacting model of holographic dark energy

    International Nuclear Information System (INIS)

    Yu Fei; Zhang Jingfei; Lu Jianbo; Wang Wei; Gui Yuanxing

    2010-01-01

    So far, there have been no theories or observational data that deny the presence of interaction between dark energy and dark matter. We extend naturally the holographic dark energy (HDE) model, proposed by Granda and Oliveros, in which the dark energy density includes not only the square of the Hubble scale, but also the time derivative of the Hubble scale to the case with interaction and the analytic forms for the cosmic parameters are obtained under the specific boundary conditions. The various behaviors concerning the cosmic expansion depend on the introduced numerical parameters which are also constrained. The more general interacting model inherits the features of the previous ones of HDE, keeping the consistency of the theory.

  8. Non-cylindrical fold growth in the Zagros fold and thrust belt (Kurdistan, NE-Iraq)

    Science.gov (United States)

    Bartl, Nikolaus; Bretis, Bernhard; Grasemann, Bernhard; Lockhart, Duncan

    2010-05-01

    The Zagros mountains extends over 1800 km from Kurdistan in N-Iraq to the Strait of Hormuz in Iran and is one of the world most promising regions for the future hydrocarbon exploration. The Zagros Mountains started to form as a result of the collision between the Eurasian and Arabian Plates, whose convergence began in the Late Cretaceous as part of the Alpine-Himalayan orogenic system. Geodetic and seismological data document that both plates are still converging and that the fold and thrust belt of the Zagros is actively growing. Extensive hydrocarbon exploration mainly focuses on the antiforms of this fold and thrust belt and therefore the growth history of the folds is of great importance. This work investigates by means of structural field work and quantitative geomorphological techniques the progressive fold growth of the Permam, Bana Bawi- and Safeen- Anticlines located in the NE of the city of Erbil in the Kurdistan region of Northern Iraq. This part of the Zagros fold and thrust belt belongs to the so-called Simply Folded Belt, which is dominated by gentle to open folding. Faults or fault related folds have only minor importance. The mechanical anisotropy of the formations consisting of a succession of relatively competent (massive dolomite and limestone) and incompetent (claystone and siltstone) sediments essentially controls the deformation pattern with open to gentle parallel folding of the competent layers and flexural flow folding of the incompetent layers. The characteristic wavelength of the fold trains is around 10 km. Due to faster erosion of the softer rock layers in the folded sequence, the more competent lithologies form sharp ridges with steeply sloping sides along the eroded flanks of the anticlines. Using an ASTER digital elevation model in combination with geological field data we quantified 250 drainage basins along the different limbs of the subcylindrical Permam, Bana Bawi- and Safeen- Anticlines. Geomorphological indices of the drainage

  9. General analysis of dark radiation in sequestered string models

    Energy Technology Data Exchange (ETDEWEB)

    Cicoli, Michele [ICTP,Strada Costiera 11, Trieste 34014 (Italy); Dipartimento di Fisica e Astronomia, Università di Bologna,via Irnerio 46, 40126 Bologna (Italy); INFN, Sezione di Bologna,via Irnerio 46, 40126 Bologna (Italy); Muia, Francesco [Dipartimento di Fisica e Astronomia, Università di Bologna,via Irnerio 46, 40126 Bologna (Italy); INFN, Sezione di Bologna,via Irnerio 46, 40126 Bologna (Italy)

    2015-12-22

    We perform a general analysis of axionic dark radiation produced from the decay of the lightest modulus in the sequestered LARGE Volume Scenario. We discuss several cases depending on the form of the Kähler metric for visible sector matter fields and the mechanism responsible for achieving a de Sitter vacuum. The leading decay channels which determine dark radiation predictions are to hidden sector axions, visible sector Higgses and SUSY scalars depending on their mass. We show that in most of the parameter space of split SUSY-like models squarks and sleptons are heavier than the lightest modulus. Hence dark radiation predictions previously obtained for MSSM-like cases hold more generally also for split SUSY-like cases since the decay channel to SUSY scalars is kinematically forbidden. However the inclusion of string loop corrections to the Kähler potential gives rise to a parameter space region where the decay channel to SUSY scalars opens up, leading to a significant reduction of dark radiation production. In this case, the simplest model with a shift-symmetric Higgs sector can suppress the excess of dark radiation ΔN{sub eff} to values as small as 0.14, in perfect agreement with current experimental bounds. Depending on the exact mass of the SUSY scalars all values in the range 0.14≲ΔN{sub eff}≲1.6 are allowed. Interestingly dark radiation overproduction can be avoided also in the absence of a Giudice-Masiero coupling.

  10. Modeling containment of large wildfires using generalized linear mixed-model analysis

    Science.gov (United States)

    Mark Finney; Isaac C. Grenfell; Charles W. McHugh

    2009-01-01

    Billions of dollars are spent annually in the United States to contain large wildland fires, but the factors contributing to suppression success remain poorly understood. We used a regression model (generalized linear mixed-model) to model containment probability of individual fires, assuming that containment was a repeated-measures problem (fixed effect) and...

  11. Diabatic models with transferrable parameters for generalized chemical reactions

    Science.gov (United States)

    Reimers, Jeffrey R.; McKemmish, Laura K.; McKenzie, Ross H.; Hush, Noel S.

    2017-05-01

    Diabatic models applied to adiabatic electron-transfer theory yield many equations involving just a few parameters that connect ground-state geometries and vibration frequencies to excited-state transition energies and vibration frequencies to the rate constants for electron-transfer reactions, utilizing properties of the conical-intersection seam linking the ground and excited states through the Pseudo Jahn-Teller effect. We review how such simplicity in basic understanding can also be obtained for general chemical reactions. The key feature that must be recognized is that electron-transfer (or hole transfer) processes typically involve one electron (hole) moving between two orbitals, whereas general reactions typically involve two electrons or even four electrons for processes in aromatic molecules. Each additional moving electron leads to new high-energy but interrelated conical-intersection seams that distort the shape of the critical lowest-energy seam. Recognizing this feature shows how conical-intersection descriptors can be transferred between systems, and how general chemical reactions can be compared using the same set of simple parameters. Mathematical relationships are presented depicting how different conical-intersection seams relate to each other, showing that complex problems can be reduced into an effective interaction between the ground-state and a critical excited state to provide the first semi-quantitative implementation of Shaik’s “twin state” concept. Applications are made (i) demonstrating why the chemistry of the first-row elements is qualitatively so different to that of the second and later rows, (ii) deducing the bond-length alternation in hypothetical cyclohexatriene from the observed UV spectroscopy of benzene, (iii) demonstrating that commonly used procedures for modelling surface hopping based on inclusion of only the first-derivative correction to the Born-Oppenheimer approximation are valid in no region of the chemical

  12. Generalized Potential Energy Finite Elements for Modeling Molecular Nanostructures.

    Science.gov (United States)

    Chatzieleftheriou, Stavros; Adendorff, Matthew R; Lagaros, Nikos D

    2016-10-24

    The potential energy of molecules and nanostructures is commonly calculated in the molecular mechanics formalism by superimposing bonded and nonbonded atomic energy terms, i.e. bonds between two atoms, bond angles involving three atoms, dihedral angles involving four atoms, nonbonded terms expressing the Coulomb and Lennard-Jones interactions, etc. In this work a new, generalized numerical simulation is presented for studying the mechanical behavior of three-dimensional nanostructures at the atomic scale. The energy gradient and Hessian matrix of such assemblies are usually computed numerically; a potential energy finite element model is proposed herein where these two components are expressed analytically. In particular, generalized finite elements are developed that express the interactions among atoms in a manner equivalent to that invoked in simulations performed based on the molecular dynamics method. Thus, the global tangent stiffness matrix for any nanostructure is formed as an assembly of the generalized finite elements and is directly equivalent to the Hessian matrix of the potential energy. The advantages of the proposed model are identified in terms of both accuracy and computational efficiency. In the case of popular force fields (e.g., CHARMM), the computation of the Hessian matrix by implementing the proposed method is of the same order as that of the gradient. This analysis can be used to minimize the potential energy of molecular systems under nodal loads in order to derive constitutive laws for molecular systems where the entropy and solvent effects are neglected and can be approximated as solids, such as double stranded DNA nanostructures. In this context, the sequence dependent stretch modulus for some typical base pairs step is calculated.

  13. Designing a Wien Filter Model with General Particle Tracer

    Science.gov (United States)

    Mitchell, John; Hofler, Alicia

    2017-09-01

    The Continuous Electron Beam Accelerator Facility injector employs a beamline component called a Wien filter which is typically used to select charged particles of a certain velocity. The Wien filter is also used to rotate the polarization of a beam for parity violation experiments. The Wien filter consists of perpendicular electric and magnetic fields. The electric field changes the spin orientation, but also imposes a transverse kick which is compensated for by the magnetic field. The focus of this project was to create a simulation of the Wien filter using General Particle Tracer. The results from these simulations were vetted against machine data to analyze the accuracy of the Wien model. Due to the close agreement between simulation and experiment, the data suggest that the Wien filter model is accurate. The model allows a user to input either the desired electric or magnetic field of the Wien filter along with the beam energy as parameters, and is able to calculate the perpendicular field strength required to keep the beam on axis. The updated model will aid in future diagnostic tests of any beamline component downstream of the Wien filter, and allow users to easily calculate the electric and magnetic fields needed for the filter to function properly. Funding support provided by DOE Office of Science's Student Undergraduate Laboratory Internship program.

  14. Singular solitons of generalized Camassa-Holm models

    International Nuclear Information System (INIS)

    Tian Lixin; Sun Lu

    2007-01-01

    Two generalizations of the Camassa-Holm system associated with the singular analysis are proposed for Painleve integrability properties and the extensions of already known analytic solitons. A remarkable feature of the physical model is that it has peakon solution which has peak form. An alternative WTC test which allowed the identifying of such models directly if formulated in terms of inserting a formed ansatz into these models. For the two models have Painleve property, Painleve-Baecklund systems can be constructed through the expansion of solitons about the singularity manifold. By the implementations of Maple, plentiful new type solitonic structures and some kink waves, which are affected by the variation of energy, are explored. If the energy is infinite in finite time, there will be a collapse in soliton systems by direct numerical simulations. Particularly, there are two collapses coexisting in our regular solitons, which occurred around its central regions. Simulation shows that in the bottom of periodic waves arises the non-zero parts of compactons and anti-compactons. We also get floating solitary waves whose amplitude is infinite. In contrary to which a finite-amplitude blow-up soliton is obtained. Periodic blow-ups are found too. Special kinks which have periodic cuspons are derived

  15. General Description of Fission Observables - JEFF Report 24. GEF Model

    International Nuclear Information System (INIS)

    Schmidt, Karl-Heinz; Jurado, Beatriz; Amouroux, Charlotte

    2014-06-01

    The Joint Evaluated Fission and Fusion (JEFF) Project is a collaborative effort among the member countries of the OECD Nuclear Energy Agency (NEA) Data Bank to develop a reference nuclear data library. The JEFF library contains sets of evaluated nuclear data, mainly for fission and fusion applications; it contains a number of different data types, including neutron and proton interaction data, radioactive decay data, fission yield data and thermal scattering law data. The General fission (GEF) model is based on novel theoretical concepts and ideas developed to model low energy nuclear fission. The GEF code calculates fission-fragment yields and associated quantities (e.g. prompt neutron and gamma) for a large range of nuclei and excitation energy. This opens up the possibility of a qualitative step forward to improve further the JEFF fission yields sub-library. This report describes the GEF model which explains the complex appearance of fission observables by universal principles of theoretical models and considerations on the basis of fundamental laws of physics and mathematics. The approach reveals a high degree of regularity and provides a considerable insight into the physics of the fission process. Fission observables can be calculated with a precision that comply with the needs for applications in nuclear technology. The relevance of the approach for examining the consistency of experimental results and for evaluating nuclear data is demonstrated. (authors)

  16. Generalized PSF modeling for optimized quantitation in PET imaging

    Science.gov (United States)

    Ashrafinia, Saeed; Mohy-ud-Din, Hassan; Karakatsanis, Nicolas A.; Jha, Abhinav K.; Casey, Michael E.; Kadrmas, Dan J.; Rahmim, Arman

    2017-06-01

    modeling does not offer optimized PET quantitation, and that PSF overestimation may provide enhanced SUV quantitation. Furthermore, generalized PSF modeling may provide a valuable approach for quantitative tasks such as treatment-response assessment and prognostication.

  17. Equi-Gaussian curvature folding

    Indian Academy of Sciences (India)

    have the same equi-Gaussian curvature 1/a2, where a is the radius of the sphere. Now let f : S2 → Pn be a cellular folding. Then we have the following possibilities: Firstly, there are no cellular foldings f : S2 → Pn, for any n > 3 [2]. Secondly, any cellular folding f : S2 → P3 for which Gf forms a regular graph is equivalent to ...

  18. Complex Environmental Data Modelling Using Adaptive General Regression Neural Networks

    Science.gov (United States)

    Kanevski, Mikhail

    2015-04-01

    The research deals with an adaptation and application of Adaptive General Regression Neural Networks (GRNN) to high dimensional environmental data. GRNN [1,2,3] are efficient modelling tools both for spatial and temporal data and are based on nonparametric kernel methods closely related to classical Nadaraya-Watson estimator. Adaptive GRNN, using anisotropic kernels, can be also applied for features selection tasks when working with high dimensional data [1,3]. In the present research Adaptive GRNN are used to study geospatial data predictability and relevant feature selection using both simulated and real data case studies. The original raw data were either three dimensional monthly precipitation data or monthly wind speeds embedded into 13 dimensional space constructed by geographical coordinates and geo-features calculated from digital elevation model. GRNN were applied in two different ways: 1) adaptive GRNN with the resulting list of features ordered according to their relevancy; and 2) adaptive GRNN applied to evaluate all possible models N [in case of wind fields N=(2^13 -1)=8191] and rank them according to the cross-validation error. In both cases training were carried out applying leave-one-out procedure. An important result of the study is that the set of the most relevant features depends on the month (strong seasonal effect) and year. The predictabilities of precipitation and wind field patterns, estimated using the cross-validation and testing errors of raw and shuffled data, were studied in detail. The results of both approaches were qualitatively and quantitatively compared. In conclusion, Adaptive GRNN with their ability to select features and efficient modelling of complex high dimensional data can be widely used in automatic/on-line mapping and as an integrated part of environmental decision support systems. 1. Kanevski M., Pozdnoukhov A., Timonin V. Machine Learning for Spatial Environmental Data. Theory, applications and software. EPFL Press

  19. General Description of Fission Observables: GEF Model Code

    Science.gov (United States)

    Schmidt, K.-H.; Jurado, B.; Amouroux, C.; Schmitt, C.

    2016-01-01

    The GEF ("GEneral description of Fission observables") model code is documented. It describes the observables for spontaneous fission, neutron-induced fission and, more generally, for fission of a compound nucleus from any other entrance channel, with given excitation energy and angular momentum. The GEF model is applicable for a wide range of isotopes from Z = 80 to Z = 112 and beyond, up to excitation energies of about 100 MeV. The results of the GEF model are compared with fission barriers, fission probabilities, fission-fragment mass- and nuclide distributions, isomeric ratios, total kinetic energies, and prompt-neutron and prompt-gamma yields and energy spectra from neutron-induced and spontaneous fission. Derived properties of delayed neutrons and decay heat are also considered. The GEF model is based on a general approach to nuclear fission that explains a great part of the complex appearance of fission observables on the basis of fundamental laws of physics and general properties of microscopic systems and mathematical objects. The topographic theorem is used to estimate the fission-barrier heights from theoretical macroscopic saddle-point and ground-state masses and experimental ground-state masses. Motivated by the theoretically predicted early localisation of nucleonic wave functions in a necked-in shape, the properties of the relevant fragment shells are extracted. These are used to determine the depths and the widths of the fission valleys corresponding to the different fission channels and to describe the fission-fragment distributions and deformations at scission by a statistical approach. A modified composite nuclear-level-density formula is proposed. It respects some features in the superfluid regime that are in accordance with new experimental findings and with theoretical expectations. These are a constant-temperature behaviour that is consistent with a considerably increased heat capacity and an increased pairing condensation energy that is

  20. A general formulation for a mathematical PEM fuel cell model

    Science.gov (United States)

    Baschuk, J. J.; Li, Xianguo

    A general formulation for a comprehensive fuel cell model, based on the conservation principle is presented. The model formulation includes the electro-chemical reactions, proton migration, and the mass transport of the gaseous reactants and liquid water. Additionally, the model formulation can be applied to all regions of the PEM fuel cell: the bipolar plates, gas flow channels, electrode backing, catalyst, and polymer electrolyte layers. The model considers the PEM fuel cell to be composed of three phases: reactant gas, liquid water, and solid. These three phases can co-exist within the gas flow channels, electrode backing, catalyst, and polymer electrolyte layers. The conservation of mass, momentum, species, and energy are applied to each phase, with the technique of volume averaging being used to incorporate the interactions between the phases as interfacial source terms. In order to avoid problems arising from phase discontinuities, the gas and liquid phases are considered as a mixture. The momentum interactions between the fluid and solid phases are modeled by the Darcy-Forchheimer term. The electro-oxidation of H and CO, the reduction of O, and the heterogeneous oxidation of H and CO are considered in the catalyst layers. Due to the small pore size of the polymer electrolyte layer, the generalized Stefan-Maxwell equations, with the polymer considered as a diffusing species, are used to describe species transport. One consequence of considering the gas and liquid phases as a mixture is that expressions for the velocity of the individual phases relative to the mixture must be developed. In the gas flow channels, the flow is assumed homogeneous, while the Darcy and Schlögl equations are used to describe liquid water transport in the electrode backing and polymer electrolyte layers. Thus, two sets of equations, one for the mixture and another for the solid phase, can be developed to describe the processes occurring within a PEM fuel cell. These equations are in

  1. Extending the linear model with R generalized linear, mixed effects and nonparametric regression models

    CERN Document Server

    Faraway, Julian J

    2005-01-01

    Linear models are central to the practice of statistics and form the foundation of a vast range of statistical methodologies. Julian J. Faraway''s critically acclaimed Linear Models with R examined regression and analysis of variance, demonstrated the different methods available, and showed in which situations each one applies. Following in those footsteps, Extending the Linear Model with R surveys the techniques that grow from the regression model, presenting three extensions to that framework: generalized linear models (GLMs), mixed effect models, and nonparametric regression models. The author''s treatment is thoroughly modern and covers topics that include GLM diagnostics, generalized linear mixed models, trees, and even the use of neural networks in statistics. To demonstrate the interplay of theory and practice, throughout the book the author weaves the use of the R software environment to analyze the data of real examples, providing all of the R commands necessary to reproduce the analyses. All of the ...

  2. Generalized multiplicative error models: Asymptotic inference and empirical analysis

    Science.gov (United States)

    Li, Qian

    This dissertation consists of two parts. The first part focuses on extended Multiplicative Error Models (MEM) that include two extreme cases for nonnegative series. These extreme cases are common phenomena in high-frequency financial time series. The Location MEM(p,q) model incorporates a location parameter so that the series are required to have positive lower bounds. The estimator for the location parameter turns out to be the minimum of all the observations and is shown to be consistent. The second case captures the nontrivial fraction of zero outcomes feature in a series and combines a so-called Zero-Augmented general F distribution with linear MEM(p,q). Under certain strict stationary and moment conditions, we establish a consistency and asymptotic normality of the semiparametric estimation for these two new models. The second part of this dissertation examines the differences and similarities between trades in the home market and trades in the foreign market of cross-listed stocks. We exploit the multiplicative framework to model trading duration, volume per trade and price volatility for Canadian shares that are cross-listed in the New York Stock Exchange (NYSE) and the Toronto Stock Exchange (TSX). We explore the clustering effect, interaction between trading variables, and the time needed for price equilibrium after a perturbation for each market. The clustering effect is studied through the use of univariate MEM(1,1) on each variable, while the interactions among duration, volume and price volatility are captured by a multivariate system of MEM(p,q). After estimating these models by a standard QMLE procedure, we exploit the Impulse Response function to compute the calendar time for a perturbation in these variables to be absorbed into price variance, and use common statistical tests to identify the difference between the two markets in each aspect. These differences are of considerable interest to traders, stock exchanges and policy makers.

  3. A Pacific Ocean general circulation model for satellite data assimilation

    Science.gov (United States)

    Chao, Y.; Halpern, D.; Mechoso, C. R.

    1991-01-01

    A tropical Pacific Ocean General Circulation Model (OGCM) to be used in satellite data assimilation studies is described. The transfer of the OGCM from a CYBER-205 at NOAA's Geophysical Fluid Dynamics Laboratory to a CRAY-2 at NASA's Ames Research Center is documented. Two 3-year model integrations from identical initial conditions but performed on those two computers are compared. The model simulations are very similar to each other, as expected, but the simulations performed with the higher-precision CRAY-2 is smoother than that with the lower-precision CYBER-205. The CYBER-205 and CRAY-2 use 32 and 64-bit mantissa arithmetic, respectively. The major features of the oceanic circulation in the tropical Pacific, namely the North Equatorial Current, the North Equatorial Countercurrent, the South Equatorial Current, and the Equatorial Undercurrent, are realistically produced and their seasonal cycles are described. The OGCM provides a powerful tool for study of tropical oceans and for the assimilation of satellite altimetry data.

  4. General relativity cosmological models without the big bang

    International Nuclear Information System (INIS)

    Rosen, N.

    1985-01-01

    Attention is given to the so-called standard model of the universe in the framework of the general theory of relativity. This model is taken to be homogeneous and isotropic and filled with an ideal fluid characterized by a density and a pressure. Taking into consideration, however, the assumption that the universe began in a singular state, it is found hard to understand why the universe is so nearly homogeneous and isotropic at present for a singularity represents a breakdown of physical laws, and the initial singularity cannot, therefore, predetermine the subsequent symmetries of the universe. The present investigation has the objective to find a way of avoiding this initial singularity, i.e., to look for a cosmological model without the big bang. The idea is proposed that there exists a limiting density of matter of the order of magnitude of the Planck density, and that this was the density of matter at the moment at which the universe began to expand

  5. A generalized model for estimating the energy density of invertebrates

    Science.gov (United States)

    James, Daniel A.; Csargo, Isak J.; Von Eschen, Aaron; Thul, Megan D.; Baker, James M.; Hayer, Cari-Ann; Howell, Jessica; Krause, Jacob; Letvin, Alex; Chipps, Steven R.

    2012-01-01

    Invertebrate energy density (ED) values are traditionally measured using bomb calorimetry. However, many researchers rely on a few published literature sources to obtain ED values because of time and sampling constraints on measuring ED with bomb calorimetry. Literature values often do not account for spatial or temporal variability associated with invertebrate ED. Thus, these values can be unreliable for use in models and other ecological applications. We evaluated the generality of the relationship between invertebrate ED and proportion of dry-to-wet mass (pDM). We then developed and tested a regression model to predict ED from pDM based on a taxonomically, spatially, and temporally diverse sample of invertebrates representing 28 orders in aquatic (freshwater, estuarine, and marine) and terrestrial (temperate and arid) habitats from 4 continents and 2 oceans. Samples included invertebrates collected in all seasons over the last 19 y. Evaluation of these data revealed a significant relationship between ED and pDM (r2  =  0.96, p cost savings compared to traditional bomb calorimetry approaches. This model should prove useful for a wide range of ecological studies because it is unaffected by taxonomic, seasonal, or spatial variability.

  6. Gauge Theory and Calibrated Geometry for Calabi-Yau 4-folds

    Science.gov (United States)

    Cao, Yalong

    This thesis is devoted to the study of gauge theory and calibrated geometry for Calabi-Yau 4-folds. More specifically, our study is along the following five directions. 1. We develop Donaldson-Thomas type theory on Calabi-Yau 4-folds. Let X be a compact complex Calabi-Yau 4-fold. We define Donaldson-Thomas type deformation invariants (DT4 invariants) by studying moduli spaces of solutions to the Donaldson- Thomas equations on X. We also study sheaves counting problems on local Calabi-Yau 4-folds. We relate DT4 invariants of KY to the Donaldson-Thomas invariants of the associated Fano 3-fold Y. When the Calabi-Yau 4-fold is toric, we adapt the virtual localization formula to define the corresponding equivariant DT4 invariants. We also discuss the non-commutative version of DT4 invariants for quivers with relations. Finally, we compute DT4 invariants for certain Calabi-Yau 4-folds when moduli spaces are smooth and find a DT 4/GW correspondence for X. Examples of wall-crossing phenomenon in DT4 theory are also given. 2. Given a complex 4-fold X with an (Calabi-Yau 3-fold) anti-canonical divisor Y, we study relative Donaldson-Thomas invariants for this pair, which are elements in the Donaldson-Thomas cohomologies of Y. We also discuss gluing formulas which relate relative invariants and DT4 invariants for Calabi-Yau 4-folds. 3. We study orientability issues of moduli spaces from gauge theories on Calabi-Yau manifolds. Our results generalize and strengthen those for Donaldson-Thomas theory on Calabi-Yau manifolds of dimensions 3 and 4. We also prove a corresponding result in the relative situation which is relevant to the gluing formula in DT theory. 4. Motivated by Strominger-Yau-Zaslow's mirror symmetry proposal and Kontsevich's homological mirror symmetry conjecture, we study mirror phenomena (in A-model) of certain results from Donaldson-Thomas theory for Calabi-Yau 4-folds. More precisely, we study calibrated geometry in the sense of Harvey-Lawson and Lagrangian

  7. Application of conditional moment tests to model checking for generalized linear models.

    Science.gov (United States)

    Pan, Wei

    2002-06-01

    Generalized linear models (GLMs) are increasingly being used in daily data analysis. However, model checking for GLMs with correlated discrete response data remains difficult. In this paper, through a case study on marginal logistic regression using a real data set, we illustrate the flexibility and effectiveness of using conditional moment tests (CMTs), along with other graphical methods, to do model checking for generalized estimation equation (GEE) analyses. Although CMTs provide an array of powerful diagnostic tests for model checking, they were originally proposed in the econometrics literature and, to our knowledge, have never been applied to GEE analyses. CMTs cover many existing tests, including the (generalized) score test for an omitted covariate, as special cases. In summary, we believe that CMTs provide a class of useful model checking tools.

  8. Spin squeezing in a generalized one-axis twisting model

    Science.gov (United States)

    Jin, Guang-Ri; Liu, Yong-Chun; Liu, Wu-Ming

    2009-07-01

    We investigate the dependence of spin squeezing on the polar angle of the initial coherent spin state |θ0, phi0rang in a generalized one-axis twisting model, where the detuning δ is taken into account. We show explicitly that regardless of δ and phi0, previous results of the ideal one-axis twisting are recovered as long as θ0=π/2. For a small departure of θ0 from π/2, however, the achievable variance (V -)min ~N2/3, which is larger than the ideal case N1/3. We also find that the maximal squeezing time tmin scales as N-5/6. Analytic expressions of (V-)min and tmin are presented and they agree with numerical simulations.

  9. dglars: An R Package to Estimate Sparse Generalized Linear Models

    Directory of Open Access Journals (Sweden)

    Luigi Augugliaro

    2014-09-01

    Full Text Available dglars is a publicly available R package that implements the method proposed in Augugliaro, Mineo, and Wit (2013, developed to study the sparse structure of a generalized linear model. This method, called dgLARS, is based on a differential geometrical extension of the least angle regression method proposed in Efron, Hastie, Johnstone, and Tibshirani (2004. The core of the dglars package consists of two algorithms implemented in Fortran 90 to efficiently compute the solution curve: a predictor-corrector algorithm, proposed in Augugliaro et al. (2013, and a cyclic coordinate descent algorithm, proposed in Augugliaro, Mineo, and Wit (2012. The latter algorithm, as shown here, is significantly faster than the predictor-corrector algorithm. For comparison purposes, we have implemented both algorithms.

  10. A general Bayes weibull inference model for accelerated life testing

    International Nuclear Information System (INIS)

    Dorp, J. Rene van; Mazzuchi, Thomas A.

    2005-01-01

    This article presents the development of a general Bayes inference model for accelerated life testing. The failure times at a constant stress level are assumed to belong to a Weibull distribution, but the specification of strict adherence to a parametric time-transformation function is not required. Rather, prior information is used to indirectly define a multivariate prior distribution for the scale parameters at the various stress levels and the common shape parameter. Using the approach, Bayes point estimates as well as probability statements for use-stress (and accelerated) life parameters may be inferred from a host of testing scenarios. The inference procedure accommodates both the interval data sampling strategy and type I censored sampling strategy for the collection of ALT test data. The inference procedure uses the well-known MCMC (Markov Chain Monte Carlo) methods to derive posterior approximations. The approach is illustrated with an example

  11. Generalized Swept Mid-structure for Polygonal Models

    KAUST Repository

    Martin, Tobias

    2012-05-01

    We introduce a novel mid-structure called the generalized swept mid-structure (GSM) of a closed polygonal shape, and a framework to compute it. The GSM contains both curve and surface elements and has consistent sheet-by-sheet topology, versus triangle-by-triangle topology produced by other mid-structure methods. To obtain this structure, a harmonic function, defined on the volume that is enclosed by the surface, is used to decompose the volume into a set of slices. A technique for computing the 1D mid-structures of these slices is introduced. The mid-structures of adjacent slices are then iteratively matched through a boundary similarity computation and triangulated to form the GSM. This structure respects the topology of the input surface model is a hybrid mid-structure representation. The construction and topology of the GSM allows for local and global simplification, used in further applications such as parameterization, volumetric mesh generation and medical applications.

  12. The review on tessellation origami inspired folded structure

    Science.gov (United States)

    Chu, Chai Chen; Keong, Choong Kok

    2017-10-01

    Existence of folds enhances the load carrying capacity of a folded structure which makes it suitable to be used for application where large open space is required such as large span roof structures and façade. Folded structure is closely related to origami especially the tessellation origami. Tessellation origami provides a folded configuration with facetted surface as a result from repeated folding pattern. Besides that, tessellation origami has flexible folding mechanism that produced a variety of 3-dimensional folded configurations. Despite the direct relationship between fold in origami and folded structure, the idea of origami inspired folded structure is not properly reviewed in the relevant engineering field. Hence, this paper aims to present the current studies from related discipline which has direct relation with application of tessellation origami in folded structure. First, tessellation origami is properly introduced and defined. Then, the review covers the topic on the origami tessellation design suitable for folded structure, its modeling and simulation method, and existing studies and applications of origami as folded structure is presented. The paper also includes the discussion on the current issues related to each topic.

  13. Cohomological Yang-Mills theories on Kähler 3-folds

    NARCIS (Netherlands)

    Hofman, C.; Park, J.-S.

    2000-01-01

    We study topological gauge theories with Nc = (2; 0) supersymmetry based on stable bundles on general Kähler 3-folds. In order to have a theory that is well defined and well behaved, we consider a model based on an extension of the usual holomorphic bundle by including a holomorphic 3-form. The

  14. Bifurcation of self-folded polygonal bilayers

    Science.gov (United States)

    Abdullah, Arif M.; Braun, Paul V.; Hsia, K. Jimmy

    2017-09-01

    Motivated by the self-assembly of natural systems, researchers have investigated the stimulus-responsive curving of thin-shell structures, which is also known as self-folding. Self-folding strategies not only offer possibilities to realize complicated shapes but also promise actuation at small length scales. Biaxial mismatch strain driven self-folding bilayers demonstrate bifurcation of equilibrium shapes (from quasi-axisymmetric doubly curved to approximately singly curved) during their stimulus-responsive morphing behavior. Being a structurally instable, bifurcation could be used to tune the self-folding behavior, and hence, a detailed understanding of this phenomenon is appealing from both fundamental and practical perspectives. In this work, we investigated the bifurcation behavior of self-folding bilayer polygons. For the mechanistic understanding, we developed finite element models of planar bilayers (consisting of a stimulus-responsive and a passive layer of material) that transform into 3D curved configurations. Our experiments with cross-linked Polydimethylsiloxane samples that change shapes in organic solvents confirmed our model predictions. Finally, we explored a design scheme to generate gripper-like architectures by avoiding the bifurcation of stimulus-responsive bilayers. Our research contributes to the broad field of self-assembly as the findings could motivate functional devices across multiple disciplines such as robotics, artificial muscles, therapeutic cargos, and reconfigurable biomedical devices.

  15. Parallelization and improvements of the generalized born model with a simple sWitching function for modern graphics processors.

    Science.gov (United States)

    Arthur, Evan J; Brooks, Charles L

    2016-04-15

    Two fundamental challenges of simulating biologically relevant systems are the rapid calculation of the energy of solvation and the trajectory length of a given simulation. The Generalized Born model with a Simple sWitching function (GBSW) addresses these issues by using an efficient approximation of Poisson-Boltzmann (PB) theory to calculate each solute atom's free energy of solvation, the gradient of this potential, and the subsequent forces of solvation without the need for explicit solvent molecules. This study presents a parallel refactoring of the original GBSW algorithm and its implementation on newly available, low cost graphics chips with thousands of processing cores. Depending on the system size and nonbonded force cutoffs, the new GBSW algorithm offers speed increases of between one and two orders of magnitude over previous implementations while maintaining similar levels of accuracy. We find that much of the algorithm scales linearly with an increase of system size, which makes this water model cost effective for solvating large systems. Additionally, we utilize our GPU-accelerated GBSW model to fold the model system chignolin, and in doing so we demonstrate that these speed enhancements now make accessible folding studies of peptides and potentially small proteins. © 2016 Wiley Periodicals, Inc.

  16. The Internal/External Frame of Reference Model Revisited: Incorporating General Cognitive Ability and General Academic Self-Concept.

    Science.gov (United States)

    Brunner, Martin; Lüdtke, Oliver; Trautwein, Ulrich

    2008-01-01

    The internal/external frame of reference model (I/E model; Marsh, 1986 ) is a highly influential model of self-concept formation, which predicts that domain-specific abilities have positive effects on academic self-concepts in the corresponding domain and negative effects across domains. Investigations of the I/E model do not typically incorporate general cognitive ability or general academic self-concept. This article investigates alternative measurement models for domain-specific and domain-general cognitive abilities and academic self-concepts within an extended I/E model framework using representative data from 25,301 9th-grade students. Empirical support was found for the external validity of a new measurement model for academic self-concepts with respect to key student characteristics (gender, school satisfaction, educational aspirations, domain-specific interests, grades). Moreover, the basic predictions of the I/E model were confirmed, and the new extension of the traditional I/E model permitted meaningful relations to be drawn between domain-general cognitive ability and domain-general academic self-concept as well as between the domain-specific elements of the model.

  17. Folding in a Cooling Crust with Elasto-visco-plastic Rheology: An Example from Venus

    Science.gov (United States)

    Ghent, R.; Phillips, R. J.; Hansen, V.

    2001-12-01

    We investigate the effects of simultaneous shortening and cooling on fold wavelengths in a crust with elasto-visco-plastic (EVP) rheology, in order to better understand the interplay between rates of shortening and cooling on the anelastic response of the crust. We apply our techniques to Venusian crustal plateaus, which show ubiquitous, low-amplitude folds with a continuous range of wavelengths from 30 km. Previous studies have proposed that these folds (and other characteristic crustal plateau structures) originated during crustal plateau formation by interaction of large mantle plumes with the surface during a time of globally thin lithosphere [1]. In this scenario, a plume arriving at the lithosphere erases existing structures and produces a mechanically homogeneous surface by heating and/or melting the crust. Subsequent cooling results in a surface layer that is capable of recording strains and that thickens with time. We investigate the conditions under which folds matching those observed in Venusian crustal plateaus are created in a finite element model simulating concurrent shortening and cooling, as motivated by the tectonic scenario in [1]. Our models are novel because a) the EVP rheology more accurately represents the actual crust than viscous or viscoelastic models; and b) other models generally specify a priori a folding layer thickness and geometry, with material properties different from those of the surrounding rock, and this pre-determines the resulting fold wavelength(s). By contrast, our models incorporate spatially uniform material properties but temperature-dependent rheology [2], so that the strength profile through the crust evolves with cooling. This allows the thermal and stress conditions to determine the instantaneous effective folding layer thickness at each time step, which in turn determines surface fold wavelengths. We investigate conditions under which short wavelength folds are initiated when the effective folding layer is very thin

  18. Digital terrain model generalization incorporating scale, semantic and cognitive constraints

    Science.gov (United States)

    Partsinevelos, Panagiotis; Papadogiorgaki, Maria

    2014-05-01

    Cartographic generalization is a well-known process accommodating spatial data compression, visualization and comprehension under various scales. In the last few years, there are several international attempts to construct tangible GIS systems, forming real 3D surfaces using a vast number of mechanical parts along a matrix formation (i.e., bars, pistons, vacuums). Usually, moving bars upon a structured grid push a stretching membrane resulting in a smooth visualization for a given surface. Most of these attempts suffer either in their cost, accuracy, resolution and/or speed. Under this perspective, the present study proposes a surface generalization process that incorporates intrinsic constrains of tangible GIS systems including robotic-motor movement and surface stretching limitations. The main objective is to provide optimized visualizations of 3D digital terrain models with minimum loss of information. That is, to minimize the number of pixels in a raster dataset used to define a DTM, while reserving the surface information. This neighborhood type of pixel relations adheres to the basics of Self Organizing Map (SOM) artificial neural networks, which are often used for information abstraction since they are indicative of intrinsic statistical features contained in the input patterns and provide concise and characteristic representations. Nevertheless, SOM remains more like a black box procedure not capable to cope with possible particularities and semantics of the application at hand. E.g. for coastal monitoring applications, the near - coast areas, surrounding mountains and lakes are more important than other features and generalization should be "biased"-stratified to fulfill this requirement. Moreover, according to the application objectives, we extend the SOM algorithm to incorporate special types of information generalization by differentiating the underlying strategy based on topologic information of the objects included in the application. The final

  19. Structural Modeling of Measurement Error in Generalized Linear Models with Rasch Measures as Covariates

    Science.gov (United States)

    Battauz, Michela; Bellio, Ruggero

    2011-01-01

    This paper proposes a structural analysis for generalized linear models when some explanatory variables are measured with error and the measurement error variance is a function of the true variables. The focus is on latent variables investigated on the basis of questionnaires and estimated using item response theory models. Latent variable…

  20. A Comparison of Generalized Hyperbolic Distribution Models for Equity Returns

    Directory of Open Access Journals (Sweden)

    Virginie Konlack Socgnia

    2014-01-01

    Full Text Available We discuss the calibration of the univariate and multivariate generalized hyperbolic distributions, as well as their hyperbolic, variance gamma, normal inverse Gaussian, and skew Student’s t-distribution subclasses for the daily log-returns of seven of the most liquid mining stocks listed on the Johannesburg Stocks Exchange. To estimate the model parameters from historic distributions, we use an expectation maximization based algorithm for the univariate case and a multicycle expectation conditional maximization estimation algorithm for the multivariate case. We assess the goodness of fit statistics using the log-likelihood, the Akaike information criterion, and the Kolmogorov-Smirnov distance. Finally, we inspect the temporal stability of parameters and note implications as criteria for distinguishing between models. To better understand the dependence structure of the stocks, we fit the MGHD and subclasses to both the stock returns and the two leading principal components derived from the price data. While the MGHD could fit both data subsets, we observed that the multivariate normality of the stock return residuals, computed by removing shared components, suggests that the departure from normality can be explained by the structure in the common factors.

  1. Prognostic cloud water in the Los Alamos general circulation model

    International Nuclear Information System (INIS)

    Kristjansson, J.E.; Kao, C.Y.J.

    1993-01-01

    Most of today's general circulation models (GCMS) have a greatly simplified treatment of condensation and clouds. Recent observational studies of the earth's radiation budget have suggested cloud-related feedback mechanisms to be of tremendous importance for the issue of global change. Thus, there has arisen an urgent need for improvements in the treatment of clouds in GCMS, especially as the clouds relate to radiation. In the present paper, we investigate the effects of introducing pregnostic cloud water into the Los Alamos GCM. The cloud water field, produced by both stratiform and convective condensation, is subject to 3-dimensional advection and vertical diffusion. The cloud water enters the radiation calculations through the long wave emissivity calculations. Results from several sensitivity simulations show that realistic cloud water and precipitation fields can be obtained with the applied method. Comparisons with observations show that the most realistic results are obtained when more sophisticated schemes for moist convection are introduced at the same time. The model's cold bias is reduced and the zonal winds become stronger, due to more realistic tropical convection

  2. General Model for Light Curves of Chromospherically Active Binary Stars

    Science.gov (United States)

    Jetsu, L.; Henry, G. W.; Lehtinen, J.

    2017-04-01

    The starspots on the surface of many chromospherically active binary stars concentrate on long-lived active longitudes separated by 180°. Shifts in activity between these two longitudes, the “flip-flop” events, have been observed in single stars like FK Comae and binary stars like σ Geminorum. Recently, interferometry has revealed that ellipticity may at least partly explain the flip-flop events in σ Geminorum. This idea was supported by the double-peaked shape of the long-term mean light curve of this star. Here we show that the long-term mean light curves of 14 chromospherically active binaries follow a general model that explains the connection between orbital motion, changes in starspot distribution, ellipticity, and flip-flop events. Surface differential rotation is probably weak in these stars, because the interference of two constant period waves may explain the observed light curve changes. These two constant periods are the active longitude period ({P}{act}) and the orbital period ({P}{orb}). We also show how to apply the same model to single stars, where only the value of P act is known. Finally, we present a tentative interference hypothesis about the origin of magnetic fields in all spectral types of stars. The CPS results are available electronically at the Vizier database.

  3. A general method for modeling population dynamics and its applications.

    Science.gov (United States)

    Shestopaloff, Yuri K

    2013-12-01

    Studying populations, be it a microbe colony or mankind, is important for understanding how complex systems evolve and exist. Such knowledge also often provides insights into evolution, history and different aspects of human life. By and large, populations' prosperity and decline is about transformation of certain resources into quantity and other characteristics of populations through growth, replication, expansion and acquisition of resources. We introduce a general model of population change, applicable to different types of populations, which interconnects numerous factors influencing population dynamics, such as nutrient influx and nutrient consumption, reproduction period, reproduction rate, etc. It is also possible to take into account specific growth features of individual organisms. We considered two recently discovered distinct growth scenarios: first, when organisms do not change their grown mass regardless of nutrients availability, and the second when organisms can reduce their grown mass by several times in a nutritionally poor environment. We found that nutrient supply and reproduction period are two major factors influencing the shape of population growth curves. There is also a difference in population dynamics between these two groups. Organisms belonging to the second group are significantly more adaptive to reduction of nutrients and far more resistant to extinction. Also, such organisms have substantially more frequent and lesser in amplitude fluctuations of population quantity for the same periodic nutrient supply (compared to the first group). Proposed model allows adequately describing virtually any possible growth scenario, including complex ones with periodic and irregular nutrient supply and other changing parameters, which present approaches cannot do.

  4. Bayes estimation of the general hazard rate model

    International Nuclear Information System (INIS)

    Sarhan, A.

    1999-01-01

    In reliability theory and life testing models, the life time distributions are often specified by choosing a relevant hazard rate function. Here a general hazard rate function h(t)=a+bt c-1 , where c, a, b are constants greater than zero, is considered. The parameter c is assumed to be known. The Bayes estimators of (a,b) based on the data of type II/item-censored testing without replacement are obtained. A large simulation study using Monte Carlo Method is done to compare the performance of Bayes with regression estimators of (a,b). The criterion for comparison is made based on the Bayes risk associated with the respective estimator. Also, the influence of the number of failed items on the accuracy of the estimators (Bayes and regression) is investigated. Estimations for the parameters (a,b) of the linearly increasing hazard rate model h(t)=a+bt, where a, b are greater than zero, can be obtained as the special case, letting c=2

  5. Generalized Functional Linear Models With Semiparametric Single-Index Interactions

    KAUST Repository

    Li, Yehua

    2010-06-01

    We introduce a new class of functional generalized linear models, where the response is a scalar and some of the covariates are functional. We assume that the response depends on multiple covariates, a finite number of latent features in the functional predictor, and interaction between the two. To achieve parsimony, the interaction between the multiple covariates and the functional predictor is modeled semiparametrically with a single-index structure. We propose a two step estimation procedure based on local estimating equations, and investigate two situations: (a) when the basis functions are pre-determined, e.g., Fourier or wavelet basis functions and the functional features of interest are known; and (b) when the basis functions are data driven, such as with functional principal components. Asymptotic properties are developed. Notably, we show that when the functional features are data driven, the parameter estimates have an increased asymptotic variance, due to the estimation error of the basis functions. Our methods are illustrated with a simulation study and applied to an empirical data set, where a previously unknown interaction is detected. Technical proofs of our theoretical results are provided in the online supplemental materials.

  6. Critical rotation of general-relativistic polytropic models revisited

    Science.gov (United States)

    Geroyannis, V.; Karageorgopoulos, V.

    2013-09-01

    We develop a perturbation method for computing the critical rotational parameter as a function of the equatorial radius of a rigidly rotating polytropic model in the "post-Newtonia approximation" (PNA). We treat our models as "initial value problems" (IVP) of ordinary differential equations in the complex plane. The computations are carried out by the code dcrkf54.f95 (Geroyannis and Valvi 2012 [P1]; modified Runge-Kutta-Fehlberg code of fourth and fifth order for solving initial value problems in the complex plane). Such a complex-plane treatment removes the syndromes appearing in this particular family of IVPs (see e.g. P1, Sec. 3) and allows continuation of the numerical integrations beyond the surface of the star. Thus all the required values of the Lane-Emden function(s) in the post-Newtonian approximation are calculated by interpolation (so avoiding any extrapolation). An interesting point is that, in our computations, we take into account the complete correction due to the gravitational term, and this issue is a remarkable difference compared to the classical PNA. We solve the generalized density as a function of the equatorial radius and find the critical rotational parameter. Our computations are extended to certain other physical characteristics (like mass, angular momentum, rotational kinetic energy, etc). We find that our method yields results comparable with those of other reliable methods. REFERENCE: V.S. Geroyannis and F.N. Valvi 2012, International Journal of Modern Physics C, 23, No 5, 1250038:1-15.

  7. Cognitive performance modeling based on general systems performance theory.

    Science.gov (United States)

    Kondraske, George V

    2010-01-01

    General Systems Performance Theory (GSPT) was initially motivated by problems associated with quantifying different aspects of human performance. It has proved to be invaluable for measurement development and understanding quantitative relationships between human subsystem capacities and performance in complex tasks. It is now desired to bring focus to the application of GSPT to modeling of cognitive system performance. Previous studies involving two complex tasks (i.e., driving and performing laparoscopic surgery) and incorporating measures that are clearly related to cognitive performance (information processing speed and short-term memory capacity) were revisited. A GSPT-derived method of task analysis and performance prediction termed Nonlinear Causal Resource Analysis (NCRA) was employed to determine the demand on basic cognitive performance resources required to support different levels of complex task performance. This approach is presented as a means to determine a cognitive workload profile and the subsequent computation of a single number measure of cognitive workload (CW). Computation of CW may be a viable alternative to measuring it. Various possible "more basic" performance resources that contribute to cognitive system performance are discussed. It is concluded from this preliminary exploration that a GSPT-based approach can contribute to defining cognitive performance models that are useful for both individual subjects and specific groups (e.g., military pilots).

  8. Prognostic cloud water in the Los Alamos general circulation model

    International Nuclear Information System (INIS)

    Kristjansson, J.E.; Kao, C.Y.J.

    1994-01-01

    Most of today's general circulation models (GCMs) have a greatly simplified treatment of condensation and clouds. Recent observational studies of the earth's radiation budget have suggested cloud-related feedback mechanisms to be of tremendous importance for the issue of global change. Thus, an urgent need for improvements in the treatment of clouds in GCMs has arisen, especially as the clouds relate to radiation. In this paper, we investigate the effects of introducing prognostic cloud water into the Los Alamos GCM. The cloud water field, produced by both stratiform and convective condensation, is subject to 3-dimensional advection and vertical diffusion. The cloud water enters the radiation calculations through the longwave emissivity calculations. Results from several sensitivity simulations show that realistic water and precipitation fields can be obtained with the applied method. Comparisons with observations show that the most realistic results are obtained when more sophisticated schemes for moist convection are introduced at the same time. The model's cold bias is reduced and the zonal winds becomes stronger because of more realistic tropical convection

  9. Neuromuscular compensation mechanisms in vocal fold paralysis and paresis.

    Science.gov (United States)

    Dewan, Karuna; Vahabzadeh-Hagh, Andrew; Soofer, Donna; Chhetri, Dinesh K

    2017-07-01

    Vocal fold paresis and paralysis are common conditions. Treatment options include augmentation laryngoplasty and voice therapy. The optimal management for this condition is unclear. The objective of this study was to assess possible neuromuscular compensation mechanisms that could potentially be used in the treatment of vocal fold paresis and paralysis. In vivo canine model. In an in vivo canine model, we examined three conditions: 1) unilateral right recurrent laryngeal nerve (RLN) paresis and paralysis, 2) unilateral superior laryngeal nerve (SLN) paralysis, and 3) unilateral vagal nerve paresis and paralysis. Phonatory acoustics and aerodynamics were measured in each of these conditions. Effective compensation was defined as improved acoustic and aerodynamic profile. The most effective compensation for all conditions was increasing RLN activation and decreasing glottal gap. Increasing RLN activation increased the percentage of possible phonatory conditions that achieved phonation onset. SLN activation generally led to decreased number of total phonation onset conditions within each category. Differential effects of SLN (cricothyroid [CT] muscle) activation were seen. Ipsilateral SLN activation could compensate for RLN paralysis; normal CT compensated well in unilateral SLN paralysis; and in vagal paresis/paralysis, contralateral SLN and RLN displayed antagonistic relationships. Methods to improve glottal closure should be the primary treatment for large glottal gaps. Neuromuscular compensation is possible for paresis. This study provides insights into possible compensatory mechanisms in vocal fold paresis and paralysis. NA Laryngoscope, 127:1633-1638, 2017. © 2017 The American Laryngological, Rhinological and Otological Society, Inc.

  10. Fractal Folding and Medium Viscoelasticity Contribute Jointly to Chromosome Dynamics

    Science.gov (United States)

    Polovnikov, K. E.; Gherardi, M.; Cosentino-Lagomarsino, M.; Tamm, M. V.

    2018-02-01

    Chromosomes are key players of cell physiology, their dynamics provides valuable information about its physical organization. In both prokaryotes and eukaryotes, the short-time motion of chromosomal loci has been described with a Rouse model in a simple or viscoelastic medium. However, little emphasis has been put on the influence of the folded organization of chromosomes on the local dynamics. Clearly, stress propagation, and thus dynamics, must be affected by such organization, but a theory allowing us to extract such information from data, e.g., on two-point correlations, is lacking. Here, we describe a theoretical framework able to answer this general polymer dynamics question. We provide a scaling analysis of the stress-propagation time between two loci at a given arclength distance along the chromosomal coordinate. The results suggest a precise way to assess folding information from the dynamical coupling of chromosome segments. Additionally, we realize this framework in a specific model of a polymer whose long-range interactions are designed to make it fold in a fractal way and immersed in a medium characterized by subdiffusive fractional Langevin motion with a tunable scaling exponent. This allows us to derive explicit analytical expressions for the correlation functions.

  11. Design and implementation of a generalized laboratory data model

    Directory of Open Access Journals (Sweden)

    Nhan Mike

    2007-09-01

    Full Text Available Abstract Background Investigators in the biological sciences continue to exploit laboratory automation methods and have dramatically increased the rates at which they can generate data. In many environments, the methods themselves also evolve in a rapid and fluid manner. These observations point to the importance of robust information management systems in the modern laboratory. Designing and implementing such systems is non-trivial and it appears that in many cases a database project ultimately proves unserviceable. Results We describe a general modeling framework for laboratory data and its implementation as an information management system. The model utilizes several abstraction techniques, focusing especially on the concepts of inheritance and meta-data. Traditional approaches commingle event-oriented data with regular entity data in ad hoc ways. Instead, we define distinct regular entity and event schemas, but fully integrate these via a standardized interface. The design allows straightforward definition of a "processing pipeline" as a sequence of events, obviating the need for separate workflow management systems. A layer above the event-oriented schema integrates events into a workflow by defining "processing directives", which act as automated project managers of items in the system. Directives can be added or modified in an almost trivial fashion, i.e., without the need for schema modification or re-certification of applications. Association between regular entities and events is managed via simple "many-to-many" relationships. We describe the programming interface, as well as techniques for handling input/output, process control, and state transitions. Conclusion The implementation described here has served as the Washington University Genome Sequencing Center's primary information system for several years. It handles all transactions underlying a throughput rate of about 9 million sequencing reactions of various kinds per month and

  12. Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction

    Science.gov (United States)

    Das, Payel; Moll, Mark; Stamati, Hernán; Kavraki, Lydia E.; Clementi, Cecilia

    2006-06-01

    The definition of reaction coordinates for the characterization of a protein-folding reaction has long been a controversial issue, even for the "simple" case in which one single free-energy barrier separates the folded and unfolded ensemble. We propose a general approach to this problem to obtain a few collective coordinates by using nonlinear dimensionality reduction. We validate the usefulness of this method by characterizing the folding landscape associated with a coarse-grained protein model of src homology 3 as sampled by molecular dynamics simulations. The folding free-energy landscape projected on the few relevant coordinates emerging from the dimensionality reduction can correctly identify the transition-state ensemble of the reaction. The first embedding dimension efficiently captures the evolution of the folding process along the main folding route. These results clearly show that the proposed method can efficiently find a low-dimensional representation of a complex process such as protein folding. reaction coordinate | transition state | manifold | embedding | ISOMAP

  13. Folding very short peptides using molecular dynamics.

    Directory of Open Access Journals (Sweden)

    Bosco K Ho

    2006-04-01

    Full Text Available Peptides often have conformational preferences. We simulated 133 peptide 8-mer fragments from six different proteins, sampled by replica-exchange molecular dynamics using Amber7 with a GB/SA (generalized-Born/solvent-accessible electrostatic approximation to water implicit solvent. We found that 85 of the peptides have no preferred structure, while 48 of them converge to a preferred structure. In 85% of the converged cases (41 peptides, the structures found by the simulations bear some resemblance to their native structures, based on a coarse-grained backbone description. In particular, all seven of the beta hairpins in the native structures contain a fragment in the turn that is highly structured. In the eight cases where the bioinformatics-based I-sites library picks out native-like structures, the present simulations are largely in agreement. Such physics-based modeling may be useful for identifying early nuclei in folding kinetics and for assisting in protein-structure prediction methods that utilize the assembly of peptide fragments.

  14. Log-normal frailty models fitted as Poisson generalized linear mixed models.

    Science.gov (United States)

    Hirsch, Katharina; Wienke, Andreas; Kuss, Oliver

    2016-12-01

    The equivalence of a survival model with a piecewise constant baseline hazard function and a Poisson regression model has been known since decades. As shown in recent studies, this equivalence carries over to clustered survival data: A frailty model with a log-normal frailty term can be interpreted and estimated as a generalized linear mixed model with a binary response, a Poisson likelihood, and a specific offset. Proceeding this way, statistical theory and software for generalized linear mixed models are readily available for fitting frailty models. This gain in flexibility comes at the small price of (1) having to fix the number of pieces for the baseline hazard in advance and (2) having to "explode" the data set by the number of pieces. In this paper we extend the simulations of former studies by using a more realistic baseline hazard (Gompertz) and by comparing the model under consideration with competing models. Furthermore, the SAS macro %PCFrailty is introduced to apply the Poisson generalized linear mixed approach to frailty models. The simulations show good results for the shared frailty model. Our new %PCFrailty macro provides proper estimates, especially in case of 4 events per piece. The suggested Poisson generalized linear mixed approach for log-normal frailty models based on the %PCFrailty macro provides several advantages in the analysis of clustered survival data with respect to more flexible modelling of fixed and random effects, exact (in the sense of non-approximate) maximum likelihood estimation, and standard errors and different types of confidence intervals for all variance parameters. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  15. Centering, Scale Indeterminacy, and Differential Item Functioning Detection in Hierarchical Generalized Linear and Generalized Linear Mixed Models

    Science.gov (United States)

    Cheong, Yuk Fai; Kamata, Akihito

    2013-01-01

    In this article, we discuss and illustrate two centering and anchoring options available in differential item functioning (DIF) detection studies based on the hierarchical generalized linear and generalized linear mixed modeling frameworks. We compared and contrasted the assumptions of the two options, and examined the properties of their DIF…

  16. Generalized equilibrium modeling: the methodology of the SRI-Gulf energy model. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Gazalet, E.G.

    1977-05-01

    The report provides documentation of the generalized equilibrium modeling methodology underlying the SRI-Gulf Energy Model and focuses entirely on the philosophical, mathematical, and computational aspects of the methodology. The model is a highly detailed regional and dynamic model of the supply and demand for energy in the US. The introduction emphasized the need to focus modeling efforts on decisions and the coordinated decomposition of complex decision problems using iterative methods. The conceptual framework is followed by a description of the structure of the current SRI-Gulf model and a detailed development of the process relations that comprise the model. The network iteration algorithm used to compute a solution to the model is described and the overall methodology is compared with other modeling methodologies. 26 references.

  17. Maximum Likelihood in a Generalized Linear Finite Mixture Model by Using the EM Algorithm

    NARCIS (Netherlands)

    Jansen, R.C.

    A generalized linear finite mixture model and an EM algorithm to fit the model to data are described. By this approach the finite mixture model is embedded within the general framework of generalized linear models (GLMs). Implementation of the proposed EM algorithm can be readily done in statistical

  18. Upright folding during extensional and transtensional tectonics

    Science.gov (United States)

    Teyssier, Christian; Fossen, Haakon; Rey, Patrice F.; Whitney, Donna L.

    2017-04-01

    Upright folds are common structures that develop in response to horizontal shortening in layered material, for example in foreland basins that surround orogens. While the contractional nature of these folds is not in doubt, interpretation of their tectonic setting needs careful consideration. Here we focus on two examples: (1) folds developed in transtension; and (2) folds developed during the flow of deep crust in response to lithospheric extension. In both cases we consider folding of nearly horizontal layers that are either primary (bedding) or secondary (foliation). Strain theory inspired by John Ramsay's work makes predictions for the behavior of material lines and planes as well as strain axes (instantaneous, finite) during transtensional deformation. Results show: folds can form in transtension; fold hinges rotate toward the direction of divergence (and not the shear zone boundary as they do in transpression), providing unique insight into ancient plate motions; fold tightness is controlled by the obliquity of divergence and not finite strain; hinge parallel stretching is always greater than hinge-perpendicular shortening, resulting in constriction strain and boudinage of fold hinges. Taken together these results provide a rigorous framework for interpreting field observations where structures are complex and boundary conditions unclear. These principles are applied to various tectonic settings ranging from active tectonic regions of oblique divergence in western North America to ancient folding that developed during oblique extension of the Western Gneiss Region, deposition of Devonian basins, and exhumation of ultrahigh-pressure rocks in the Norwegian Caledonides. The other class of upright folds that form during extension may require revision of the tectonic interpretation of structural overprints in orogenic cores, for example in gneiss/migmatite domes. Dynamic modeling of extension of thick/hot crust predicts a positive feedback between extension of

  19. Explicit prediction of ice clouds in general circulation models

    Science.gov (United States)

    Kohler, Martin

    1999-11-01

    Although clouds play extremely important roles in the radiation budget and hydrological cycle of the Earth, there are large quantitative uncertainties in our understanding of their generation, maintenance and decay mechanisms, representing major obstacles in the development of reliable prognostic cloud water schemes for General Circulation Models (GCMs). Recognizing their relative neglect in the past, both observationally and theoretically, this work places special focus on ice clouds. A recent version of the UCLA - University of Utah Cloud Resolving Model (CRM) that includes interactive radiation is used to perform idealized experiments to study ice cloud maintenance and decay mechanisms under various conditions in term of: (1) background static stability, (2) background relative humidity, (3) rate of cloud ice addition over a fixed initial time-period and (4) radiation: daytime, nighttime and no-radiation. Radiation is found to have major effects on the life-time of layer-clouds. Optically thick ice clouds decay significantly slower than expected from pure microphysical crystal fall-out (taucld = 0.9--1.4 h as opposed to no-motion taumicro = 0.5--0.7 h). This is explained by the upward turbulent fluxes of water induced by IR destabilization, which partially balance the downward transport of water by snowfall. Solar radiation further slows the ice-water decay by destruction of the inversion above cloud-top and the resulting upward transport of water. Optically thin ice clouds, on the other hand, may exhibit even longer life-times (>1 day) in the presence of radiational cooling. The resulting saturation mixing ratio reduction provides for a constant cloud ice source. These CRM results are used to develop a prognostic cloud water scheme for the UCLA-GCM. The framework is based on the bulk water phase model of Ose (1993). The model predicts cloud liquid water and cloud ice separately, and which is extended to split the ice phase into suspended cloud ice (predicted

  20. Factors that affect coseismic folds in an overburden layer

    Science.gov (United States)

    Zeng, Shaogang; Cai, Yongen

    2018-03-01

    Coseismic folds induced by blind thrust faults have been observed in many earthquake zones, and they have received widespread attention from geologists and geophysicists. Numerous studies have been conducted regarding fold kinematics; however, few have studied fold dynamics quantitatively. In this paper, we establish a conceptual model with a thrust fault zone and tectonic stress load to study the factors that affect coseismic folds and their formation mechanisms using the finite element method. The numerical results show that the fault dip angle is a key factor that controls folding. The greater the dip angle is, the steeper the fold slope. The second most important factor is the overburden thickness. The thicker the overburden is, the more gradual the fold. In this case, folds are difficult to identify in field surveys. Therefore, if a fold can be easily identified with the naked eye, the overburden is likely shallow. The least important factors are the mechanical parameters of the overburden. The larger the Young's modulus of the overburden is, the smaller the displacement of the fold and the fold slope. Strong horizontal compression and vertical extension in the overburden near the fault zone are the main mechanisms that form coseismic folds.