Folding-type coupling potentials in the context of the generalized rotation-vibration model
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.
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...
Folding models for elastic and inelastic scattering
International Nuclear Information System (INIS)
Satchler, G.R.
1982-01-01
The most widely used models are the optical model potential (OMP) for elastic scattering, and its generalization to non-spherical shapes, the deformed optical model potential (DOMP) for inelastic scattering. These models are simple and phenomenological; their parameters are adjusted so as to reproduce empirical data. Nonetheless, there are certain, not always well-defined, constraints to be imposed. The potential shapes and their parameter values must be reasonable and should vary in a smooth and systematic way with the masses of the colliding nuclei and their energy. One way of satisfying these constraints, without going back to a much more fundamental theory, is through the use of folding models. The basic justification for using potentials of the Woods-Saxon shape for nucleon-nucleus scattering, for example, is our knowledge that a nuclear density distribution is more-or-less constant in the nuclear interior with a diffuse surface. When this is folded with a short-range nucleon-nucleon interaction, the result is a similar shape with a more diffuse surface. Folding procedures allow us to incorporate many aspects of nuclear structure (although the nuclear size is one of the most important), as well as theoretical ideas about the effective interaction of two nucleons within nuclear matter. It also provides us with a means of linking information obtained from nuclear (hadronic) interactions with that from other sources, as well as correlating that from the use of different hadronic probes. Folding model potentials, single-folded potentials, and the double-folding model including applications to heavy-ion scattering are discussed
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).
SDEM modelling of fault-propagation folding
DEFF Research Database (Denmark)
Clausen, O.R.; Egholm, D.L.; Poulsen, Jane Bang
2009-01-01
and variations in Mohr-Coulomb parameters including internal friction. Using SDEM modelling, we have mapped the propagation of the tip-line of the fault, as well as the evolution of the fold geometry across sedimentary layers of contrasting rheological parameters, as a function of the increased offset......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...... a precise indication of when faults develop and hence also the sequential evolution of secondary faults. Here we focus on the generation of a fault -propagated fold with a reverse sense of motion at the master fault, and varying only the dip of the master fault and the mechanical behaviour of the deformed...
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.
Protein folding simulations by generalized-ensemble algorithms.
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.
Folding model analysis of alpha radioactivity
International Nuclear Information System (INIS)
Basu, D N
2003-01-01
Radioactive decay of nuclei via emission of α-particles has been studied theoretically in the framework of a superasymmetric fission model using the double folding (DF) procedure for obtaining the α-nucleus interaction potential. The DF nuclear potential has been obtained by folding in the density distribution functions of the α nucleus and the daughter nucleus with a realistic effective interaction. The M3Y effective interaction has been used for calculating the nuclear interaction potential which has been supplemented by a zero-range pseudo-potential for exchange along with the density dependence. The nuclear microscopic α-nucleus potential thus obtained has been used along with the Coulomb interaction potential to calculate the action integral within the WKB approximation. This subsequently yields calculations for the half-lives of α decays of nuclei. The density dependence and the exchange effects have not been found to be very significant. These calculations provide reasonable estimates for the lifetimes of α-radioactivity of nuclei
A Rat Excised Larynx Model of Vocal Fold Scar
Welham, Nathan V.; Montequin, Douglas W.; Tateya, Ichiro; Tateya, Tomoko; Choi, Seong Hee; Bless, Diane M.
2009-01-01
Purpose: To develop and evaluate a rat excised larynx model for the measurement of acoustic, aerodynamic, and vocal fold vibratory changes resulting from vocal fold scar. Method: Twenty-four 4-month-old male Sprague-Dawley rats were assigned to 1 of 4 experimental groups: chronic vocal fold scar, chronic vocal fold scar treated with 100-ng basic…
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.
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)
Approximate self-similarity in models of geological folding
Budd, C.J.; Peletier, M.A.
2000-01-01
We propose a model for the folding of rock under the compression of tectonic plates. This models an elastic rock layer imbedded in a viscous foundation by a fourth-order parabolic equation with a nonlinear constraint. The large-time behavior of solutions of this problem is examined and found to be
Exact solution of the generalized Peierls equation for arbitrary n-fold screw dislocation
Wang, Shaofeng; Hu, Xiangsheng
2018-05-01
The exact solution of the generalized Peierls equation is presented and proved for arbitrary n-fold screw dislocation. The displacement field, stress field and the energy of the n-fold dislocation are also evaluated explicitly. It is found that the solution defined on each individual fold is given by the tail cut from the original Peierls solution. In viewpoint of energetics, a screw dislocation has a tendency to spread the distribution on all possible slip planes which are contained in the dislocation line zone. Based on the exact solution, the approximated solution of the improved Peierls equation is proposed for the modified γ-surface.
Visualization of protein folding funnels in lattice models.
Directory of Open Access Journals (Sweden)
Antonio B Oliveira
Full Text Available Protein folding occurs in a very high dimensional phase space with an exponentially large number of states, and according to the energy landscape theory it exhibits a topology resembling a funnel. In this statistical approach, the folding mechanism is unveiled by describing the local minima in an effective one-dimensional representation. Other approaches based on potential energy landscapes address the hierarchical structure of local energy minima through disconnectivity graphs. In this paper, we introduce a metric to describe the distance between any two conformations, which also allows us to go beyond the one-dimensional representation and visualize the folding funnel in 2D and 3D. In this way it is possible to assess the folding process in detail, e.g., by identifying the connectivity between conformations and establishing the paths to reach the native state, in addition to regions where trapping may occur. Unlike the disconnectivity maps method, which is based on the kinetic connections between states, our methodology is based on structural similarities inferred from the new metric. The method was developed in a 27-mer protein lattice model, folded into a 3×3×3 cube. Five sequences were studied and distinct funnels were generated in an analysis restricted to conformations from the transition-state to the native configuration. Consistent with the expected results from the energy landscape theory, folding routes can be visualized to probe different regions of the phase space, as well as determine the difficulty in folding of the distinct sequences. Changes in the landscape due to mutations were visualized, with the comparison between wild and mutated local minima in a single map, which serves to identify different trapping regions. The extension of this approach to more realistic models and its use in combination with other approaches are discussed.
Protein folding simulations: from coarse-grained model to all-atom model.
Zhang, Jian; Li, Wenfei; Wang, Jun; Qin, Meng; Wu, Lei; Yan, Zhiqiang; Xu, Weixin; Zuo, Guanghong; Wang, Wei
2009-06-01
Protein folding is an important and challenging problem in molecular biology. During the last two decades, molecular dynamics (MD) simulation has proved to be a paramount tool and was widely used to study protein structures, folding kinetics and thermodynamics, and structure-stability-function relationship. It was also used to help engineering and designing new proteins, and to answer even more general questions such as the minimal number of amino acid or the evolution principle of protein families. Nowadays, the MD simulation is still undergoing rapid developments. The first trend is to toward developing new coarse-grained models and studying larger and more complex molecular systems such as protein-protein complex and their assembling process, amyloid related aggregations, and structure and motion of chaperons, motors, channels and virus capsides; the second trend is toward building high resolution models and explore more detailed and accurate pictures of protein folding and the associated processes, such as the coordination bond or disulfide bond involved folding, the polarization, charge transfer and protonate/deprotonate process involved in metal coupled folding, and the ion permeation and its coupling with the kinetics of channels. On these new territories, MD simulations have given many promising results and will continue to offer exciting views. Here, we review several new subjects investigated by using MD simulations as well as the corresponding developments of appropriate protein models. These include but are not limited to the attempt to go beyond the topology based Gō-like model and characterize the energetic factors in protein structures and dynamics, the study of the thermodynamics and kinetics of disulfide bond involved protein folding, the modeling of the interactions between chaperonin and the encapsulated protein and the protein folding under this circumstance, the effort to clarify the important yet still elusive folding mechanism of protein BBL
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/
Mechanical Modeling and Computer Simulation of Protein Folding
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…
Glottal aerodynamics in compliant, life-sized vocal fold models
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.
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)
Developing guinea pig brain as a model for cortical folding.
Hatakeyama, Jun; Sato, Haruka; Shimamura, Kenji
2017-05-01
The cerebral cortex in mammals, the neocortex specifically, is highly diverse among species with respect to its size and morphology, likely reflecting the immense adaptiveness of this lineage. In particular, the pattern and number of convoluted ridges and fissures, called gyri and sulci, respectively, on the surface of the cortex are variable among species and even individuals. However, little is known about the mechanism of cortical folding, although there have been several hypotheses proposed. Recent studies on embryonic neurogenesis revealed the differences in cortical progenitors as a critical factor of the process of gyrification. Here, we investigated the gyrification processes using developing guinea pig brains that form a simple but fundamental pattern of gyri. In addition, we established an electroporation-mediated gene transfer method for guinea pig embryos. We introduce the guinea pig brain as a useful model system to understand the mechanisms and basic principle of cortical folding. © 2017 Japanese Society of Developmental Biologists.
Wang, Fei; Gong, Haoran; Chen, Xi; Chen, C. Q.
2016-09-01
Origami structures enrich the field of mechanical metamaterials with the ability to convert morphologically and systematically between two-dimensional (2D) thin sheets and three-dimensional (3D) spatial structures. In this study, an in-plane design method is proposed to approximate curved surfaces of interest with generalized Miura-ori units. Using this method, two combination types of crease lines are unified in one reprogrammable procedure, generating multiple types of cylindrical structures. Structural completeness conditions of the finite-thickness counterparts to the two types are also proposed. As an example of the design method, the kinematics and elastic properties of an origami-based circular cylindrical shell are analysed. The concept of Poisson’s ratio is extended to the cylindrical structures, demonstrating their auxetic property. An analytical model of rigid plates linked by elastic hinges, consistent with numerical simulations, is employed to describe the mechanical response of the structures. Under particular load patterns, the circular shells display novel mechanical behaviour such as snap-through and limiting folding positions. By analysing the geometry and mechanics of the origami structures, we extend the design space of mechanical metamaterials and provide a basis for their practical applications in science and engineering.
Roles of beta-turns in protein folding: from peptide models to protein engineering.
Marcelino, Anna Marie C; Gierasch, Lila M
2008-05-01
Reverse turns are a major class of protein secondary structure; they represent sites of chain reversal and thus sites where the globular character of a protein is created. It has been speculated for many years that turns may nucleate the formation of structure in protein folding, as their propensity to occur will favor the approximation of their flanking regions and their general tendency to be hydrophilic will favor their disposition at the solvent-accessible surface. Reverse turns are local features, and it is therefore not surprising that their structural properties have been extensively studied using peptide models. In this article, we review research on peptide models of turns to test the hypothesis that the propensities of turns to form in short peptides will relate to the roles of corresponding sequences in protein folding. Turns with significant stability as isolated entities should actively promote the folding of a protein, and by contrast, turn sequences that merely allow the chain to adopt conformations required for chain reversal are predicted to be passive in the folding mechanism. We discuss results of protein engineering studies of the roles of turn residues in folding mechanisms. Factors that correlate with the importance of turns in folding indeed include their intrinsic stability, as well as their topological context and their participation in hydrophobic networks within the protein's structure.
Separable potential approach in the folding model. Pt. 2
International Nuclear Information System (INIS)
Lee, C.L.; Robson, D.
1982-01-01
A microscopic folding formalism using a separable potential approach is applied to the elastic scattering of the n-α system. Starting with a separable nucleon-nucleon (NN) potential model, a sum of separable nucleon-nucleus potentials is obtained. A simple structure of the α-particle is assumed and the Tabakin, the Doleschall and the Strobel NN potentials are considered. These phenomenological interactions are of Yukawa or gaussian form with variable parameters for each partial wave. Spin-orbit and tensor forces are included. The resulting potentials developed from our folding calculations give approximately the same ssub(1/2) phase shifts for the n-α elastic scattering. However, in the psub(1/2) and psub(3/2) phase-shift analysis, an effective interaction derived from the NN potential is necessary to reproduce the resonances. One free energy independent parameter is introduced in our approximate G-matrix concept to give a good fit for the phase shifts. Single-nucleon knockout exchange (SNKE) is considered throughout. (orig.)
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
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.
Characteristics of phonation onset in a two-layer vocal fold model.
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.
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.
DEFF Research Database (Denmark)
Amatori, Andrea; Ferkinghoff-Borg, Jesper; Tiana, Guido
2008-01-01
The thermodynamics of proteins designed on three common folds (SH3, chymotrypsin inhibitor 2 [CI2], and protein G) is studied with a simplified C alpha, model and compared with the thermodynamics of proteins designed on random-generated folds. The model allows to design sequences to fold within a...
Allen, Johnie J.; Anderson, Craig A.; Bushman, Brad J.
The General Aggression Model (GAM) is a comprehensive, integrative, framework for understanding aggression. It considers the role of social, cognitive, personality, developmental, and biological factors on aggression. Proximate processes of GAM detail how person and situation factors influence
Modeling Vocal Fold Intravascular Flow using Synthetic Replicas
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.
Moisik, Scott R.; Esling, John H.
2014-01-01
Purpose: Physiological and phonetic studies suggest that, at moderate levels of epilaryngeal stricture, the ventricular folds impinge upon the vocal folds and influence their dynamical behavior, which is thought to be responsible for constricted laryngeal sounds. In this work, the authors examine this hypothesis through biomechanical modeling.…
Self-organized critical model for protein folding
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.
The generalized circular model
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
Generalized Nonlinear Yule Models
Lansky, Petr; Polito, Federico; Sacerdote, Laura
2016-01-01
With the aim of considering models with persistent memory we propose a fractional nonlinear modification of the classical Yule model often studied in the context of macrovolution. Here the model is analyzed and interpreted in the framework of the development of networks such as the World Wide Web. Nonlinearity is introduced by replacing the linear birth process governing the growth of the in-links of each specific webpage with a fractional nonlinear birth process with completely general birth...
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
Galindo, Gabriel E.; Peterson, Sean D.; Erath, Byron D.; Castro, Christian; Hillman, Robert E.; Zañartu, Matías
2017-01-01
Purpose: Our goal was to test prevailing assumptions about the underlying biomechanical and aeroacoustic mechanisms associated with phonotraumatic lesions of the vocal folds using a numerical lumped-element model of voice production. Method: A numerical model with a triangular glottis, posterior glottal opening, and arytenoid posturing is…
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
Computational Modeling of Proteins based on Cellular Automata: A Method of HP Folding Approximation.
Madain, Alia; Abu Dalhoum, Abdel Latif; Sleit, Azzam
2018-06-01
The design of a protein folding approximation algorithm is not straightforward even when a simplified model is used. The folding problem is a combinatorial problem, where approximation and heuristic algorithms are usually used to find near optimal folds of proteins primary structures. Approximation algorithms provide guarantees on the distance to the optimal solution. The folding approximation approach proposed here depends on two-dimensional cellular automata to fold proteins presented in a well-studied simplified model called the hydrophobic-hydrophilic model. Cellular automata are discrete computational models that rely on local rules to produce some overall global behavior. One-third and one-fourth approximation algorithms choose a subset of the hydrophobic amino acids to form H-H contacts. Those algorithms start with finding a point to fold the protein sequence into two sides where one side ignores H's at even positions and the other side ignores H's at odd positions. In addition, blocks or groups of amino acids fold the same way according to a predefined normal form. We intend to improve approximation algorithms by considering all hydrophobic amino acids and folding based on the local neighborhood instead of using normal forms. The CA does not assume a fixed folding point. The proposed approach guarantees one half approximation minus the H-H endpoints. This lower bound guaranteed applies to short sequences only. This is proved as the core and the folds of the protein will have two identical sides for all short sequences.
Self-organization and mismatch tolerance in protein folding: General theory and an application
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.
Ansari, M. H.; Karami, M. Amin
2016-03-01
This paper studies energy harvesting from heartbeat vibrations for powering leadless pacemakers. Unlike traditional pacemakers, leadless pacemakers are implanted inside the heart and the pacemaker is in direct contact with the myocardium. A leadless pacemaker is in the shape of a cylinder. Thus, in order to utilize the available 3-dimensional space for the energy harvester, we choose a fan-folded 3D energy harvester. The proposed device consists of several piezoelectric beams stacked on top of each other. The volume of the energy harvester is 1 cm3 and its dimensions are 2 cm × 0.5 cm × 1 cm. Although high natural frequency is generally a major concern with micro-scale energy harvesters, by utilizing the fan-folded geometry and adding tip mass and link mass to the configuration, we reduced the natural frequency to the desired range. This fan-folded design makes it possible to generate more than 10 μ W of power per cubic centimeter. The proposed device is compatible with Magnetic Resonance Imaging. Although the proposed device is a linear energy harvester, it is relatively insensitive to the heart rate. The natural frequencies and the mode shapes of the device are calculated analytically. The accuracy of the analytical model is verified by experimental investigations. We use a closed loop shaker system to precisely replicate heartbeat vibrations in vitro.
Generalized Nonlinear Yule Models
Lansky, Petr; Polito, Federico; Sacerdote, Laura
2016-11-01
With the aim of considering models related to random graphs growth exhibiting persistent memory, we propose a fractional nonlinear modification of the classical Yule model often studied in the context of macroevolution. Here the model is analyzed and interpreted in the framework of the development of networks such as the World Wide Web. Nonlinearity is introduced by replacing the linear birth process governing the growth of the in-links of each specific webpage with a fractional nonlinear birth process with completely general birth rates. Among the main results we derive the explicit distribution of the number of in-links of a webpage chosen uniformly at random recognizing the contribution to the asymptotics and the finite time correction. The mean value of the latter distribution is also calculated explicitly in the most general case. Furthermore, in order to show the usefulness of our results, we particularize them in the case of specific birth rates giving rise to a saturating behaviour, a property that is often observed in nature. The further specialization to the non-fractional case allows us to extend the Yule model accounting for a nonlinear growth.
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...... of evolutionary processes in simulations derived from the mechanistic assumptions of the GDM corresponded broadly to those initially suggested, with the exception of trends in extinction rates. Expanding the model to incorporate different scenarios of island ontogeny and isolation revealed a sensitivity...
Modeling and imaging of the vocal fold vibration for voice health
DEFF Research Database (Denmark)
Granados, Alba
Identication of abnormalities on the vocal fold by means of dierent diagnostic methods is a key step to determine the cause or causes of a voice disorder, and subsequently give an adequate treatment. To this end, clinical investigations benet from accurate mathematical models for prediction......, 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...
Anomaly General Circulation Models.
Navarra, Antonio
The feasibility of the anomaly model is assessed using barotropic and baroclinic models. In the barotropic case, both a stationary and a time-dependent model has been formulated and constructed, whereas only the stationary, linear case is considered in the baroclinic case. Results from the barotropic model indicate that a relation between the stationary solution and the time-averaged non-linear solution exists. The stationary linear baroclinic solution can therefore be considered with some confidence. The linear baroclinic anomaly model poses a formidable mathematical problem because it is necessary to solve a gigantic linear system to obtain the solution. A new method to find solution of large linear system, based on a projection on the Krylov subspace is shown to be successful when applied to the linearized baroclinic anomaly model. The scheme consists of projecting the original linear system on the Krylov subspace, thereby reducing the dimensionality of the matrix to be inverted to obtain the solution. With an appropriate setting of the damping parameters, the iterative Krylov method reaches a solution even using a Krylov subspace ten times smaller than the original space of the problem. This generality allows the treatment of the important problem of linear waves in the atmosphere. A larger class (nonzonally symmetric) of basic states can now be treated for the baroclinic primitive equations. These problem leads to large unsymmetrical linear systems of order 10000 and more which can now be successfully tackled by the Krylov method. The (R7) linear anomaly model is used to investigate extensively the linear response to equatorial and mid-latitude prescribed heating. The results indicate that the solution is deeply affected by the presence of the stationary waves in the basic state. The instability of the asymmetric flows, first pointed out by Simmons et al. (1983), is active also in the baroclinic case. However, the presence of baroclinic processes modifies the
Allen, Johnie J; Anderson, Craig A; Bushman, Brad J
2018-02-01
The General Aggression Model (GAM) is a comprehensive, integrative, framework for understanding aggression. It considers the role of social, cognitive, personality, developmental, and biological factors on aggression. Proximate processes of GAM detail how person and situation factors influence cognitions, feelings, and arousal, which in turn affect appraisal and decision processes, which in turn influence aggressive or nonaggressive behavioral outcomes. Each cycle of the proximate processes serves as a learning trial that affects the development and accessibility of aggressive knowledge structures. Distal processes of GAM detail how biological and persistent environmental factors can influence personality through changes in knowledge structures. GAM has been applied to understand aggression in many contexts including media violence effects, domestic violence, intergroup violence, temperature effects, pain effects, and the effects of global climate change. Copyright © 2017 Elsevier Ltd. All rights reserved.
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.
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.
Scattering of long folded strings and mixed correlators in the two-matrix model
International Nuclear Information System (INIS)
Bourgine, J.-E.; Hosomichi, K.; Kostov, I.; Matsuo, Y.
2008-01-01
We study the interactions of Maldacena's long folded strings in two-dimensional string theory. We find the amplitude for a state containing two long folded strings to come and go back to infinity. We calculate this amplitude both in the worldsheet theory and in the dual matrix model, the matrix quantum mechanics. The matrix model description allows to evaluate the amplitudes involving any number of long strings, which are given by the mixed trace correlators in an effective two-matrix model
The generalized collective model
International Nuclear Information System (INIS)
Troltenier, D.
1992-07-01
In this thesis a new way of proceeding, basing on the method of the finite elements, for the solution of the collective Schroedinger equation in the framework of the Generalized Collective Model was presented. The numerically reachable accuracy was illustrated by the comparison to analytically known solutions by means of numerous examples. Furthermore the potential-energy surfaces of the 182-196 Hg, 242-248 Cm, and 242-246 Pu isotopes were determined by the fitting of the parameters of the Gneuss-Greiner potential to the experimental data. In the Hg isotopes a shape consistency of nearly spherical and oblate deformations is shown, while the Cm and Pu isotopes possess an essentially equal remaining prolate deformation. By means of the pseudo-symplectic model the potential-energy surfaces of 24 Mg, 190 Pt, and 238 U were microscopically calculated. Using a deformation-independent kinetic energy so the collective excitation spectra and the electrical properties (B(E2), B(E4) values, quadrupole moments) of these nuclei were calculated and compared with the experiment. Finally an analytic relation between the (g R -Z/A) value and the quadrupole moment was derived. The study of the experimental data of the 166-170 Er isotopes shows an in the framework of the measurement accuracy a sufficient agreement with this relation. Furthermore it is by this relation possible to determine the effective magnetic dipole moment parameter-freely. (orig./HSI) [de
Thermodynamics of protein folding using a modified Wako-Saitô-Muñoz-Eaton model.
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.
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.
A numerical strategy for finite element modeling of frictionless asymmetric vocal fold collision.
Granados, Alba; Misztal, Marek Krzysztof; Brunskog, Jonas; Visseq, Vincent; Erleben, Kenny
2017-02-01
Analysis of voice pathologies may require vocal fold models that include relevant features such as vocal fold asymmetric collision. The present study numerically addresses the problem of frictionless asymmetric collision in a self-sustained three-dimensional continuum model of the vocal folds. 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 schemes. Finally, vocal fold contact enforcement is shown to affect asymmetric oscillations. The present model may be adapted to existing vocal fold models, which may contribute to a better understanding of the effect of the nonlinear contact phenomenon on phonation. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.
Calculation of real optical model potential for heavy ions in the framework of the folding model
International Nuclear Information System (INIS)
Goncharov, S.A.; Timofeyuk, N.K.; Kazacha, G.S.
1987-01-01
The code for calculation of a real optical model potential in the framework of the folding model is realized. The program of numerical Fourier-Bessel transformation based on Filon's integration rule is used. The accuracy of numerical calculations is ∼ 10 -4 for a distance interval up to a bout (2.5-3) times the size of nuclei. The potentials are calculated for interactions of 3,4 He with nuclei from 9 Be to 27 Al with different effective NN-interactions and densities obtained from electron scattering data. Calculated potentials are similar to phenomenological potentials in Woods-Saxon form. With calculated potentials the available elastic scattering data for the considered nuclei in the energy interval 18-56 MeV are analysed. The needed renormalizations for folding potentials are < or approx. 20%
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.)
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/.
Fold catastrophe model of dynamic pillar failure in asymmetric mining
Energy Technology Data Exchange (ETDEWEB)
Yue Pan; Ai-wu Li; Yun-song Qi [Qingdao Technological University, Qingdao (China). College of Civil Engineering
2009-01-15
A rock burst disaster not only destroys the pit facilities and results in economic loss but it also threatens the life of the miners. Pillar rock burst has a higher frequency of occurrence in the pit compared to other kinds of rock burst. Understanding the cause, magnitude and prevention of pillar rock burst is a significant undertaking. Equations describing the bending moment and displacement of the rock beam in asymmetric mining have been deduced for simplified asymmetric beam-pillar systems. Using the symbolic operation software MAPLE 9.5 a catastrophe model of the dynamic failure of an asymmetric rock-beam pillar system has been established. The differential form of the total potential function deduced from the law of conservation of energy was used for this deduction. The critical conditions and the initial and final positions of the pillar during failure have been given in analytical form. The amount of elastic energy released by the rock beam at the instant of failure is determined as well. A diagrammatic form showing the pillar failure was plotted using MATLAB software. This graph contains a wealth of information and is important for understanding the behavior during each deformation phase of the rock-beam pillar system. The graphic also aids in distinguishing the equivalent stiffness of the rock beam in different directions. 11 refs., 8 figs.
Performance of a reduced-order FSI model for flow-induced vocal fold vibration
Luo, Haoxiang; Chang, Siyuan; Chen, Ye; Rousseau, Bernard; PhonoSim Team
2017-11-01
Vocal fold vibration during speech production involves a three-dimensional unsteady glottal jet flow and three-dimensional nonlinear tissue mechanics. A full 3D fluid-structure interaction (FSI) model is computationally expensive even though it provides most accurate information about the system. On the other hand, an efficient reduced-order FSI model is useful for fast simulation and analysis of the vocal fold dynamics, which can be applied in procedures such as optimization and parameter estimation. In this work, we study performance of a reduced-order model as compared with the corresponding full 3D model in terms of its accuracy in predicting the vibration frequency and deformation mode. In the reduced-order model, we use a 1D flow model coupled with a 3D tissue model that is the same as in the full 3D model. Two different hyperelastic tissue behaviors are assumed. In addition, the vocal fold thickness and subglottal pressure are varied for systematic comparison. The result shows that the reduced-order model provides consistent predictions as the full 3D model across different tissue material assumptions and subglottal pressures. However, the vocal fold thickness has most effect on the model accuracy, especially when the vocal fold is thin.
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.
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.
Kinematic evolution of fold and thrust belts. Insights from experimental modeling
International Nuclear Information System (INIS)
Ueta, Keiichi
2011-01-01
Physical experiments were performed to gain a better understanding on the kinematic evolution of fold and thrust belts. The present study focuses on deformation of sedimentary cover caused by thrust and reverse movements along the basement fault. Our physical models comprise dry quartz sand representing brittle sedimentary rock and viscous silicone polymer representing overpressured mudstone. Computerized X-ray tomography was applied to the experiments to analyze the kinematic evolution of fold and thrust belts. In the sand models, the width of deformation zone above thrust was wider than that above reverse fault, because back thrust developed on the hanging wall of reverse fault. Within the physical models composed of dry sand and silicone polymer, minor folds and thrusts with minor displacement developed on the footwall of the major monoclinal flexure. These results compare well with the geometry and kinematic evolution of the fold and thrust belts in Japan. (author)
Orogen-transverse tectonic window in the Eastern Himalayan fold belt: A superposed buckling model
Bose, Santanu; Mandal, Nibir; Acharyya, S. K.; Ghosh, Subhajit; Saha, Puspendu
2014-09-01
The Eastern Lesser Himalayan fold-thrust belt is punctuated by a row of orogen-transverse domal tectonic windows. To evaluate their origin, a variety of thrust-stack models have been proposed, assuming that the crustal shortening occurred dominantly by brittle deformations. However, the Rangit Window (RW) in the Darjeeling-Sikkim Himalaya (DSH) shows unequivocal structural imprints of ductile deformations of multiple episodes. Based on new structural maps, coupled with outcrop-scale field observations, we recognize at least four major episodes of folding in the litho-tectonic units of DSH. The last episode has produced regionally orogen-transverse upright folds (F4), the interference of which with the third-generation (F3) orogen-parallel folds has shaped the large-scale structural patterns in DSH. We propose a new genetic model for the RW, invoking the mechanics of superposed buckling in the mechanically stratified litho-tectonic systems. We substantiate this superposed buckling model with results obtained from analogue experiments. The model explains contrasting F3-F4 interferences in the Lesser Himalayan Sequence (LHS). The lower-order (terrain-scale) folds have undergone superposed buckling in Mode 1, producing large-scale domes and basins, whereas the RW occurs as a relatively higher-order dome nested in the first-order Tista Dome. The Gondwana and the Proterozoic rocks within the RW underwent superposed buckling in Modes 3 and 4, leading to Type 2 fold interferences, as evident from their structural patterns.
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 l...... to capture different deformation patterns between the computed optical flow and the finite element deformation, controlled by the choice of the model tissue parameters........ 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...
An optical flow-based state-space model of the vocal folds.
Granados, Alba; Brunskog, Jonas
2017-06-01
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 to capture different deformation patterns between the computed optical flow and the finite element deformation, controlled by the choice of the model tissue parameters.
Suzuki, Ryo; Kawai, Yoshitaka; Tsuji, Takuya; Hiwatashi, Nao; Kishimoto, Yo; Tateya, Ichiro; Nakamura, Tatsuo; Hirano, Shigeru
2017-02-01
Vocal fold scarring, which causes severe hoarseness, is intractable. The optimal treatment for vocal fold scarring has not been established; therefore, prevention of scarring is important. The aim of this study was to clarify the effectiveness of basic fibroblast growth factor (bFGF) for prevention of postsurgical vocal fold scarring. Prospective animal experiments with controls. The vocal folds of Sprague-Dawley rats were injured unilaterally or bilaterally after local application of a 10 μL solution of bFGF. Larynges ware harvested for histological and immunohistochemical examination 2 months postoperation and for quantitative real-time polymerase chain reaction (qRT-PCR) analysis 1 week postoperation. Histological examination showed significantly increased hyaluronic acid and decreased deposition of dense collagen in the bFGF-treated group at 100 ng/10 μL compared with the sham-treated group. Immunohistochemical examination showed significantly decreased collagen type III deposition in the bFGF-treated group at 100 ng/10 μL compared with the sham-treated group. qRT-PCR revealed that hyaluronan synthase 2 (Has2), Has3, and hepatocyte growth factor were upregulated in bFGF-treated groups compared with sham-treated group. The current results suggest that local application of bFGF at the time of injury has the potential to prevent vocal fold scarring. Preventive injection of bFGF could be applied at the time of phonomicrosurgery to avoid postoperative scar formation. N/A. Laryngoscope, 2016 127:E67-E74, 2017. © 2016 The American Laryngological, Rhinological and Otological Society, Inc.
General Protein Data Bank-Based Collective Variables for Protein Folding.
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.
International Nuclear Information System (INIS)
Lammert, Heiko; Noel, Jeffrey K.; Haglund, Ellinor; Onuchic, José N.; Schug, Alexander
2015-01-01
The diversity in a set of protein nuclear magnetic resonance (NMR) structures provides an estimate of native state fluctuations that can be used to refine and enrich structure-based protein models (SBMs). Dynamics are an essential part of a protein’s functional native state. The dynamics in the native state are controlled by the same funneled energy landscape that guides the entire folding process. SBMs apply the principle of minimal frustration, drawn from energy landscape theory, to construct a funneled folding landscape for a given protein using only information from the native structure. On an energy landscape smoothed by evolution towards minimal frustration, geometrical constraints, imposed by the native structure, control the folding mechanism and shape the native dynamics revealed by the model. Native-state fluctuations can alternatively be estimated directly from the diversity in the set of NMR structures for a protein. Based on this information, we identify a highly flexible loop in the ribosomal protein S6 and modify the contact map in a SBM to accommodate the inferred dynamics. By taking into account the probable native state dynamics, the experimental transition state is recovered in the model, and the correct order of folding events is restored. Our study highlights how the shared energy landscape connects folding and function by showing that a better description of the native basin improves the prediction of the folding mechanism
Distinct Element Method modelling of fold-related fractures in a multilayer sequence
Kaserer, Klemens; Schöpfer, Martin P. J.; Grasemann, Bernhard
2017-04-01
Natural fractures have a significant impact on the performance of hydrocarbon systems/reservoirs. In a multilayer sequence, both the fracture density within the individual layers and the type of fracture intersection with bedding contacts are key parameters controlling fluid pathways. In the present study the influence of layer stacking and interlayer friction on fracture density and connectivity within a folded sequence is systematically investigated using 2D Distinct Element Method modelling. Our numerical approach permits forward modelling of both fracture nucleation/propagation/arrest and (contemporaneous) frictional slip along bedding planes in a robust and mechanically sound manner. Folding of the multilayer sequence is achieved by enforcing constant curvature folding by means of a velocity boundary condition at the model base, while a constant overburden pressure is maintained at the model top. The modelling reveals that with high bedding plane friction the multilayer stack behaves mechanically as a single layer so that the neutral surface develops in centre of the sequence and fracture spacing is controlled by the total thickness of the folded sequence. In contrast, low bedding plane friction leads to decoupling of the individual layers (flexural slip folding) so that a neutral surface develops in the centre of each layer and fracture spacing is controlled by the thickness of the individual layers. The low interfacial friction models illustrate that stepping of fractures across bedding planes is a common process, which can however have two contrasting origins: The mechanical properties of the interface cause fracture stepping during fracture propagation. Originally through-going fractures are later offset by interfacial slip during folding. A combination of these two different origins may lead to (apparently) inconsistent fracture offsets across bedding planes within a flexural slip fold.
A Corner-Point-Grid-Based Voxelization Method for Complex Geological Structure Model with Folds
Chen, Qiyu; Mariethoz, Gregoire; Liu, Gang
2017-04-01
3D voxelization is the foundation of geological property modeling, and is also an effective approach to realize the 3D visualization of the heterogeneous attributes in geological structures. The corner-point grid is a representative data model among all voxel models, and is a structured grid type that is widely applied at present. When carrying out subdivision for complex geological structure model with folds, we should fully consider its structural morphology and bedding features to make the generated voxels keep its original morphology. And on the basis of which, they can depict the detailed bedding features and the spatial heterogeneity of the internal attributes. In order to solve the shortage of the existing technologies, this work puts forward a corner-point-grid-based voxelization method for complex geological structure model with folds. We have realized the fast conversion from the 3D geological structure model to the fine voxel model according to the rule of isocline in Ramsay's fold classification. In addition, the voxel model conforms to the spatial features of folds, pinch-out and other complex geological structures, and the voxels of the laminas inside a fold accords with the result of geological sedimentation and tectonic movement. This will provide a carrier and model foundation for the subsequent attribute assignment as well as the quantitative analysis and evaluation based on the spatial voxels. Ultimately, we use examples and the contrastive analysis between the examples and the Ramsay's description of isoclines to discuss the effectiveness and advantages of the method proposed in this work when dealing with the voxelization of 3D geologic structural model with folds based on corner-point grids.
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
Frequency Response of Synthetic Vocal Fold Models with Linear and Nonlinear Material Properties
Shaw, Stephanie M.; Thomson, Scott L.; Dromey, Christopher; Smith, Simeon
2012-01-01
Purpose: The purpose of this study was to create synthetic vocal fold models with nonlinear stress-strain properties and to investigate the effect of linear versus nonlinear material properties on fundamental frequency (F[subscript 0]) during anterior-posterior stretching. Method: Three materially linear and 3 materially nonlinear models were…
Bergasa-Caceres, Fernando; Rabitz, Herschel A.
2013-06-01
A model of protein folding kinetics is applied to study the effects of macromolecular crowding on protein folding rate and stability. Macromolecular crowding is found to promote a decrease of the entropic cost of folding of proteins that produces an increase of both the stability and the folding rate. The acceleration of the folding rate due to macromolecular crowding is shown to be a topology-dependent effect. The model is applied to the folding dynamics of the murine prion protein (121-231). The differential effect of macromolecular crowding as a function of protein topology suffices to make non-native configurations relatively more accessible.
Correlation of phonatory behavior with vocal fold structure, observed in a physical model
Krane, Michael; Walters, Gage; McPhail, Michael
2017-11-01
The effect of vocal fold shape and internal structure on phonation was studied experimentally using a physical model of the human airway. Model folds used a ``M5'' or a swept ellipse coronal cross-section shape. Models were molded in either 2 or three layers. Two-layer models included a more stiff ``body'' layer and a much softer ``cover'' layer, while the 3-layer models also incorporated an additional, thin, ``ligament/conus'' layer stiffer than the body layer. The elliptical section models were all molded in 3 such layers. Measurements of transglottal pressure, volume flow, mouth sound pressure, and high-speed imaging of vocal fold vibration were performed. These show that models with the ``ligament'' layer experienced much attenuated vertical deformation, that glottal closure was more likely, and that phonation was much easier to initiate. These findings suggest that the combination of the vocal ligament and the conus elasticus stabilize the vocal fold for efficient phonation by limiting vertical deformation, while allowing transverse deformations to occur. Acknowledge support from NIH DC R01005642-11.
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
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.
Zhang, Dawei; Lazim, Raudah; Mun Yip, Yew
2017-09-01
We conducted an all-atom ab initio folding of FSD-EY, a protein with a ββα configuration using non-polarizable (AMBER) and polarizable force fields (PHB designed by Gao et al.) in implicit solvent. The effect of reducing the polarization effect integrated into the force field by the PHB model, termed the PHB0.7 was also examined in the folding of FSD-EY. This model incorporates into the force field 70% of the original polarization effect to minimize the likelihood of over-stabilizing the backbone hydrogen bonds. Precise folding of the β-sheet of FSD-EY was further achieved by relaxing the REMD structure obtained in explicit water.
Three-Dimensional Flow Separation Induced by a Model Vocal Fold Polyp
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).
Time-resolved transglottal pressure measurements in a scaled up vocal fold model
Ringenberg, Hunter; Krane, Michael; Rogers, Dylan; Misfeldt, Mitchel; Wei, Timothy
2016-11-01
Experimental measurements of flow through a scaled up dynamic human vocal fold model are presented. The simplified 10x scale vocal fold model from Krane, et al. (2007) was used to examine fundamental features of vocal fold oscillatory motion. Of particular interest was the temporal variation of transglottal pressure multiplied by the volume flow rate through the glottis throughout an oscillation cycle. Experiments were dynamically scaled to examine a range of frequencies, 100 - 200 Hz, corresponding to the male and female voice. By using water as the working fluid, very high resolution, both spatial and temporal resolution, was achieved. Time resolved movies of flow through symmetrically oscillating vocal folds will be presented. Both individual realizations as well as phase-averaged data will be shown. Key features, such as randomness and development time of the Coanda effect, vortex shedding, and volume flow rate data have been presented in previous APS-DFD meetings. This talk will focus more on the relation between the flow and aeroacoustics associated with vocal fold oscillations. Supported by the NIH.
Heterotic line bundle models on elliptically fibered Calabi-Yau three-folds
Braun, Andreas P.; Brodie, Callum R.; Lukas, Andre
2018-04-01
We analyze heterotic line bundle models on elliptically fibered Calabi-Yau three-folds over weak Fano bases. In order to facilitate Wilson line breaking to the standard model group, we focus on elliptically fibered three-folds with a second section and a freely-acting involution. Specifically, we consider toric weak Fano surfaces as base manifolds and identify six such manifolds with the required properties. The requisite mathematical tools for the construction of line bundle models on these spaces, including the calculation of line bundle cohomology, are developed. A computer scan leads to more than 400 line bundle models with the right number of families and an SU(5) GUT group which could descend to standard-like models after taking the ℤ2 quotient. A common and surprising feature of these models is the presence of a large number of vector-like states.
Finite Element Modelling of Bends and Creases during Folding Ultra Thin Stainless Steel Foils
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
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...
Cross-tropopause Transport In Tropopause Folds: Mechanisms and Sensitivity To Model Resolution
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.
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 ...
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.
Generalized, Linear, and Mixed Models
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
International Nuclear Information System (INIS)
Guo, Wei; Zhou, Jinxiong; Li, Meie
2013-01-01
Combination of soft active hydrogels with hard passive polymers gives rise to all-polymer composites. The hydrogel is sensitive to external stimuli while the passive polymer is inert. Utilizing the different behaviors of two materials subject to environmental variation, for example temperature, results in self-folding soft machines. We report our efforts to model the programmable deformation of self-folding structures with temperature-sensitive hydrogels. The self-folding structures are realized either by constructing a bilayer structure or by incorporating hydrogels as hinges. The methodology and the results may aid the design, control and fabrication of 3D complex structures from 2D simple configurations through self-assembly. (paper)
Xu, Chet C; Chan, Roger W; Sun, Han; Zhan, Xiaowei
2017-11-01
A mixed-effects model approach was introduced in this study for the statistical analysis of rheological data of vocal fold tissues, in order to account for the data correlation caused by multiple measurements of each tissue sample across the test frequency range. Such data correlation had often been overlooked in previous studies in the past decades. The viscoelastic shear properties of the vocal fold lamina propria of two commonly used laryngeal research animal species (i.e. rabbit, porcine) were measured by a linear, controlled-strain simple-shear rheometer. Along with published canine and human rheological data, the vocal fold viscoelastic shear moduli of these animal species were compared to those of human over a frequency range of 1-250Hz using the mixed-effects models. Our results indicated that tissues of the rabbit, canine and porcine vocal fold lamina propria were significantly stiffer and more viscous than those of human. Mixed-effects models were shown to be able to more accurately analyze rheological data generated from repeated measurements. Copyright © 2017 Elsevier Ltd. All rights reserved.
Generic framework for mining cellular automata models on protein-folding simulations.
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.
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…
Introduction to generalized linear models
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 ...
Three-dimensional laryngeal flow fields induced by a model vocal fold polyp
Energy Technology Data Exchange (ETDEWEB)
Erath, Byron D., E-mail: erath@gwu.edu [Department of Mechanical and Aerospace Engineering, George Washington University, 801 22nd Street NW, 739 Phillips Hall, Washington, DC 20052 (United States); Plesniak, Michael W., E-mail: plesniak@gwu.edu [Department of Mechanical and Aerospace Engineering, George Washington University, 801 22nd Street NW, 739 Phillips Hall, Washington, DC 20052 (United States)
2012-06-15
Highlights: Black-Right-Pointing-Pointer Pathological speech with a unilateral polyp is modeled in a scaled-up flow facility. Black-Right-Pointing-Pointer Vortex shedding from the polyp disrupts normal flow behavior. Black-Right-Pointing-Pointer Hairpin vortices create spatial velocity asymmetries in the glottal flow. - Abstract: Pathological laryngeal flow fields are investigated in a dynamically-driven, scaled-up model of the vocal folds. Disruption of the flow field due to the presence of a geometric protuberance, representative of a sessile unilateral polyp, is investigated in both the streamwise and transverse flow directions using phase-averaged particle image velocimetry. It is shown that the protuberance disrupts the normal flow behavior of the glottal jet throughout the phonatory cycle. During the divergent portions of the glottal cycle, the flow is characterized by the formation of hairpin vortices downstream of the protuberance. The protuberance also introduces significant velocity gradients in the anterior-posterior direction, which cover {approx}30 - 40% of the vocal fold length. It is proposed that the disruption of the normal velocity behavior owing to the presence of a polyp will adversely impact the aerodynamic loadings that drive vocal fold motion, contributing to the temporal and spatial vocal fold asymmetries that are clinically-observed in patients with unilateral polyps.
Three-dimensional laryngeal flow fields induced by a model vocal fold polyp
International Nuclear Information System (INIS)
Erath, Byron D.; Plesniak, Michael W.
2012-01-01
Highlights: ► Pathological speech with a unilateral polyp is modeled in a scaled-up flow facility. ► Vortex shedding from the polyp disrupts normal flow behavior. ► Hairpin vortices create spatial velocity asymmetries in the glottal flow. - Abstract: Pathological laryngeal flow fields are investigated in a dynamically-driven, scaled-up model of the vocal folds. Disruption of the flow field due to the presence of a geometric protuberance, representative of a sessile unilateral polyp, is investigated in both the streamwise and transverse flow directions using phase-averaged particle image velocimetry. It is shown that the protuberance disrupts the normal flow behavior of the glottal jet throughout the phonatory cycle. During the divergent portions of the glottal cycle, the flow is characterized by the formation of hairpin vortices downstream of the protuberance. The protuberance also introduces significant velocity gradients in the anterior-posterior direction, which cover ∼30 − 40% of the vocal fold length. It is proposed that the disruption of the normal velocity behavior owing to the presence of a polyp will adversely impact the aerodynamic loadings that drive vocal fold motion, contributing to the temporal and spatial vocal fold asymmetries that are clinically-observed in patients with unilateral polyps.
A kinetic model of trp-cage folding from multiple biased molecular dynamics simulations.
Directory of Open Access Journals (Sweden)
Fabrizio Marinelli
2009-08-01
Full Text Available Trp-cage is a designed 20-residue polypeptide that, in spite of its size, shares several features with larger globular proteins.Although the system has been intensively investigated experimentally and theoretically, its folding mechanism is not yet fully understood. Indeed, some experiments suggest a two-state behavior, while others point to the presence of intermediates. In this work we show that the results of a bias-exchange metadynamics simulation can be used for constructing a detailed thermodynamic and kinetic model of the system. The model, although constructed from a biased simulation, has a quality similar to those extracted from the analysis of long unbiased molecular dynamics trajectories. This is demonstrated by a careful benchmark of the approach on a smaller system, the solvated Ace-Ala3-Nme peptide. For theTrp-cage folding, the model predicts that the relaxation time of 3100 ns observed experimentally is due to the presence of a compact molten globule-like conformation. This state has an occupancy of only 3% at 300 K, but acts as a kinetic trap.Instead, non-compact structures relax to the folded state on the sub-microsecond timescale. The model also predicts the presence of a state at Calpha-RMSD of 4.4 A from the NMR structure in which the Trp strongly interacts with Pro12. This state can explain the abnormal temperature dependence of the Pro12-delta3 and Gly11-alpha3 chemical shifts. The structures of the two most stable misfolded intermediates are in agreement with NMR experiments on the unfolded protein. Our work shows that, using biased molecular dynamics trajectories, it is possible to construct a model describing in detail the Trp-cage folding kinetics and thermodynamics in agreement with experimental data.
Multimodal imaging of vocal fold scarring in a rabbit model by multiphoton microscopy
Kazarine, Alexei; Bouhabel, Sarah; Douillette, Annie H.; Kost, Karen; Li-Jessen, Nicole Y. K.; Mongeau, Luc; Wiseman, Paul W.
2017-02-01
Vocal fold scarring as a result of injury or disease can lead to voice disorders which can significantly affect the quality of life. During the scarring process, the normally elastic tissue of the vocal fold lamina propria is replaced by a much stiffer collagen-based fibrotic tissue, which impacts the fold's ability to vibrate. Surgical removal of this tissue is often ineffective and can result in further scarring. Injectable biomaterials, a form of tissue engineering, have been proposed as a potential solution to reduce existing scars or prevent scarring altogether. In order to properly evaluate the effectiveness of these new materials, multiphoton microscopy emerges as an effective tool due to its intrinsic multiple label free contrast mechanisms that highlight extracellular matrix elements. In this study, we evaluate the spatial distribution of collagen and elastin fibers in a rabbit model using second harmonic generation (SHG), third harmonic generation (THG) and two photon autofluorescence (TPAF) applied to unlabeled tissue sections. In comparison to traditional methods that rely on histological staining or immunohistochemistry, SHG, THG and TPAF provide a more reliable detection of these native proteins. The evaluation of collagen levels allows us to follow the extent of scarring, while the presence of elastin fibers is thought to be indicative of the level of healing of the injured fold. Using these imaging modalities, we characterize the outcome of injectable biomaterial treatments in order to direct future treatments for tissue engineering.
The parametrization of Coulomb barrier heights and positions using the double folding model
International Nuclear Information System (INIS)
Qu, W.W.; Zhang, G.L.; Le, X.Y.
2011-01-01
The Coulomb barrier heights and positions are systematically shown with mass numbers and charge radii of the interacting nuclei. The nuclear potential is calculated by using the double folding model with the density-dependence nucleon-nucleon interaction (CDM3Y6). The pocket formulas are obtained for the Coulomb barrier heights and positions by analyzing several hundreds of heavy-ion systems with mass numbers from light nuclei to heavy nuclei. The parameterized formulas can reproduce the calculated barrier heights and positions by using the double folding model within the accuracy of ±1%. Moreover, the results are agreeable with the experimental data. The relation between the barrier height and the barrier position is also studied.
Cluster folding-model for quasi-elastic scattering of 23Na from 208Pb
International Nuclear Information System (INIS)
Kabir, A.; Johnson, R.C.; Tostevin, M.H.
1991-01-01
A cluster model of 23 Na is used to calculate the 23 Na-target interaction potentials by folding the cluster wavefunction with the cluster-target interaction potentials. Coupled channels calculations are carried out for the quasi-elastic scattering of polarized 23 Na from 208 Pb at 170 MeV and compared with recent experiments. Qualitative agreement with experiment is obtained when the interaction is adjusted by a single overall normalization constant. (author)
A Self-Folding Hydrogel In Vitro Model for Ductal Carcinoma.
Kwag, Hye Rin; Serbo, Janna V; Korangath, Preethi; Sukumar, Saraswati; Romer, Lewis H; Gracias, David H
2016-04-01
A significant challenge in oncology is the need to develop in vitro models that accurately mimic the complex microenvironment within and around normal and diseased tissues. Here, we describe a self-folding approach to create curved hydrogel microstructures that more accurately mimic the geometry of ducts and acini within the mammary glands, as compared to existing three-dimensional block-like models or flat dishes. The microstructures are composed of photopatterned bilayers of poly (ethylene glycol) diacrylate (PEGDA), a hydrogel widely used in tissue engineering. The PEGDA bilayers of dissimilar molecular weights spontaneously curve when released from the underlying substrate due to differential swelling ratios. The photopatterns can be altered via AutoCAD-designed photomasks so that a variety of ductal and acinar mimetic structures can be mass-produced. In addition, by co-polymerizing methacrylated gelatin (methagel) with PEGDA, microstructures with increased cell adherence are synthesized. Biocompatibility and versatility of our approach is highlighted by culturing either SUM159 cells, which were seeded postfabrication, or MDA-MB-231 cells, which were encapsulated in hydrogels; cell viability is verified over 9 and 15 days, respectively. We believe that self-folding processes and associated tubular, curved, and folded constructs like the ones demonstrated here can facilitate the design of more accurate in vitro models for investigating ductal carcinoma.
The ModFOLD4 server for the quality assessment of 3D protein models
McGuffin, Liam J.; Buenavista, Maria T.; Roche, Daniel B.
2013-01-01
Once you have generated a 3D model of a protein,\\ud how do you know whether it bears any resemblance\\ud to the actual structure? To determine the usefulness\\ud of 3D models of proteins, they must be assessed in\\ud terms of their quality by methods that predict their\\ud similarity to the native structure. The ModFOLD4\\ud server is the latest version of our leading independent\\ud server for the estimation of both the global and\\ud local (per-residue) quality of 3D protein models. The\\ud server ...
Study of elastic scattering of polarized proton with 6He by folding model
International Nuclear Information System (INIS)
Iseri, Y.; Tanifuji, M.; Ishikawa, S.; Hiyama, E.; Yamamoto, Y.
2005-01-01
Experimental data of the elastic scattering of 6 He with polarized proton target has been analyzed using a simple folding model. As we regard 6 He as three bodies consisting of 4 He+n+n, the potential between the proton and 6 He is obtained by folding the two potentials, one between a proton and 4 He and another between a proton and a neutron, with the density distribution of 6 He. Calculated results of both the differential cross section and the vector analyzing power reproduce the experimental data satisfactorily. It is shown that the vector analyzing power of the p- 6 He scattering is mainly due to the spin orbit interaction between the proton and 4 He. (S. Funahashi)
Folding paper swans, modeling lives: the ritual of Filipina eldercare in Israel.
Mazuz, Keren
2013-06-01
This article examines the practices of folding paper swans by Filipina migrants employed as live-in caregivers for elderly, dying patients in Israel. These practices create a microsystem model of adjustment through precise, small-scale, and repetitive movements. This microsystem synchronizes a tripartite process: the swan's process of construction, the patient's process of decay, and the caregiver's process of self-creation. In the short term, the microsystem is sustained, but in the long term, the microsystem contains within it the seeds of its own self-destruction, as the patient eventually dies, the caregiver is reassigned to another patient or deported, and the swans are gifted. Therefore, the swan folding expands both medical anthropology understanding of caregiving as a ritual and the phenomenology of global caregivers who use immediately accessible materials-paper and glue-as an imaginative tool for ordering their daily experiences as dislocated and marginalized workers. © 2013 by the American Anthropological Association.
ModFOLD6: an accurate web server for the global and local quality estimation of 3D protein models.
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.
Generalized Ordinary Differential Equation Models.
Miao, Hongyu; Wu, Hulin; Xue, Hongqi
2014-10-01
Existing estimation methods for ordinary differential equation (ODE) models are not applicable to discrete data. The generalized ODE (GODE) model is therefore proposed and investigated for the first time. We develop the likelihood-based parameter estimation and inference methods for GODE models. We propose robust computing algorithms and rigorously investigate the asymptotic properties of the proposed estimator by considering both measurement errors and numerical errors in solving ODEs. The simulation study and application of our methods to an influenza viral dynamics study suggest that the proposed methods have a superior performance in terms of accuracy over the existing ODE model estimation approach and the extended smoothing-based (ESB) method.
Kosinski, Jan; Gajda, Michal J; Cymerman, Iwona A; Kurowski, Michal A; Pawlowski, Marcin; Boniecki, Michal; Obarska, Agnieszka; Papaj, Grzegorz; Sroczynska-Obuchowicz, Paulina; Tkaczuk, Karolina L; Sniezynska, Paulina; Sasin, Joanna M; Augustyn, Anna; Bujnicki, Janusz M; Feder, Marcin
2005-01-01
In the course of CASP6, we generated models for all targets using a new version of the "FRankenstein's monster approach." Previously (in CASP5) we were able to build many very accurate full-atom models by selection and recombination of well-folded fragments obtained from crude fold recognition (FR) results, followed by optimization of the sequence-structure fit and assessment of alternative alignments on the structural level. This procedure was however very arduous, as most of the steps required extensive visual and manual input from the human modeler. Now, we have automated the most tedious steps, such as superposition of alternative models, extraction of best-scoring fragments, and construction of a hybrid "monster" structure, as well as generation of alternative alignments in the regions that remain poorly scored in the refined hybrid model. We have also included the ROSETTA method to construct those parts of the target for which no reasonable structures were generated by FR methods (such as long insertions and terminal extensions). The analysis of successes and failures of the current version of the FRankenstein approach in modeling of CASP6 targets reveals that the considerably streamlined and automated method performs almost as well as the initial, mostly manual version, which suggests that it may be a useful tool for accurate protein structure prediction even in the hands of nonexperts. 2005 Wiley-Liss, Inc.
Saidi, Hiba; Erath, Byron D.
2015-11-01
The vocal folds play a major role in human communication by initiating voiced sound production. During voiced speech, the vocal folds are set into sustained vibrations. Synthetic self-oscillating vocal fold models are regularly employed to gain insight into flow-structure interactions governing the phonation process. Commonly, a fixed boundary condition is applied to the lateral, anterior, and posterior sides of the synthetic vocal fold models. However, physiological observations reveal the presence of adipose tissue on the lateral surface between the thyroid cartilage and the vocal folds. The goal of this study is to investigate the influence of including this substrate layer of adipose tissue on the dynamics of phonation. For a more realistic representation of the human vocal folds, synthetic multi-layer vocal fold models have been fabricated and tested while including a soft lateral layer representative of adipose tissue. Phonation parameters have been collected and are compared to those of the standard vocal fold models. Results show that vocal fold kinematics are affected by adding the adipose tissue layer as a new boundary condition.
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.
Communication: Role of explicit water models in the helix folding/unfolding processes
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.
A Self-Assisting Protein Folding Model for Teaching Structural Molecular Biology.
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.
Folding model analysis of Λ binding energies and three-body ΛNN force
International Nuclear Information System (INIS)
Mian, M.; Rahman Khan, M.Z.
1988-02-01
Working within the framework of the folding model, we analyze the Λ binding energy data of light hypernuclei with effective two-body ΛN plus three-body ΛNN interaction. The two-body density for the core nucleus required for evaluating the three-body force contribution is obtained in terms of the centre of mass pair correlation. It is found that except for Λ 5 He the data are fairly well explained. The three-body force seems to account for the density dependence of the effective two-body ΛN interaction proposed earlier. (author). 13 refs, 2 tabs
Pratt, William B; Morishima, Yoshihiro; Gestwicki, Jason E; Lieberman, Andrew P; Osawa, Yoichi
2014-11-01
In an EBM Minireview published in 2010, we proposed that the heat shock protein (Hsp)90/Hsp70-based chaperone machinery played a major role in determining the selection of proteins that have undergone oxidative or other toxic damage for ubiquitination and proteasomal degradation. The proposal was based on a model in which the Hsp90 chaperone machinery regulates signaling by modulating ligand-binding clefts. The model provides a framework for thinking about the development of neuroprotective therapies for protein-folding diseases like Alzheimer's disease (AD), Parkinson's disease (PD), and the polyglutamine expansion disorders, such as Huntington's disease (HD) and spinal and bulbar muscular atrophy (SBMA). Major aberrant proteins that misfold and accumulate in these diseases are "client" proteins of the abundant and ubiquitous stress chaperone Hsp90. These Hsp90 client proteins include tau (AD), α-synuclein (PD), huntingtin (HD), and the expanded glutamine androgen receptor (polyQ AR) (SBMA). In this Minireview, we update our model in which Hsp90 acts on protein-folding clefts and show how it forms a rational basis for developing drugs that promote the targeted elimination of these aberrant proteins. © 2014 by the Society for Experimental Biology and Medicine.
Use of the peritracheal fold in the dog tracheal transplantation model.
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.
Spherical aberration correction with an in-lens N-fold symmetric line currents model.
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.
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
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.
Ban, Myung Jin; Park, Jae Hong; Kim, Jae Wook; Park, Ki Nam; Lee, Jae Yong; Kim, Hee Kyung; Lee, Seung Won
2017-12-01
This study assessed the regenerative efficacy of basic fibroblast growth factor (FGF) in a rabbit model of chronic vocal fold scarring and then confirmed its utility and safety in a prospective trial of patients with this condition. FGF was injected three times, at 1-week intervals, into a chronic vocal fold scar created in a rabbit model. After 1 month, mRNA level of procollagen I, hyaluronic acid synthetase 2 (HAS 2), and matrix metalloproteinase 2 (MMP 2) were analyzed by real-time polymerase chain reaction. The relative densities of hyaluronic acid (HA) and collagen were examined 3 months post-injection. From April 2012 to September 2014, a prospective clinical trial was conducted at a tertiary hospital in Korea. FGF was injected into the mild vocal fold scar of 17 consecutive patients with a small glottic gap. The patients underwent perceptual, stroboscopic, acoustic aerodynamic test, and Voice Handicap Index (VHI) survey prior to and 3, 6, and 12 months after FGF injection. FGF injection of the vocal fold scar decreased the density of collagen and increased mRNA level of HAS 2 and MMP 2 expression significantly compared to the control group injected with phosphate buffered solution in a rabbit model (Pvocal fold injections of FGF in patients with mild chronic vocal fold scarring can significantly improve voice quality for as long as 1 year and without side effects. Our results recommend the use of FGF vocal fold injection as an alternative treatment modality for mild chronic vocal fold scarring.
Generalized waste package containment model
International Nuclear Information System (INIS)
Liebetrau, A.M.; Apted, M.J.
1985-02-01
The US Department of Energy (DOE) is developing a performance assessment strategy to demonstrate compliance with standards and technical requirements of the Environmental Protection Agency (EPA) and the Nuclear Regulatory Commission (NRC) for the permanent disposal of high-level nuclear wastes in geologic repositories. One aspect of this strategy is the development of a unified performance model of the entire geologic repository system. Details of a generalized waste package containment (WPC) model and its relationship with other components of an overall repository model are presented in this paper. The WPC model provides stochastically determined estimates of the distributions of times-to-failure of the barriers of a waste package by various corrosion mechanisms and degradation processes. The model consists of a series of modules which employ various combinations of stochastic (probabilistic) and mechanistic process models, and which are individually designed to reflect the current state of knowledge. The WPC model is designed not only to take account of various site-specific conditions and processes, but also to deal with a wide range of site, repository, and waste package configurations. 11 refs., 3 figs., 2 tabs
Multivariate covariance generalized linear models
DEFF Research Database (Denmark)
Bonat, W. H.; Jørgensen, Bent
2016-01-01
are fitted by using an efficient Newton scoring algorithm based on quasi-likelihood and Pearson estimating functions, using only second-moment assumptions. This provides a unified approach to a wide variety of types of response variables and covariance structures, including multivariate extensions......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...
Yang, Anxiong; Berry, David A.; Kaltenbacher, Manfred; Döllinger, Michael
2012-01-01
The human voice signal originates from the vibrations of the two vocal folds within the larynx. The interactions of several intrinsic laryngeal muscles adduct and shape the vocal folds to facilitate vibration in response to airflow. Three-dimensional vocal fold dynamics are extracted from in vitro hemilarynx experiments and fitted by a numerical three-dimensional-multi-mass-model (3DM) using an optimization procedure. In this work, the 3DM dynamics are optimized over 24 experimental data sets to estimate biomechanical vocal fold properties during phonation. Accuracy of the optimization is verified by low normalized error (0.13 ± 0.02), high correlation (83% ± 2%), and reproducible subglottal pressure values. The optimized, 3DM parameters yielded biomechanical variations in tissue properties along the vocal fold surface, including variations in both the local mass and stiffness of vocal folds. That is, both mass and stiffness increased along the superior-to-inferior direction. These variations were statistically analyzed under different experimental conditions (e.g., an increase in tension as a function of vocal fold elongation and an increase in stiffness and a decrease in mass as a function of glottal airflow). The study showed that physiologically relevant vocal fold tissue properties, which cannot be directly measured during in vivo human phonation, can be captured using this 3D-modeling technique. PMID:22352511
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.
Anisotropic charged generalized polytropic models
Nasim, A.; Azam, M.
2018-06-01
In this paper, we found some new anisotropic charged models admitting generalized polytropic equation of state with spherically symmetry. An analytic solution of the Einstein-Maxwell field equations is obtained through the transformation introduced by Durgapal and Banerji (Phys. Rev. D 27:328, 1983). The physical viability of solutions corresponding to polytropic index η =1/2, 2/3, 1, 2 is analyzed graphically. For this, we plot physical quantities such as radial and tangential pressure, anisotropy, speed of sound which demonstrated that these models achieve all the considerable physical conditions required for a relativistic star. Further, it is mentioned here that previous results for anisotropic charged matter with linear, quadratic and polytropic equation of state can be retrieved.
Theoretical models for designing a 220-GHz folded waveguide backward wave oscillator
International Nuclear Information System (INIS)
Cai Jin-Chi; Chen Huai-Bi; Hu Lin-Lin; Ma Guo-Wu; Chen Hong-Bin; Jin Xiao
2015-01-01
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. (paper)
Investigation of the three-dimensional lattice HP protein folding model using a genetic algorithm
Directory of Open Access Journals (Sweden)
Fábio L. Custódio
2004-01-01
Full Text Available An approach to the hydrophobic-polar (HP protein folding model was developed using a genetic algorithm (GA to find the optimal structures on a 3D cubic lattice. A modification was introduced to the scoring system of the original model to improve the model's capacity to generate more natural-like structures. The modification was based on the assumption that it may be preferable for a hydrophobic monomer to have a polar neighbor than to be in direct contact with the polar solvent. The compactness and the segregation criteria were used to compare structures created by the original HP model and by the modified one. An islands' algorithm, a new selection scheme and multiple-points crossover were used to improve the performance of the algorithm. Ten sequences, seven with length 27 and three with length 64 were analyzed. Our results suggest that the modified model has a greater tendency to form globular structures. This might be preferable, since the original HP model does not take into account the positioning of long polar segments. The algorithm was implemented in the form of a program with a graphical user interface that might have a didactical potential in the study of GA and on the understanding of hydrophobic core formation.
Rf modeling and design of a folded waveguide launcher for the Alcator C-Mod tokamak
International Nuclear Information System (INIS)
Bigelow, T.S.; Fogelman, C.F.; Baity, F.W.; Carter, M.D.; Hoffman, D.J.; Ryan, P.M.; Yugo, J.J.; Golovato, S.N.; Bonoli, P.
1993-01-01
The folded waveguide (FWG) launcher is being investigated as an improved antenna configuration for plasma heating in the ion cyclotron range of frequencies (ICRF). A development FWG launcher was successfully tested at Oak Ridge National Laboratory (ORNL) with a low-density plasma load and found to have significantly greater power density capability than current strap-type antennas operating in similar plasmas. To further test the concept on a high density tokamak plasma, a collaboration has been set up between ORNL and Massachusetts Institute of Technology (MIT) to develop and test an 80-MHz, 2-MW FWG on the Alcator C-Mod tokamak at MIT. The radio frequency (rf) electromagnetic modeling techniques and laboratory measurements used in the design of this antenna are described in this paper. A companion paper describes the mechanical design of the FWG
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
Discrete gauge groups in F-theory models on genus-one fibered Calabi-Yau 4-folds without section
International Nuclear Information System (INIS)
Kimura, Yusuke
2017-01-01
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.
Histological Effect of Basic Fibroblast Growth Factor on Chronic Vocal Fold Scarring in a Rat Model.
Tateya, Ichiro; Tateya, Tomoko; Sohn, Jin-Ho; Bless, Diane M
2016-03-01
Vocal fold scarring is one of the most challenging laryngeal disorders to treat and there are currently no consistently effective treatments available. Our previous studies have shown the therapeutic potential of basic fibroblast growth factor (bFGF) for vocal fold scarring. However, the histological effects of bFGF on scarred vocal fold have not been elucidated. The aim of this study was to examine the histological effects of bFGF on chronic vocal fold scarring. Sprague-Dawley rats were divided into phosphate buffered saline (sham) and bFGF groups. Unilateral vocal fold stripping was performed and the drug was injected into the scarred vocal fold for each group 2 months postoperatively. Injections were performed weekly for 4 weeks. Two months after the last injection, larynges were harvested and histologically analyzed. A significant increase of hyaluronic acid was observed in the vocal fold of the bFGF group compared with that of the sham group. However, there was no remarkable change in collagen expression nor in vocal fold contraction. Significant increase of hyaluronic acid by local bFGF injection was thought to contribute to the therapeutic effects on chronic vocal fold scarring.
The influence of material anisotropy on vibration at onset in a three-dimensional vocal fold model
Zhang, Zhaoyan
2014-01-01
Although vocal folds are known to be anisotropic, the influence of material anisotropy on vocal fold vibration remains largely unknown. Using a linear stability analysis, phonation onset characteristics were investigated in a three-dimensional anisotropic vocal fold model. The results showed that isotropic models had a tendency to vibrate in a swing-like motion, with vibration primarily along the superior-inferior direction. Anterior-posterior (AP) out-of-phase motion was also observed and large vocal fold vibration was confined to the middle third region along the AP length. In contrast, increasing anisotropy or increasing AP-transverse stiffness ratio suppressed this swing-like motion and allowed the vocal fold to vibrate in a more wave-like motion with strong medial-lateral motion over the entire medial surface. Increasing anisotropy also suppressed the AP out-of-phase motion, allowing the vocal fold to vibrate in phase along the entire AP length. Results also showed that such improvement in vibration pattern was the most effective with large anisotropy in the cover layer alone. These numerical predictions were consistent with previous experimental observations using self-oscillating physical models. It was further hypothesized that these differences may facilitate complete glottal closure in finite-amplitude vibration of anisotropic models as observed in recent experiments. PMID:24606284
Generalized model of island biodiversity
Kessler, David A.; Shnerb, Nadav M.
2015-04-01
The dynamics of a local community of competing species with weak immigration from a static regional pool is studied. Implementing the generalized competitive Lotka-Volterra model with demographic noise, a rich dynamics with four qualitatively distinct phases is unfolded. When the overall interspecies competition is weak, the island species recapitulate the mainland species. For higher values of the competition parameter, the system still admits an equilibrium community, but now some of the mainland species are absent on the island. Further increase in competition leads to an intermittent "disordered" phase, where the dynamics is controlled by invadable combinations of species and the turnover rate is governed by the migration. Finally, the strong competition phase is glasslike, dominated by uninvadable states and noise-induced transitions. Our model contains, as a special case, the celebrated neutral island theories of Wilson-MacArthur and Hubbell. Moreover, we show that slight deviations from perfect neutrality may lead to each of the phases, as the Hubbell point appears to be quadracritical.
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.
Expression of tenascin-C in a rat vocal fold injury model and its regulation of fibroblasts.
Li, Juan; Liu, Yiqiong; Wang, Yiming; Xu, Wen
2018-03-23
Tenascin-C (Tnc) is an extracellular matrix (ECM) glycoprotein that plays a vital role in wound healing and fibrotic disease. Tnc is highly upregulated soon after vocal fold injury, but its function in the vocal fold has not yet been defined. In this study, we investigated Tnc expression in a rat vocal fold injury model in vivo and its roles in fibroblasts in vitro. In vivo and in vitro. Tnc mRNA and protein expression levels were quantified on days 3, 7, 14, 28, and 56 after vocal fold injury in Sprague-Dawley rats. In vitro, immunocytochemistry, Western blot, and quantitative real-time polymerase chain reaction (qRT-PCR) analyses were performed in primary rat vocal fold fibroblasts following Tnc or transforming growth factor (TGF)-β1 stimulation to investigate the phenotypic effects. Tnc mRNA and protein expression was upregulated dramatically on days 3 and 7 after injury, and significant differences were observed by qRT-PCR (P vocal fold fibroblasts. Following incubation with Tnc for 72 hours, α-smooth muscle actin, collagen I, and fibronectin expression was significantly upregulated (P vocal fold fibroblast migration, transdifferentiation, and ECM protein synthesis in vitro. Tnc was induced by TGF-β1 in a SMAD3-dependent manner. Transient expression of Tnc is likely to promote regeneration, but its potential role in fibrosis requires further study. NA Laryngoscope, 2018. © 2018 The American Laryngological, Rhinological and Otological Society, Inc.
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.
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.
Multimodality pH imaging in a mouse dorsal skin fold window chamber model
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.
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
Double folding model of nucleus-nucleus potential: formulae, iteration method and computer code
International Nuclear Information System (INIS)
Luk'yanov, K.V.
2008-01-01
Method of construction of the nucleus-nucleus double folding potential is described. Iteration procedure for the corresponding integral equation is presented. Computer code and numerical results are presented
Implementation of a 3d numerical model of a folded multilayer carbonate aquifer
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
Martin-Rojas, Ivan; Alfaro, Pedro; Estévez, Antonio
2014-05-01
We present a study that encompasses several software tools (iGIS©, ArcGIS©, Autocad©, etc.) and data (geological mapping, high resolution digital topographic data, high resolution aerial photographs, etc.) to create a detailed 3D geometric model of an active fault propagation growth fold. This 3D model clearly shows structural features of the analysed fold, as well as growth relationships and sedimentary patterns. The results obtained permit us to discuss the kinematics and structural evolution of the fold and the fault in time and space. The study fault propagation fold is the Crevillente syncline. This fold represents the northern limit of the Bajo Segura Basin, an intermontane basin in the Eastern Betic Cordillera (SE Spain) developed from upper Miocene on. 3D features of the Crevillente syncline, including growth pattern, indicate that limb rotation and, consequently, fault activity was higher during Messinian than during Tortonian; consequently, fault activity was also higher. From Pliocene on our data point that limb rotation and fault activity steadies or probably decreases. This in time evolution of the Crevillente syncline is not the same all along the structure; actually the 3D geometric model indicates that observed lateral heterogeneity is related to along strike variation of fault displacement.
Generalized complex geometry, generalized branes and the Hitchin sigma model
International Nuclear Information System (INIS)
Zucchini, Roberto
2005-01-01
Hitchin's generalized complex geometry has been shown to be relevant in compactifications of superstring theory with fluxes and is expected to lead to a deeper understanding of mirror symmetry. Gualtieri's notion of generalized complex submanifold seems to be a natural candidate for the description of branes in this context. Recently, we introduced a Batalin-Vilkovisky field theoretic realization of generalized complex geometry, the Hitchin sigma model, extending the well known Poisson sigma model. In this paper, exploiting Gualtieri's formalism, we incorporate branes into the model. A detailed study of the boundary conditions obeyed by the world sheet fields is provided. Finally, it is found that, when branes are present, the classical Batalin-Vilkovisky cohomology contains an extra sector that is related non trivially to a novel cohomology associated with the branes as generalized complex submanifolds. (author)
Zhang, Lucy T; Yang, Jubiao
2016-12-01
In this work we explore the aerodynamics flow characteristics of a coupled fluid-structure interaction system using a generalized Bernoulli equation derived directly from the Cauchy momentum equations. Unlike the conventional Bernoulli equation where incompressible, inviscid, and steady flow conditions are assumed, this generalized Bernoulli equation includes the contributions from compressibility, viscous, and unsteadiness, which could be essential in defining aerodynamic characteristics. The application of the derived Bernoulli's principle is on a fully-coupled fluid-structure interaction simulation of the vocal folds vibration. The coupled system is simulated using the immersed finite element method where compressible Navier-Stokes equations are used to describe the air and an elastic pliable structure to describe the vocal fold. The vibration of the vocal fold works to open and close the glottal flow. The aerodynamics flow characteristics are evaluated using the derived Bernoulli's principles for a vibration cycle in a carefully partitioned control volume based on the moving structure. The results agree very well to experimental observations, which validate the strategy and its use in other types of flow characteristics that involve coupled fluid-structure interactions.
Zhang, Lucy T.; Yang, Jubiao
2017-01-01
In this work we explore the aerodynamics flow characteristics of a coupled fluid-structure interaction system using a generalized Bernoulli equation derived directly from the Cauchy momentum equations. Unlike the conventional Bernoulli equation where incompressible, inviscid, and steady flow conditions are assumed, this generalized Bernoulli equation includes the contributions from compressibility, viscous, and unsteadiness, which could be essential in defining aerodynamic characteristics. The application of the derived Bernoulli’s principle is on a fully-coupled fluid-structure interaction simulation of the vocal folds vibration. The coupled system is simulated using the immersed finite element method where compressible Navier-Stokes equations are used to describe the air and an elastic pliable structure to describe the vocal fold. The vibration of the vocal fold works to open and close the glottal flow. The aerodynamics flow characteristics are evaluated using the derived Bernoulli’s principles for a vibration cycle in a carefully partitioned control volume based on the moving structure. The results agree very well to experimental observations, which validate the strategy and its use in other types of flow characteristics that involve coupled fluid-structure interactions. PMID:29527541
Ringenberg, Hunter; Rogers, Dylan; Wei, Nathaniel; Krane, Michael; Wei, Timothy
2017-11-01
The objective of this study is to apply experimental data to theoretical framework of Krane (2013) in which the principal aeroacoustic source is expressed in terms of vocal fold drag, glottal jet dynamic head, and glottal exit volume flow, reconciling formal theoretical aeroacoustic descriptions of phonation with more traditional lumped-element descriptions. These quantities appear in the integral equations of motion for phonatory flow. In this way time resolved velocity field measurements can be used to compute time-resolved estimates of the relevant terms in the integral equations of motion, including phonation aeroacoustic source strength. A simplified 10x scale vocal fold model from Krane, et al. (2007) was used to examine symmetric, i.e. `healthy', oscillatory motion of the vocal folds. By using water as the working fluid, very high spatial and temporal resolution was achieved. Temporal variation of transglottal pressure was simultaneously measured with flow on the vocal fold model mid-height. Experiments were dynamically scaled to examine a range of frequencies corresponding to male and female voice. The simultaneity of the pressure and flow provides new insights into the aeroacoustics associated with vocal fold oscillations. Supported by NIH Grant No. 2R01 DC005642-11.
General introduction to simulation models
DEFF Research Database (Denmark)
Hisham Beshara Halasa, Tariq; Boklund, Anette
2012-01-01
trials. However, if simulation models would be used, good quality input data must be available. To model FMD, several disease spread models are available. For this project, we chose three simulation model; Davis Animal Disease Spread (DADS), that has been upgraded to DTU-DADS, InterSpread Plus (ISP......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 field...... trials to investigate the effect of alternative conditions or actions on a specific system. Nonetheless, field trials are expensive and sometimes not possible to conduct, as in case of foot-and-mouth disease (FMD). Instead, simulation models can be a good and cheap substitute for experiments and field...
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.
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 injury...... pro cess. To infer material parameters via an inverse optimization problem from recorded deformation, a self sustained theoretical mo del of the vo cal folds is needed. With this purp ose, a transversely isotropic three-dimensional nite element mo del is prop osed and investigated. Sp ecial attention...
Multivariate generalized linear mixed models using R
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...
Prompers, J.J.; Brüschweiler, R.
2002-01-01
A general framework is presented for the interpretation of NMR relaxation data of proteins. The method, termed isotropic reorientational eigenmode dynamics (iRED), relies on a principal component analysis of the isotropically averaged covariance matrix of the lattice functions of the spin
Yin, Jun; Zhang, Zhaoyan
2013-01-01
The influence of the thyroarytenoid (TA) and cricothyroid (CT) muscle activation on vocal fold stiffness and eigenfrequencies was investigated in a muscularly controlled continuum model of the vocal folds. Unlike the general understanding that vocal fold fundamental frequency was determined by vocal fold tension, this study showed that vocal fold eigenfrequencies were primarily determined by vocal fold stiffness. This study further showed that, with reference to the resting state of zero stra...
Samlan, Robin A.; Story, Brad H.
2011-01-01
Purpose: To relate vocal fold structure and kinematics to 2 acoustic measures: cepstral peak prominence (CPP) and the amplitude of the first harmonic relative to the second (H1-H2). Method: The authors used a computational, kinematic model of the medial surfaces of the vocal folds to specify features of vocal fold structure and vibration in a…
Geometric U-folds in four dimensions
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 \
Rogers, Dylan; Wei, Nathaniel; Ringenber, Hunter; Krane, Michael; Wei, Timothy
2017-11-01
This study builds on the parallel presentation of Ringenberg, et al. (APS-DFD 2017) involving simultaneous, temporally and spatially resolved flow and pressure measurements in a scaled-up vocal fold model. In this talk, data from experiments replicating characteristics of diseased vocal folds are presented. This begins with vocal folds that do not fully close and continues with asymmetric oscillations. Data are compared to symmetric, i.e. `healthy', oscillatory motions presented in the companion talk. Having pressure and flow data for individual as well as phase averaged oscillations for these diseased cases highlights the potential for aeroacoustic analysis in this complex system. Supported by NIH Grant No. 2R01 DC005642-11.
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
Self-similar voiding solutions for a single layered model of folding rocks
Dodwell, T.J.; Peletier, M.A.; Budd, C.J.; Hunt, G.W.
2011-01-01
In this paper we derive an obstacle problem with a free boundary to describe the formation of voids at areas of intense geological folding. An elastic layer is forced by overburden pressure against a V-shaped rigid obstacle. Energy minimization leads to representation as a non-linear fourth-order
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
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
Generalized latent variable modeling multilevel, longitudinal, and structural equation models
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.
General Pressurization Model in Simscape
Servin, Mario; Garcia, Vicky
2010-01-01
System integration is an essential part of the engineering design process. The Ares I Upper Stage (US) is a complex system which is made up of thousands of components assembled into subsystems including a J2-X engine, liquid hydrogen (LH2) and liquid oxygen (LO2) tanks, avionics, thrust vector control, motors, etc. System integration is the task of connecting together all of the subsystems into one large system. To ensure that all the components will "fit together" as well as safety and, quality, integration analysis is required. Integration analysis verifies that, as an integrated system, the system will behave as designed. Models that represent the actual subsystems are built for more comprehensive analysis. Matlab has been an instrument widely use by engineers to construct mathematical models of systems. Simulink, one of the tools offered by Matlab, provides multi-domain graphical environment to simulate and design time-varying systems. Simulink is a powerful tool to analyze the dynamic behavior of systems over time. Furthermore, Simscape, a tool provided by Simulink, allows users to model physical (such as mechanical, thermal and hydraulic) systems using physical networks. Using Simscape, a model representing an inflow of gas to a pressurized tank was created where the temperature and pressure of the tank are measured over time to show the behavior of the gas. By further incorporation of Simscape into model building, the full potential of this software can be discovered and it hopefully can become a more utilized tool.
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.
Process generalization in conceptual models
Wieringa, Roelf J.
In conceptual modeling, the universe of discourse (UoD) is divided into classes which have a taxonomic structure. The classes are usually defined in terms of attributes (all objects in a class share attribute names) and possibly of events. For enmple, the class of employees is the set of objects to
Vector models and generalized SYK models
Energy Technology Data Exchange (ETDEWEB)
Peng, Cheng [Department of Physics, Brown University,Providence RI 02912 (United States)
2017-05-23
We consider the relation between SYK-like models and vector models by studying a toy model where a tensor field is coupled with a vector field. By integrating out the tensor field, the toy model reduces to the Gross-Neveu model in 1 dimension. On the other hand, a certain perturbation can be turned on and the toy model flows to an SYK-like model at low energy. A chaotic-nonchaotic phase transition occurs as the sign of the perturbation is altered. We further study similar models that possess chaos and enhanced reparameterization symmetries.
Testing the generalized partial credit model
Glas, Cornelis A.W.
1996-01-01
The partial credit model (PCM) (G.N. Masters, 1982) can be viewed as a generalization of the Rasch model for dichotomous items to the case of polytomous items. In many cases, the PCM is too restrictive to fit the data. Several generalizations of the PCM have been proposed. In this paper, a generalization of the PCM (GPCM), a further generalization of the one-parameter logistic model, is discussed. The model is defined and the conditional maximum likelihood procedure for the method is describe...
Structurally and functionally characterized in vitro model of rabbit vocal fold epithelium.
Mizuta, Masanobu; Kurita, Takashi; Kimball, Emily E; Rousseau, Bernard
2017-06-01
In this paper, we describe a method for primary culture of a well differentiated electrically tight rabbit vocal fold epithelial cell multilayer and the measurement of transepithelial electrical resistance (TEER) for the evaluation of epithelial barrier function in vitro. Rabbit larynges were harvested and enzymatically treated to isolate vocal fold epithelial cells and to establish primary culture. Vocal fold epithelial cells were co-cultured with mitomycin C-treated feeder cells on collagen-coated plates. After 10-14 days in primary culture, cells were passaged and cultured until they achieved 70-90% confluence on collagen-coated plates. Epithelial cells were then passaged onto collagen-coated cell culture inserts using 4.5cm 2 membrane filters (1.0μm pore size) with 10% fetal bovine serum or 30μg/mL bovine pituitary extract to investigate the effects of growth-promoting additives on TEER. Additional experiments were performed to investigate optimal seeding density (1.1, 2.2, 4.4, or 8.9×10 5 cells/cm 2 ), the effect of co-culture with feeder cells, and the effect of passage number on epithelial barrier function. Characterization of in vitro cultures was performed using hematoxylin and eosin staining and immunostaining for vocal fold epithelial cell markers and tight junctions. Results revealed higher TEER in cells supplemented with fetal bovine serum compared to bovine pituitary extract. TEER was highest in cells passaged at a seeding density of 2.2×10 4 cells/cm 2 , and TEER was higher in cells at passage two than passage three. Ultrastructural experiments revealed a well-differentiated epithelial cell multilayer, expressing the epithelial cell markers CK13, CK14 and the tight junction proteins occludin and ZO-1. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.
Actuarial statistics with generalized linear mixed models
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
Testing the generalized partial credit model
Glas, Cornelis A.W.
1996-01-01
The partial credit model (PCM) (G.N. Masters, 1982) can be viewed as a generalization of the Rasch model for dichotomous items to the case of polytomous items. In many cases, the PCM is too restrictive to fit the data. Several generalizations of the PCM have been proposed. In this paper, a
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...
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.
A general consumer-resource population model
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.
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
A Generalized Random Regret Minimization Model
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
EOP MIT General Circulation Model (MITgcm)
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...
Generalized Reduced Order Model Generation, Phase I
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...
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.
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
Foundations of linear and generalized linear models
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,
Chistolini, Filippo; Bistacchi, Andrea; Massironi, Matteo; Consonni, Davide; Cortinovis, Silvia
2014-05-01
performed a dip-domain analysis that allowed to categorize the different fold limbs and reduce the uncertainty in the reconstruction of the fault network topology in map view. This enabled us to reconstruct a high-quality, low-uncertainty 3D structural and geological model, which unambiguously proves that deformations with a top-to-WSW Dinaric transport direction propagate farther to the west than previously supposed in this part of the Southern Alps. Our new structural reconstruction of the Vajont valley have also clarified the structural control on the 1963 catastrophic landslide (which caused over 2000 losses). Besides being a challenging natural laboratory for testing analysis and modelling methodologies to be used when reconstructing in 3D this kind of complex interference structures, the Vajont area also provides useful clues on the still-enigmatic structures in the frontal part of the Friuli-Venetian Southern Alps, buried in the Venetian Plain foredeep. These include active seismogenic thrust-faults and, at the same time, represent a growing interest for the oil industry.
Simple implementation of general dark energy models
International Nuclear Information System (INIS)
Bloomfield, Jolyon K.; Pearson, Jonathan A.
2014-01-01
We present a formalism for the numerical implementation of general theories of dark energy, combining the computational simplicity of the equation of state for perturbations approach with the generality of the effective field theory approach. An effective fluid description is employed, based on a general action describing single-scalar field models. The formalism is developed from first principles, and constructed keeping the goal of a simple implementation into CAMB in mind. Benefits of this approach include its straightforward implementation, the generality of the underlying theory, the fact that the evolved variables are physical quantities, and that model-independent phenomenological descriptions may be straightforwardly investigated. We hope this formulation will provide a powerful tool for the comparison of theoretical models of dark energy with observational data
NoFold: RNA structure clustering without folding or alignment.
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.
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
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.)
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.
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
Generalized Born Models of Macromolecular Solvation Effects
Bashford, Donald; Case, David A.
2000-10-01
It would often be useful in computer simulations to use a simple description of solvation effects, instead of explicitly representing the individual solvent molecules. Continuum dielectric models often work well in describing the thermodynamic aspects of aqueous solvation, and approximations to such models that avoid the need to solve the Poisson equation are attractive because of their computational efficiency. Here we give an overview of one such approximation, the generalized Born model, which is simple and fast enough to be used for molecular dynamics simulations of proteins and nucleic acids. We discuss its strengths and weaknesses, both for its fidelity to the underlying continuum model and for its ability to replace explicit consideration of solvent molecules in macromolecular simulations. We focus particularly on versions of the generalized Born model that have a pair-wise analytical form, and therefore fit most naturally into conventional molecular mechanics calculations.
Crash data modeling with a generalized estimator.
Ye, Zhirui; Xu, Yueru; Lord, Dominique
2018-05-11
The investigation of relationships between traffic crashes and relevant factors is important in traffic safety management. Various methods have been developed for modeling crash data. In real world scenarios, crash data often display the characteristics of over-dispersion. However, on occasions, some crash datasets have exhibited under-dispersion, especially in cases where the data are conditioned upon the mean. The commonly used models (such as the Poisson and the NB regression models) have associated limitations to cope with various degrees of dispersion. In light of this, a generalized event count (GEC) model, which can be generally used to handle over-, equi-, and under-dispersed data, is proposed in this study. This model was first applied to case studies using data from Toronto, characterized by over-dispersion, and then to crash data from railway-highway crossings in Korea, characterized with under-dispersion. The results from the GEC model were compared with those from the Negative binomial and the hyper-Poisson models. The cases studies show that the proposed model provides good performance for crash data characterized with over- and under-dispersion. Moreover, the proposed model simplifies the modeling process and the prediction of crash data. Copyright © 2018 Elsevier Ltd. All rights reserved.
A Three Dimension Model to Demonstrate Head and Tail Fold Formation in Mammalian Embryos
Bressler, Robert S.
1977-01-01
Many students have difficulty visualizing the delineation of the embryonic body from the flat germ disc. An easily-constructed model is described that has been used successfully to convey the dynamics of embryological events at Mount Sinai School of Medicine. (LBH)
Generalized formal model of Big Data
Shakhovska, N.; Veres, O.; Hirnyak, M.
2016-01-01
This article dwells on the basic characteristic features of the Big Data technologies. It is analyzed the existing definition of the “big data” term. The article proposes and describes the elements of the generalized formal model of big data. It is analyzed the peculiarities of the application of the proposed model components. It is described the fundamental differences between Big Data technology and business analytics. Big Data is supported by the distributed file system Google File System ...
A new General Lorentz Transformation model
International Nuclear Information System (INIS)
Novakovic, Branko; Novakovic, Alen; Novakovic, Dario
2000-01-01
A new general structure of Lorentz Transformations, in the form of General Lorentz Transformation model (GLT-model), has been derived. This structure includes both Lorentz-Einstein and Galilean Transformations as its particular (special) realizations. Since the free parameters of GLT-model have been identified in a gravitational field, GLT-model can be employed both in Special and General Relativity. Consequently, the possibilities of an unification of Einstein's Special and General Theories of Relativity, as well as an unification of electromagnetic and gravitational fields are opened. If GLT-model is correct then there exist four new observation phenomena (a length and time neutrality, and a length dilation and a time contraction). Besides, the well-known phenomena (a length contraction, and a time dilation) are also the constituents of GLT-model. It means that there is a symmetry in GLT-model, where the center of this symmetry is represented by a length and a time neutrality. A time and a length neutrality in a gravitational field can be realized if the velocity of a moving system is equal to the free fall velocity. A time and a length neutrality include an observation of a particle mass neutrality. A special consideration has been devoted to a correlation between GLT-model and a limitation on particle velocities in order to investigate the possibility of a travel time reduction. It is found out that an observation of a particle speed faster then c=299 792 458 m/s, is possible in a gravitational field, if certain conditions are fulfilled
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
Adaptive Inference on General Graphical Models
Acar, Umut A.; Ihler, Alexander T.; Mettu, Ramgopal; Sumer, Ozgur
2012-01-01
Many algorithms and applications involve repeatedly solving variations of the same inference problem; for example we may want to introduce new evidence to the model or perform updates to conditional dependencies. The goal of adaptive inference is to take advantage of what is preserved in the model and perform inference more rapidly than from scratch. In this paper, we describe techniques for adaptive inference on general graphs that support marginal computation and updates to the conditional ...
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
The General Education Collaboration Model: A Model for Successful Mainstreaming.
Simpson, Richard L.; Myles, Brenda Smith
1990-01-01
The General Education Collaboration Model is designed to support general educators teaching mainstreamed disabled students, through collaboration with special educators. The model is based on flexible departmentalization, program ownership, identification and development of supportive attitudes, student assessment as a measure of program…
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
Diffusion maps, clustering and fuzzy Markov modeling in peptide folding transitions
Energy Technology Data Exchange (ETDEWEB)
Nedialkova, Lilia V.; Amat, Miguel A. [Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544 (United States); Kevrekidis, Ioannis G., E-mail: yannis@princeton.edu, E-mail: gerhard.hummer@biophys.mpg.de [Department of Chemical and Biological Engineering and Program in Applied and Computational Mathematics, Princeton University, Princeton, New Jersey 08544 (United States); Hummer, Gerhard, E-mail: yannis@princeton.edu, E-mail: gerhard.hummer@biophys.mpg.de [Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main (Germany)
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.
Numerical seismic modelling of fault-fold structures in a mountainous setting
Energy Technology Data Exchange (ETDEWEB)
Kirtland Grech, M.G.; Lawton, D.C.; Spratt, D.A. (Calgary Univ., AB (Canada))
1999-01-01
Experiments were conducted to determine the performance of different prestack migration algorithms in complex structural areas, particularly in the presence of rugged topography and thrust faults that result in severe lateral and vertical velocity changes, using a series of numerical seismic models. The numerical model used was based on a cross section through the Rocky Mountains Front Ranges of Western Canada and is 33 km wide and 11 km deep. The best migrated section was obtained with FD shot migration in depth and from topography, using the known velocity model. This result was superior to Kirchhoff depth migration from topography and from a flat datum. As the velocities departed from their true value, the deeper events were most affected, because of the accumulation of velocity errors with depth. The small-scale features of Target A, in the shallower part of the section, could still be interpreted even when the velocities were inaccurate. In the presence of velocity errors, the different structures could still be interpreted, but were at the wrong depth and had the wrong structural shape and size. Layers that were of the order of 1 km in width and 500 km in thickness, such as Layer 4, were the most poorly imaged and focussed, both with time migration and with depth migration. Fault planes were not imaged in the absence of a velocity contrast across them, making some FW cutoffs difficult to interpret. 2 refs.
Numerical seismic modelling of fault-fold structures in a mountainous setting
Energy Technology Data Exchange (ETDEWEB)
Kirtland Grech, M.G.; Lawton, D.C.; Spratt, D.A. [Calgary Univ., AB (Canada)
1999-11-01
Experiments were conducted to determine the performance of different prestack migration algorithms in complex structural areas, particularly in the presence of rugged topography and thrust faults that result in severe lateral and vertical velocity changes, using a series of numerical seismic models. The numerical model used was based on a cross section through the Rocky Mountains Front Ranges of Western Canada and is 33 km wide and 11 km deep. The best migrated section was obtained with FD shot migration in depth and from topography, using the known velocity model. This result was superior to Kirchhoff depth migration from topography and from a flat datum. As the velocities departed from their true value, the deeper events were most affected, because of the accumulation of velocity errors with depth. The small-scale features of Target A, in the shallower part of the section, could still be interpreted even when the velocities were inaccurate. In the presence of velocity errors, the different structures could still be interpreted, but were at the wrong depth and had the wrong structural shape and size. Layers that were of the order of 1 km in width and 500 km in thickness, such as Layer 4, were the most poorly imaged and focussed, both with time migration and with depth migration. Fault planes were not imaged in the absence of a velocity contrast across them, making some FW cutoffs difficult to interpret. 2 refs.
General Equilibrium Models: Improving the Microeconomics Classroom
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…
Yin, Jun; Zhang, Zhaoyan
2013-01-01
The influence of the thyroarytenoid (TA) and cricothyroid (CT) muscle activation on vocal fold stiffness and eigenfrequencies was investigated in a muscularly controlled continuum model of the vocal folds. Unlike the general understanding that vocal fold fundamental frequency was determined by vocal fold tension, this study showed that vocal fold eigenfrequencies were primarily determined by vocal fold stiffness. This study further showed that, with reference to the resting state of zero strain, vocal fold stiffness in both body and cover layers increased with either vocal fold elongation or shortening. As a result, whether vocal fold eigenfrequencies increased or decreased with CT/TA activation depended on how the CT/TA interaction influenced vocal fold deformation. For conditions of strong CT activation and thus an elongated vocal fold, increasing TA contraction reduced the degree of vocal fold elongation and thus reduced vocal fold eigenfrequencies. For conditions of no CT activation and thus a resting or slightly shortened vocal fold, increasing TA contraction increased the degree of vocal fold shortening and thus increased vocal fold eigenfrequencies. In the transition region of a slightly elongated vocal fold, increasing TA contraction first decreased and then increased vocal fold eigenfrequencies. PMID:23654401
The generalized spherical model of ferromagnetic films
International Nuclear Information System (INIS)
Costache, G.
1977-12-01
The D→ infinity of the D-vectorial model of a ferromagnetic film with free surfaces is exactly solved. The mathematical mechanism responsible for the onset of a phase transition in the system is a generalized sticking phenomenon. It is shown that the temperature at which the sticking appears, the transition temperature of the model is monotonously increasing with increasing the number of layers of the film, contrary to what happens in the spherical model with overall constraint. Certain correlation inequalities of Griffiths type are shown to hold. (author)
New insights into chromatin folding and dynamics from multi-scale modeling
Olson, Wilma
The dynamic organization of chromatin plays an essential role in the regulation of gene expression and in other fundamental cellular processes. The underlying physical basis of these activities lies in the sequential positioning, chemical composition, and intermolecular interactions of the nucleosomes-the familiar assemblies of roughly 150 DNA base pairs and eight histone proteins-found on chromatin fibers. We have developed a mesoscale model of short nucleosomal arrays and a computational framework that make it possible to incorporate detailed structural features of DNA and histones in simulations of short chromatin constructs with 3-25 evenly spaced nucleosomes. The correspondence between the predicted and observed effects of nucleosome composition, spacing, and numbers on long-range communication between regulatory proteins bound to the ends of designed nucleosome arrays lends credence to the model and to the molecular insights gleaned from the simulated structures. We have extracted effective nucleosome-nucleosome potentials from the mesoscale simulations and introduced the potentials in a larger scale computational treatment of regularly repeating chromatin fibers. Our results reveal a remarkable influence of nucleosome spacing on chromatin flexibility. Small changes in the length of the DNA fragments linking successive nucleosomes introduce marked changes in the local interactions of the nucleosomes and in the spatial configurations of the fiber as a whole. The changes in nucleosome positioning influence the statistical properties of longer chromatin constructs with 100-10,000 nucleosomes. We are investigating the extent to which the `local' interactions of regularly spaced nucleosomes contribute to the corresponding interactions in chains with mixed spacings as a step toward the treatment of fibers with nucleosomes positioned at the sites mapped at base-pair resolution on genomic sequences. Support of the work by USPHS R01 GM 34809 is gratefully acknowledged.
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.
The Complexity of Folding Self-Folding Origami
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.
A General Model for Estimating Macroevolutionary Landscapes.
Boucher, Florian C; Démery, Vincent; Conti, Elena; Harmon, Luke J; Uyeda, Josef
2018-03-01
The evolution of quantitative characters over long timescales is often studied using stochastic diffusion models. The current toolbox available to students of macroevolution is however limited to two main models: Brownian motion and the Ornstein-Uhlenbeck process, plus some of their extensions. Here, we present a very general model for inferring the dynamics of quantitative characters evolving under both random diffusion and deterministic forces of any possible shape and strength, which can accommodate interesting evolutionary scenarios like directional trends, disruptive selection, or macroevolutionary landscapes with multiple peaks. This model is based on a general partial differential equation widely used in statistical mechanics: the Fokker-Planck equation, also known in population genetics as the Kolmogorov forward equation. We thus call the model FPK, for Fokker-Planck-Kolmogorov. We first explain how this model can be used to describe macroevolutionary landscapes over which quantitative traits evolve and, more importantly, we detail how it can be fitted to empirical data. Using simulations, we show that the model has good behavior both in terms of discrimination from alternative models and in terms of parameter inference. We provide R code to fit the model to empirical data using either maximum-likelihood or Bayesian estimation, and illustrate the use of this code with two empirical examples of body mass evolution in mammals. FPK should greatly expand the set of macroevolutionary scenarios that can be studied since it opens the way to estimating macroevolutionary landscapes of any conceivable shape. [Adaptation; bounds; diffusion; FPK model; macroevolution; maximum-likelihood estimation; MCMC methods; phylogenetic comparative data; selection.].
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.
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.
Higher dimensional generalizations of the SYK model
Energy Technology Data Exchange (ETDEWEB)
Berkooz, Micha [Department of Particle Physics and Astrophysics, Weizmann Institute of Science,Rehovot 7610001 (Israel); Narayan, Prithvi [International Centre for Theoretical Sciences, Hesaraghatta,Bengaluru North, 560 089 (India); Rozali, Moshe [Department of Physics and Astronomy, University of British Columbia,Vancouver, BC V6T 1Z1 (Canada); Simón, Joan [School of Mathematics and Maxwell Institute for Mathematical Sciences, University of Edinburgh,King’s Buildings, Edinburgh EH9 3FD (United Kingdom)
2017-01-31
We discuss a 1+1 dimensional generalization of the Sachdev-Ye-Kitaev model. The model contains N Majorana fermions at each lattice site with a nearest-neighbour hopping term. The SYK random interaction is restricted to low momentum fermions of definite chirality within each lattice site. This gives rise to an ordinary 1+1 field theory above some energy scale and a low energy SYK-like behavior. We exhibit a class of low-pass filters which give rise to a rich variety of hyperscaling behaviour in the IR. We also discuss another set of generalizations which describes probing an SYK system with an external fermion, together with the new scaling behavior they exhibit in the IR.
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
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...
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
A General Business Model for Marine Reserves
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
A proposed general model of information behaviour.
Directory of Open Access Journals (Sweden)
2003-01-01
Full Text Available Presents a critical description of Wilson's (1996 global model of information behaviour and proposes major modification on the basis of research into information behaviour of managers, conducted in Poland. The theoretical analysis and research results suggest that Wilson's model has certain imperfections, both in its conceptual content, and in graphical presentation. The model, for example, cannot be used to describe managers' information behaviour, since managers basically are not the end users of external from organization or computerized information services, and they acquire information mainly through various intermediaries. Therefore, the model cannot be considered as a general model, applicable to every category of information users. The proposed new model encompasses the main concepts of Wilson's model, such as: person-in-context, three categories of intervening variables (individual, social and environmental, activating mechanisms, cyclic character of information behaviours, and the adoption of a multidisciplinary approach to explain them. However, the new model introduces several changes. They include: 1. identification of 'context' with the intervening variables; 2. immersion of the chain of information behaviour in the 'context', to indicate that the context variables influence behaviour at all stages of the process (identification of needs, looking for information, processing and using it; 3. stress is put on the fact that the activating mechanisms also can occur at all stages of the information acquisition process; 4. introduction of two basic strategies of looking for information: personally and/or using various intermediaries.
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...
Generalized model of the microwave auditory effect
International Nuclear Information System (INIS)
Yitzhak, N M; Ruppin, R; Hareuveny, R
2009-01-01
A generalized theoretical model for evaluating the amplitudes of the sound waves generated in a spherical head model, which is irradiated by microwave pulses, is developed. The thermoelastic equation of motion is solved for a spherically symmetric heating pattern of arbitrary form. For previously treated heating patterns that are peaked at the sphere centre, the results reduce to those presented before. The generalized model is applied to the case in which the microwave absorption is concentrated near the sphere surface. It is found that, for equal average specific absorption rates, the sound intensity generated by a surface localized heating pattern is comparable to that generated by a heating pattern that is peaked at the centre. The dependence of the induced sound pressure on the shape of the microwave pulse is explored. Another theoretical extension, to the case of repeated pulses, is developed and applied to the interpretation of existing experimental data on the dependence of the human hearing effect threshold on the pulse repetition frequency.
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
A generalized model for compact stars
Energy Technology Data Exchange (ETDEWEB)
Aziz, Abdul [Bodai High School (H.S.), Department of Physics, Kolkata, West Bengal (India); Ray, Saibal [Government College of Engineering and Ceramic Technology, Department of Physics, Kolkata, West Bengal (India); Rahaman, Farook [Jadavpur University, Department of Mathematics, Kolkata, West Bengal (India)
2016-05-15
By virtue of the maximum entropy principle, we get an Euler-Lagrange equation which is a highly nonlinear differential equation containing the mass function and its derivatives. Solving the equation by a homotopy perturbation method we derive a generalized expression for the mass which is a polynomial function of the radial distance. Using the mass function we find a partially stable configuration and its characteristics. We show that different physical features of the known compact stars, viz. Her X-1, RX J 1856-37, SAX J (SS1), SAX J (SS2), and PSR J 1614-2230, can be explained by the present model. (orig.)
Testing Parametric versus Semiparametric Modelling in Generalized Linear Models
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.
A Model Fit Statistic for Generalized Partial Credit Model
Liang, Tie; Wells, Craig S.
2009-01-01
Investigating the fit of a parametric model is an important part of the measurement process when implementing item response theory (IRT), but research examining it is limited. A general nonparametric approach for detecting model misfit, introduced by J. Douglas and A. S. Cohen (2001), has exhibited promising results for the two-parameter logistic…
The Generalized Quantum Episodic Memory Model.
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.
RNA folding: structure prediction, folding kinetics and ion electrostatics.
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.
The epistemological status of general circulation models
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.
Generalized Penner models and multicritical behavior
International Nuclear Information System (INIS)
Tan, C.
1992-01-01
In this paper, we are interested in the critical behavior of generalized Penner models at t∼-1+μ/N where the topological expansion for the free energy develops logarithmic singularities: Γ∼-(χ 0 μ 2 lnμ+χ 1 lnμ+...). We demonstrate that these criticalities can best be characterized by the fact that the large-N generating function becomes meromorphic with a single pole term of unit residue, F(z)→1/(z-a), where a is the location of the ''sink.'' For a one-band eigenvalue distribution, we identify multicritical potentials; we find that none of these can be associated with the c=1 string compactified at an integral multiple of the self-dual radius. We also give an exact solution to the Gaussian Penner model and explicitly demonstrate that, at criticality, this solution does not correspond to a c=1 string compactified at twice the self-dual radius
Aspects of general linear modelling of migration.
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
Generalized Linear Models in Vehicle Insurance
Directory of Open Access Journals (Sweden)
Silvie Kafková
2014-01-01
Full Text Available Actuaries in insurance companies try to find the best model for an estimation of insurance premium. It depends on many risk factors, e.g. the car characteristics and the profile of the driver. In this paper, an analysis of the portfolio of vehicle insurance data using a generalized linear model (GLM is performed. The main advantage of the approach presented in this article is that the GLMs are not limited by inflexible preconditions. Our aim is to predict the relation of annual claim frequency on given risk factors. Based on a large real-world sample of data from 57 410 vehicles, the present study proposed a classification analysis approach that addresses the selection of predictor variables. The models with different predictor variables are compared by analysis of deviance and Akaike information criterion (AIC. Based on this comparison, the model for the best estimate of annual claim frequency is chosen. All statistical calculations are computed in R environment, which contains stats package with the function for the estimation of parameters of GLM and the function for analysis of deviation.
... here Home » Health Info » Voice, Speech, and Language Vocal Fold Paralysis On this page: What is vocal fold ... Where can I get additional information? What is vocal fold paralysis? Structures involved in speech and voice production ...
A general phenomenological model for work function
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.
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
A generalized model for coincidence counting
International Nuclear Information System (INIS)
Lu, Ming-Shih; Teichmann, T.
1992-01-01
The aim of this paper is to provide a description of the multiplicative processes associated with coincidence counting techniques, for example in the NDA of plutonium bearing materials. The model elucidates both the physical processes and the underlying mathematical formalism in a relatively simple but comprehensive way. In particular, it includes the effect of absorption by impurities or poisons, as well as that of neutron leakage on a parallel basis to the treatment of induced fission itself. The work thus parallels and generalizes the methods of Boehnel of Hage and Cifarelli, and more recently of Yanjushkin. This paper introduces the concept of a dual probability generating function to account for both the basic physical multiplication phenomena, as well as the detection phenomena. The underlying approach extends the idea of a simple probability generating function, due to De Moivre. The basic mathematical background may be found, for example, in Feller 1966
Corti, Alessio
2007-01-01
This edited collection of chapters, authored by leading experts, provides a complete and essentially self-contained construction of 3-fold and 4-fold klt flips. A large part of the text is a digest of Shokurov's work in the field and a concise, complete and pedagogical proof of the existence of 3-fold flips is presented. The text includes a ten page glossary and is accessible to students and researchers in algebraic geometry.
Dynamical reduction models with general gaussian noises
International Nuclear Information System (INIS)
Bassi, Angelo; Ghirardi, GianCarlo
2002-02-01
We consider the effect of replacing in stochastic differential equations leading to the dynamical collapse of the statevector, white noise stochastic processes with non white ones. We prove that such a modification can be consistently performed without altering the most interesting features of the previous models. One of the reasons to discuss this matter derives from the desire of being allowed to deal with physical stochastic fields, such as the gravitational one, which cannot give rise to white noises. From our point of view the most relevant motivation for the approach we propose here derives from the fact that in relativistic models the occurrence of white noises is the main responsible for the appearance of untractable divergences. Therefore, one can hope that resorting to non white noises one can overcome such a difficulty. We investigate stochastic equations with non white noises, we discuss their reduction properties and their physical implications. Our analysis has a precise interest not only for the above mentioned subject but also for the general study of dissipative systems and decoherence. (author)
Dynamical reduction models with general Gaussian noises
International Nuclear Information System (INIS)
Bassi, Angelo; Ghirardi, GianCarlo
2002-01-01
We consider the effect of replacing in stochastic differential equations leading to the dynamical collapse of the state vector, white-noise stochastic processes with nonwhite ones. We prove that such a modification can be consistently performed without altering the most interesting features of the previous models. One of the reasons to discuss this matter derives from the desire of being allowed to deal with physical stochastic fields, such as the gravitational one, which cannot give rise to white noises. From our point of view, the most relevant motivation for the approach we propose here derives from the fact that in relativistic models intractable divergences appear as a consequence of the white nature of the noises. Therefore, one can hope that resorting to nonwhite noises, one can overcome such a difficulty. We investigate stochastic equations with nonwhite noises, we discuss their reduction properties and their physical implications. Our analysis has a precise interest not only for the above-mentioned subject but also for the general study of dissipative systems and decoherence
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.
Evaluating the double Poisson generalized linear model.
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.
Generalized Reduced Order Modeling of Aeroservoelastic Systems
Gariffo, James Michael
Transonic aeroelastic and aeroservoelastic (ASE) modeling presents a significant technical and computational challenge. Flow fields with a mixture of subsonic and supersonic flow, as well as moving shock waves, can only be captured through high-fidelity CFD analysis. With modern computing power, it is realtively straightforward to determine the flutter boundary for a single structural configuration at a single flight condition, but problems of larger scope remain quite costly. Some such problems include characterizing a vehicle's flutter boundary over its full flight envelope, optimizing its structural weight subject to aeroelastic constraints, and designing control laws for flutter suppression. For all of these applications, reduced-order models (ROMs) offer substantial computational savings. ROM techniques in general have existed for decades, and the methodology presented in this dissertation builds on successful previous techniques to create a powerful new scheme for modeling aeroelastic systems, and predicting and interpolating their transonic flutter boundaries. In this method, linear ASE state-space models are constructed from modal structural and actuator models coupled to state-space models of the linearized aerodynamic forces through feedback loops. Flutter predictions can be made from these models through simple eigenvalue analysis of their state-transition matrices for an appropriate set of dynamic pressures. Moreover, this analysis returns the frequency and damping trend of every aeroelastic branch. In contrast, determining the critical dynamic pressure by direct time-marching CFD requires a separate run for every dynamic pressure being analyzed simply to obtain the trend for the critical branch. The present ROM methodology also includes a new model interpolation technique that greatly enhances the benefits of these ROMs. This enables predictions of the dynamic behavior of the system for flight conditions where CFD analysis has not been explicitly
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...
Finkelstein, A. V.; Galzitskaya, O. V.
2004-04-01
Protein physics is grounded on three fundamental experimental facts: protein, this long heteropolymer, has a well defined compact three-dimensional structure; this structure can spontaneously arise from the unfolded protein chain in appropriate environment; and this structure is separated from the unfolded state of the chain by the “all-or-none” phase transition, which ensures robustness of protein structure and therefore of its action. The aim of this review is to consider modern understanding of physical principles of self-organization of protein structures and to overview such important features of this process, as finding out the unique protein structure among zillions alternatives, nucleation of the folding process and metastable folding intermediates. Towards this end we will consider the main experimental facts and simple, mostly phenomenological theoretical models. We will concentrate on relatively small (single-domain) water-soluble globular proteins (whose structure and especially folding are much better studied and understood than those of large or membrane and fibrous proteins) and consider kinetic and structural aspects of transition of initially unfolded protein chains into their final solid (“native”) 3D structures.
Bayesian Subset Modeling for High-Dimensional Generalized Linear Models
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.
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)
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
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.)
Directory of Open Access Journals (Sweden)
M. Mihalikova
2012-09-01
Full Text Available Tropopause folds are one of the mechanisms of stratosphere–troposphere exchange, which can bring ozone rich stratospheric air to low altitudes in the extra-tropical regions. They have been widely studied at northern mid- or high latitudes, but so far almost no studies have been made at mid- or high southern latitudes. The Moveable Atmospheric Radar for Antarctica (MARA, a 54.5 MHz wind-profiler radar, has operated at the Swedish summer station Wasa, Antarctica (73° S, 13.5° W during austral summer seasons from 2007 to 2011 and has observed on several occasions signatures similar to those caused by tropopause folds at comparable Arctic latitudes. Here a case study is presented of one of these events when an ozonesonde successfully sampled the fold. Analysis from European Center for Medium Range Weather Forecasting (ECMWF is used to study the circumstances surrounding the event, and as boundary conditions for a mesoscale simulation using the Weather Research and Forecasting (WRF model. The fold is well resolved by the WRF simulation, and occurs on the poleward side of the polar jet stream. However, MARA resolves fine-scale layering associated with the fold better than the WRF simulation.
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
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.
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......Sensory discrimination tests such as the triangle, duo-trio, 2-AFC and 3-AFC tests produce binary data and the Thurstonian decision rule links the underlying sensory difference 6 to the observed number of correct responses. In this paper it is shown how each of these four situations can be viewed...
Ruh, Jonas B.; Gerya, Taras
2015-04-01
The Simply Folded Belt of the Zagros orogen is characterized by elongated fold trains symptomatically defining the geomorphology along this mountain range. The Zagros orogen results from the collision of the Arabian and the Eurasian plates. The Simply Folded Belt is located southwest of the Zagros suture zone. An up to 2 km thick salt horizon below the sedimentary sequence enables mechanical and structural detachment from the underlying Arabian basement. Nevertheless, deformation within the basement influences the structural evolution of the Simply Folded Belt. It has been shown that thrusts in form of reactivated normal faults can trigger out-of-sequence deformation within the sedimentary stratigraphy. Furthermore, deeply rooted strike-slip faults, such as the Kazerun faults between the Fars zone in the southeast and the Dezful embayment and the Izeh zone, are largely dispersing into the overlying stratigraphy, strongly influencing the tectonic evolution and mechanical behaviour. The aim of this study is to reveal the influence of basement thrusts and strike-slip faults on the structural evolution of the Simply Folded Belt depending on the occurrence of intercrustal weak horizons (Hormuz salt) and the rheology and thermal structure of the basement. Therefore, we present high-resolution 3D thermo-mechnical models with pre-existing, inversively reactivated normal faults or strike-slip faults within the basement. Numerical models are based on finite difference, marker-in-cell technique with (power-law) visco-plastic rheology accounting for brittle deformation. Preliminary results show that deep tectonic structures present in the basement may have crucial effects on the morphology and evolution of a fold-and-thrust belt above a major detachment horizon.
A generalization of the quantum Rabi model: exact solution and spectral structure
International Nuclear Information System (INIS)
Eckle, Hans-Peter; Johannesson, Henrik
2017-01-01
We consider a generalization of the quantum Rabi model where the two-level system and the single-mode cavity oscillator are coupled by an additional Stark-like term. By adapting a method recently introduced by Braak (2011 Phys. Rev. Lett . 107 100401), we solve the model exactly. The low-lying spectrum in the experimentally relevant ultrastrong and deep strong regimes of the Rabi coupling is found to exhibit two striking features absent from the original quantum Rabi model: avoided level crossings for states of the same parity and an anomalously rapid onset of two-fold near-degenerate levels as the Rabi coupling increases. (paper)
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.
Multivariate statistical modelling based on generalized linear models
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...
A generalized multivariate regression model for modelling ocean wave heights
Wang, X. L.; Feng, Y.; Swail, V. R.
2012-04-01
In this study, a generalized multivariate linear regression model is developed to represent the relationship between 6-hourly ocean significant wave heights (Hs) and the corresponding 6-hourly mean sea level pressure (MSLP) fields. The model is calibrated using the ERA-Interim reanalysis of Hs and MSLP fields for 1981-2000, and is validated using the ERA-Interim reanalysis for 2001-2010 and ERA40 reanalysis of Hs and MSLP for 1958-2001. The performance of the fitted model is evaluated in terms of Pierce skill score, frequency bias index, and correlation skill score. Being not normally distributed, wave heights are subjected to a data adaptive Box-Cox transformation before being used in the model fitting. Also, since 6-hourly data are being modelled, lag-1 autocorrelation must be and is accounted for. The models with and without Box-Cox transformation, and with and without accounting for autocorrelation, are inter-compared in terms of their prediction skills. The fitted MSLP-Hs relationship is then used to reconstruct historical wave height climate from the 6-hourly MSLP fields taken from the Twentieth Century Reanalysis (20CR, Compo et al. 2011), and to project possible future wave height climates using CMIP5 model simulations of MSLP fields. The reconstructed and projected wave heights, both seasonal means and maxima, are subject to a trend analysis that allows for non-linear (polynomial) trends.
Origami-Inspired Folding of Thick, Rigid Panels
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.
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)
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.
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.
INFORMATION MODEL OF A GENERAL PRACTITIONER
Directory of Open Access Journals (Sweden)
S. M. Zlepko
2016-06-01
Full Text Available In the paper the authors developed information model family doctor shows its innovation and functionality. The proposed model meets the requirements of the current job description and criteria World Organization of Family Doctors.
Generalization of Random Intercept Multilevel Models
Directory of Open Access Journals (Sweden)
Rehan Ahmad Khan
2013-10-01
Full Text Available The concept of random intercept models in a multilevel model developed by Goldstein (1986 has been extended for k-levels. The random variation in intercepts at individual level is marginally split into components by incorporating higher levels of hierarchy in the single level model. So, one can control the random variation in intercepts by incorporating the higher levels in the model.
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.
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
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.
A Generalized Deduction of the Ideal-Solution Model
Leo, Teresa J.; Perez-del-Notario, Pedro; Raso, Miguel A.
2006-01-01
A new general procedure for deriving the Gibbs energy of mixing is developed through general thermodynamic considerations, and the ideal-solution model is obtained as a special particular case of the general one. The deduction of the Gibbs energy of mixing for the ideal-solution model is a rational one and viewed suitable for advanced students who…
Stratospheric General Circulation with Chemistry Model (SGCCM)
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).
Development of a generalized integral jet model
DEFF Research Database (Denmark)
Duijm, Nijs Jan; Kessler, A.; Markert, Frank
2017-01-01
Integral type models to describe stationary plumes and jets in cross-flows (wind) have been developed since about 1970. These models are widely used for risk analysis, to describe the consequences of many different scenarios. Alternatively, CFD codes are being applied, but computational requireme......Integral type models to describe stationary plumes and jets in cross-flows (wind) have been developed since about 1970. These models are widely used for risk analysis, to describe the consequences of many different scenarios. Alternatively, CFD codes are being applied, but computational...... requirements still limit the number of scenarios that can be dealt with using CFD only. The integral models, however, are not suited to handle transient releases, such as releases from pressurized equipment, where the initially high release rate decreases rapidly with time. Further, on gas ignition, a second...... 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...
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....
Smooth generalized linear models for aggregated data
Ayma Anza, Diego Armando
2016-01-01
Mención Internacional en el título de doctor Aggregated data commonly appear in areas such as epidemiology, demography, and public health. Generally, the aggregation process is done to protect the privacy of patients, to facilitate compact presentation, or to make it comparable with other coarser datasets. However, this process may hinder the visualization of the underlying distribution that follows the data. Also, it prohibits the direct analysis of relationships between ag...
Universality in generalized models of inflation
Energy Technology Data Exchange (ETDEWEB)
Binétruy, P.; Pieroni, M. [AstroParticule et Cosmologie, Université Paris Diderot, CNRS, CEA, Observatoire de Paris, Sorbonne Paris Cité, 10, rue Alice Domon et Léonie Duquet, F-75205 Paris Cedex 13 (France); Mabillard, J., E-mail: pierre.binetruy@apc.univ-paris7.fr, E-mail: joel.mabillard@ed.ac.uk, E-mail: mauro.pieroni@apc.in2p3.fr [School of Physics and Astronomy, University of Edinburgh, Edinburgh, EH9 3JZ (United Kingdom)
2017-03-01
We discuss the cosmological evolution of a scalar field with non standard kinetic term in terms of a Renormalization Group Equation (RGE). In this framework inflation corresponds to the slow evolution in a neighborhood of a fixed point and universality classes for inflationary models naturally arise. Using some examples we show the application of the formalism. The predicted values for the speed of sound c {sub s} {sup 2} and for the amount of non-Gaussianities produced in these models are discussed. In particular, we show that it is possible to introduce models with c {sub s} {sup 2} ≠ 1 that can be in agreement with present cosmological observations.
Energy Technology Data Exchange (ETDEWEB)
Li, Chunhua [College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124 (China); Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 45108 (United States); Lv, Dashuai; Zhang, Lei; Yang, Feng; Wang, Cunxin [College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124 (China); Su, Jiguo, E-mail: jiguosu@ysu.edu.cn, E-mail: zhng@umich.edu [College of Science, Yanshan University, Qinhuangdao 066004 (China); Zhang, Yang, E-mail: jiguosu@ysu.edu.cn, E-mail: zhng@umich.edu [Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 45108 (United States)
2016-07-07
Riboswitches are noncoding mRNA segments that can regulate the gene expression via altering their structures in response to specific metabolite binding. We proposed a coarse-grained Gaussian network model (GNM) to examine the unfolding and folding dynamics of adenosine deaminase (add) A-riboswitch upon the adenine dissociation, in which the RNA is modeled by a nucleotide chain with interaction networks formed by connecting adjoining atomic contacts. It was shown that the adenine binding is critical to the folding of the add A-riboswitch while the removal of the ligand can result in drastic increase of the thermodynamic fluctuations especially in the junction regions between helix domains. Under the assumption that the native contacts with the highest thermodynamic fluctuations break first, the iterative GNM simulations showed that the unfolding process of the adenine-free add A-riboswitch starts with the denature of the terminal helix stem, followed by the loops and junctions involving ligand binding pocket, and then the central helix domains. Despite the simplified coarse-grained modeling, the unfolding dynamics and pathways are shown in close agreement with the results from atomic-level MD simulations and the NMR and single-molecule force spectroscopy experiments. Overall, the study demonstrates a new avenue to investigate the binding and folding dynamics of add A-riboswitch molecule which can be readily extended for other RNA molecules.
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
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…
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...... implementation and illustrate the application of double generalized linear compound Poisson models using a data set about car insurances....
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.
Esperanto: A Unique Model for General Linguistics.
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)
Folding model analysis of 58Ni + 64Ni elastic and inelastic scattering at Elab=203.8 and 219.2 MeV
International Nuclear Information System (INIS)
Ruiz, J.A.; Ferrero, J.L.; Bilwes, B.; Bilwes, R.
1992-01-01
Angular distributions of elastic scattering of 58 Ni by 64 Ni and inelastic scattering leading to the first 2 + state in 58 Ni or in 64 Ni were measured at E lab =203.8 and 219.2 MeV. The data were analyzed in the frame of the folding model. A renormalization N of the folding potential consistently lower than unity (N∼0.65) is needed to reproduce the elastic scattering data. Coupled-channel calculations including the main inelastic channels explain partly this discrepancy. They reproduce the elastic and inelastic scattering data with a renormalization of N∼0.8 at both energies. Interference between Coulomb and nuclear excitation is shown to play an important role in the repulsive character of the polarization potential. (author) 38 refs.; 6 figs.; 1 tab
Multiple phase transitions in the generalized Curie-Weiss model
International Nuclear Information System (INIS)
Eisele, T.; Ellis, R.S.
1988-01-01
The generalized Curie-Weiss model is an extension of the classical Curie-Weiss model in which the quadratic interaction function of the mean spin value is replaced by a more general interaction function. It is shown that the generalized Curie-Weiss model can have a sequence of phase transitions at different critical temperatures. Both first-order and second-order phase transitions can occur, and explicit criteria for the two types are given. Three examples of generalized Curie-Weiss models are worked out in detail, including one example with infinitely many phase transitions. A number of results are derived using large-deviation techniques
On A General Frame For Macroeconomic Modelling
Directory of Open Access Journals (Sweden)
Emil DINGA
2012-03-01
Full Text Available The purpose of the research project was to identify the methodological bases for the aggregate description of the Romanian national economy, both logically and in terms of the sources of empirical data for modelling. The specific objectives of the project were: a description of the economic markets in correlation with the logic description of the economic behaviours; b determination of the sectoral blocks of the Romanian economy, on the basis of the homogeneity of the economic; activity and behaviour; c association of the sectoral blocks to the national accounts, so as to ensure the sources of empirical data for the calibration and utilisation of the model; d association of the sectoral blocks to the economic markets; e association of the national accounts with the economic markets; f identification of the classes of interactions between the determined sectoral blocks.
Generalized Mathai-Quillen Topological Sigma Models
Llatas, Pablo M.
1995-01-01
A simple field theoretical approach to Mathai-Quillen topological field theories of maps $X: M_I \\to M_T$ from an internal space to a target space is presented. As an example of applications of our formalism we compute by applying our formulas the action and Q-variations of the fields of two well known topological systems: Topological Quantum Mechanics and type-A topological Sigma Model.
Reduced Order Modeling in General Relativity
Tiglio, Manuel
2014-03-01
Reduced Order Modeling is an emerging yet fast developing filed in gravitational wave physics. The main goals are to enable fast modeling and parameter estimation of any detected signal, along with rapid matched filtering detecting. I will focus on the first two. Some accomplishments include being able to replace, with essentially no lost of physical accuracy, the original models with surrogate ones (which are not effective ones, that is, they do not simplify the physics but go on a very different track, exploiting the particulars of the waveform family under consideration and state of the art dimensional reduction techniques) which are very fast to evaluate. For example, for EOB models they are at least around 3 orders of magnitude faster than solving the original equations, with physically equivalent results. For numerical simulations the speedup is at least 11 orders of magnitude. For parameter estimation our current numbers are about bringing ~100 days for a single SPA inspiral binary neutron star Bayesian parameter estimation analysis to under a day. More recently, it has been shown that the full precessing problem for, say, 200 cycles, can be represented, through some new ideas, by a remarkably compact set of carefully chosen reduced basis waveforms (~10-100, depending on the accuracy requirements). I will highlight what I personally believe are the challenges to face next in this subarea of GW physics and where efforts should be directed. This talk will summarize work in collaboration with: Harbir Antil (GMU), Jonathan Blackman (Caltech), Priscila Canizares (IoA, Cambridge, UK), Sarah Caudill (UWM), Jonathan Gair (IoA. Cambridge. UK), Scott Field (UMD), Chad R. Galley (Caltech), Frank Herrmann (Germany), Han Hestahven (EPFL, Switzerland), Jason Kaye (Brown, Stanford & Courant). Evan Ochsner (UWM), Ricardo Nochetto (UMD), Vivien Raymond (LIGO, Caltech), Rory Smith (LIGO, Caltech) Bela Ssilagyi (Caltech) and MT (UMD & Caltech).
Models and materials for generalized Kitaev magnetism
Winter, Stephen M.; Tsirlin, Alexander A.; Daghofer, Maria; van den Brink, Jeroen; Singh, Yogesh; Gegenwart, Philipp; Valentí, Roser
2017-12-01
The exactly solvable Kitaev model on the honeycomb lattice has recently received enormous attention linked to the hope of achieving novel spin-liquid states with fractionalized Majorana-like excitations. In this review, we analyze the mechanism proposed by Jackeli and Khaliullin to identify Kitaev materials based on spin-orbital dependent bond interactions and provide a comprehensive overview of its implications in real materials. We set the focus on experimental results and current theoretical understanding of planar honeycomb systems (Na2IrO3, α-Li2IrO3, and α-RuCl3), three-dimensional Kitaev materials (β- and γ-Li2IrO3), and other potential candidates, completing the review with the list of open questions awaiting new insights.
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.
The DART general equilibrium model: A technical description
Springer, Katrin
1998-01-01
This paper provides a technical description of the Dynamic Applied Regional Trade (DART) General Equilibrium Model. The DART model is a recursive dynamic, multi-region, multi-sector computable general equilibrium model. All regions are fully specified and linked by bilateral trade flows. The DART model can be used to project economic activities, energy use and trade flows for each of the specified regions to simulate various trade policy as well as environmental policy scenarios, and to analy...
Generalized bi-additive modelling for categorical data
P.J.F. Groenen (Patrick); A.J. Koning (Alex)
2004-01-01
textabstractGeneralized linear modelling (GLM) is a versatile technique, which may be viewed as a generalization of well-known techniques such as least squares regression, analysis of variance, loglinear modelling, and logistic regression. In may applications, low-order interaction (such as
A QCD Model Using Generalized Yang-Mills Theory
International Nuclear Information System (INIS)
Wang Dianfu; Song Heshan; Kou Lina
2007-01-01
Generalized Yang-Mills theory has a covariant derivative, which contains both vector and scalar gauge bosons. Based on this theory, we construct a strong interaction model by using the group U(4). By using this U(4) generalized Yang-Mills model, we also obtain a gauge potential solution, which can be used to explain the asymptotic behavior and color confinement.
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.
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.
Directory of Open Access Journals (Sweden)
Balaji Petety V
2006-04-01
Full Text Available Abstract Background The 3-D structure of none of the eukaryotic sialyltransferases (SiaTs has been determined so far. Sequence alignment algorithms such as BLAST and PSI-BLAST could not detect a homolog of these enzymes from the protein databank. SiaTs, thus, belong to the hard/medium target category in the CASP experiments. The objective of the current work is to model the 3-D structures of human SiaTs which transfer the sialic acid in α2,3-linkage viz., ST3Gal I, II, III, IV, V, and VI, using fold-recognition and comparative modeling methods. The pair-wise sequence similarity among these six enzymes ranges from 41 to 63%. Results Unlike the sequence similarity servers, fold-recognition servers identified CstII, a α2,3/8 dual-activity SiaT from Campylobacter jejuni as the homolog of all the six ST3Gals; the level of sequence similarity between CstII and ST3Gals is only 15–20% and the similarity is restricted to well-characterized motif regions of ST3Gals. Deriving template-target sequence alignments for the entire ST3Gal sequence was not straightforward: the fold-recognition servers could not find a template for the region preceding the L-motif and that between the L- and S-motifs. Multiple structural templates were identified to model these regions and template identification-modeling-evaluation had to be performed iteratively to choose the most appropriate templates. The modeled structures have acceptable stereochemical properties and are also able to provide qualitative rationalizations for some of the site-directed mutagenesis results reported in literature. Apart from the predicted models, an unexpected but valuable finding from this study is the sequential and structural relatedness of family GT42 and family GT29 SiaTs. Conclusion The modeled 3-D structures can be used for docking and other modeling studies and for the rational identification of residues to be mutated to impart desired properties such as altered stability, substrate
International Nuclear Information System (INIS)
Terazawa, H.
1986-01-01
The four-fold way is proposed in a minimal composite model of quarks and leptons. Various new pictures and consequences are presented and discussed. They include 1) generation, 2) quark-lepton mass spectrum, 3) quark mixing, 4) supersymmetry, 5) effective gauge theory. (author)
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.
Kinematics, structural mechanics, and design of origami structures with smooth folds
Peraza Hernandez, Edwin Alexander
Origami provides novel approaches to the fabrication, assembly, and functionality of engineering structures in various fields such as aerospace, robotics, etc. With the increase in complexity of the geometry and materials for origami structures that provide engineering utility, computational models and design methods for such structures have become essential. Currently available models and design methods for origami structures are generally limited to the idealization of the folds as creases of zeroth-order geometric continuity. Such an idealization is not proper for origami structures having non-negligible thickness or maximum curvature at the folds restricted by material limitations. Thus, for general structures, creased folds of merely zeroth-order geometric continuity are not appropriate representations of structural response and a new approach is needed. The first contribution of this dissertation is a model for the kinematics of origami structures having realistic folds of non-zero surface area and exhibiting higher-order geometric continuity, here termed smooth folds. The geometry of the smooth folds and the constraints on their associated kinematic variables are presented. A numerical implementation of the model allowing for kinematic simulation of structures having arbitrary fold patterns is also described. Examples illustrating the capability of the model to capture realistic structural folding response are provided. Subsequently, a method for solving the origami design problem of determining the geometry of a single planar sheet and its pattern of smooth folds that morphs into a given three-dimensional goal shape, discretized as a polygonal mesh, is presented. The design parameterization of the planar sheet and the constraints that allow for a valid pattern of smooth folds and approximation of the goal shape in a known folded configuration are presented. Various testing examples considering goal shapes of diverse geometries are provided. Afterwards, a
Learning general phonological rules from distributional information: a computational model.
Calamaro, Shira; Jarosz, Gaja
2015-04-01
Phonological rules create alternations in the phonetic realizations of related words. These rules must be learned by infants in order to identify the phonological inventory, the morphological structure, and the lexicon of a language. Recent work proposes a computational model for the learning of one kind of phonological alternation, allophony (Peperkamp, Le Calvez, Nadal, & Dupoux, 2006). This paper extends the model to account for learning of a broader set of phonological alternations and the formalization of these alternations as general rules. In Experiment 1, we apply the original model to new data in Dutch and demonstrate its limitations in learning nonallophonic rules. In Experiment 2, we extend the model to allow it to learn general rules for alternations that apply to a class of segments. In Experiment 3, the model is further extended to allow for generalization by context; we argue that this generalization must be constrained by linguistic principles. Copyright © 2014 Cognitive Science Society, Inc.
DEFF Research Database (Denmark)
Jin, Emma Yu; Nebel, M. E.
2016-01-01
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...... sparsification) may reduce the runtime to n2 on average, assuming that nucleotides of distance d form a hydrogen bond (i.e. are paired) with probability (Formula Presented.) for some constants b > 0, c > 1. The latter is called the polymer-zeta model and plays a crucial role in speeding up the above mentioned...... 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...
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...
On a Generalized Squared Gaussian Diffusion Model for Option Valuation
Directory of Open Access Journals (Sweden)
Edeki S.O.
2017-01-01
Full Text Available In financial mathematics, option pricing models are vital tools whose usefulness cannot be overemphasized. Modern approaches and modelling of financial derivatives are therefore required in option pricing and valuation settings. In this paper, we derive via the application of Ito lemma, a pricing model referred to as Generalized Squared Gaussian Diffusion Model (GSGDM for option pricing and valuation. Same approach can be considered via Stratonovich stochastic dynamics. We also show that the classical Black-Scholes, and the square root constant elasticity of variance models are special cases of the GSGDM. In addition, general solution of the GSGDM is obtained using modified variational iterative method (MVIM.
Kalman Filter for Generalized 2-D Roesser Models
Institute of Scientific and Technical Information of China (English)
SHENG Mei; ZOU Yun
2007-01-01
The design problem of the state filter for the generalized stochastic 2-D Roesser models, which appears when both the state and measurement are simultaneously subjected to the interference from white noise, is discussed. The wellknown Kalman filter design is extended to the generalized 2-D Roesser models. Based on the method of "scanning line by line", the filtering problem of generalized 2-D Roesser models with mode-energy reconstruction is solved. The formula of the optimal filtering, which minimizes the variance of the estimation error of the state vectors, is derived. The validity of the designed filter is verified by the calculation steps and the examples are introduced.
Generalized Linear Models with Applications in Engineering and the Sciences
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
Fold and Fit: Space Conserving Shape Editing
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.
Critical Comments on the General Model of Instructional Communication
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…
Membrane models and generalized Z2 gauge theories
International Nuclear Information System (INIS)
Lowe, M.J.; Wallace, D.J.
1980-01-01
We consider models of (d-n)-dimensional membranes fluctuating in a d-dimensional space under the action of surface tension. We investigate the renormalization properties of these models perturbatively and in 1/n expansion. The potential relationships of these models to generalized Z 2 gauge theories are indicated. (orig.)
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.
A Generalized Partial Credit Model: Application of an EM Algorithm.
Muraki, Eiji
1992-01-01
The partial credit model with a varying slope parameter is developed and called the generalized partial credit model (GPCM). Analysis results for simulated data by this and other polytomous item-response models demonstrate that the rating formulation of the GPCM is adaptable to the analysis of polytomous item responses. (SLD)
Linear and Generalized Linear Mixed Models and Their Applications
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
a Proposal for Generalization of 3d Models
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.
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
Czech Academy of Sciences Publication Activity Database
Horáček, Jaromír; Šidlof, Petr; Uruba, Václav; Veselý, Jan; Radolf, Vojtěch; Bula, Vítězslav
2010-01-01
Roč. 55, č. 4 (2010), s. 327-343 ISSN 0001-7043 R&D Projects: GA ČR GA101/08/1155 Institutional research plan: CEZ:AV0Z20760514 Keywords : biomechanics of voice * voice production modeling * PIV method * coherent structures Subject RIV: BI - Acoustics
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
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...
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...
Dividend taxation in an infinite-horizon general equilibrium model
Pham, Ngoc-Sang
2017-01-01
We consider an infinite-horizon general equilibrium model with heterogeneous agents and financial market imperfections. We investigate the role of dividend taxation on economic growth and asset price. The optimal dividend taxation is also studied.
Two point function for a simple general relativistic quantum model
Colosi, Daniele
2007-01-01
We study the quantum theory of a simple general relativistic quantum model of two coupled harmonic oscillators and compute the two-point function following a proposal first introduced in the context of loop quantum gravity.
Generalized model for Memristor-based Wien family oscillators
Talukdar, Abdul Hafiz Ibne; Radwan, Ahmed G.; Salama, Khaled N.
2012-01-01
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
The DINA model as a constrained general diagnostic model: Two variants of a model equivalency.
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.
A Generalized QMRA Beta-Poisson Dose-Response Model.
Xie, Gang; Roiko, Anne; Stratton, Helen; Lemckert, Charles; Dunn, Peter K; Mengersen, Kerrie
2016-10-01
Quantitative microbial risk assessment (QMRA) is widely accepted for characterizing the microbial risks associated with food, water, and wastewater. Single-hit dose-response models are the most commonly used dose-response models in QMRA. Denoting PI(d) as the probability of infection at a given mean dose d, a three-parameter generalized QMRA beta-Poisson dose-response model, PI(d|α,β,r*), is proposed in which the minimum number of organisms required for causing infection, K min , is not fixed, but a random variable following a geometric distribution with parameter 0Poisson model, PI(d|α,β), is a special case of the generalized model with K min = 1 (which implies r*=1). The generalized beta-Poisson model is based on a conceptual model with greater detail in the dose-response mechanism. Since a maximum likelihood solution is not easily available, a likelihood-free approximate Bayesian computation (ABC) algorithm is employed for parameter estimation. By fitting the generalized model to four experimental data sets from the literature, this study reveals that the posterior median r* estimates produced fall short of meeting the required condition of r* = 1 for single-hit assumption. However, three out of four data sets fitted by the generalized models could not achieve an improvement in goodness of fit. These combined results imply that, at least in some cases, a single-hit assumption for characterizing the dose-response process may not be appropriate, but that the more complex models may be difficult to support especially if the sample size is small. The three-parameter generalized model provides a possibility to investigate the mechanism of a dose-response process in greater detail than is possible under a single-hit model. © 2016 Society for Risk Analysis.
Specific and General Human Capital in an Endogenous Growth Model
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...
Dynamical CP violation of the generalized Yang-Mills model
International Nuclear Information System (INIS)
Wang Dianfu; Chang Xiaojing; Sun Xiaoyu
2011-01-01
Starting from the generalized Yang-Mills model which contains, besides the vector part V μ , also a scalar part S and a pseudoscalar part P . It is shown, in terms of the Nambu-Jona-Lasinio (NJL) mechanism, that CP violation can be realized dynamically. The combination of the generalized Yang-Mills model and the NJL mechanism provides a new way to explain CP violation. (authors)
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...
Generalized continua as models for classical and advanced materials
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.
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.
International Competition and Inequality: A Generalized Ricardian Model
Adolfo Figueroa
2014-01-01
Why does the gap in real wage rates persist between the First World and the Third World after so many years of increasing globalization? The standard neoclassical trade model predicts that real wage rates will be equalized with international trade, whereas the standard Ricardian trade model does not. Facts are thus consistent with the Ricardian model. However, this model leaves undetermined income distribution. The objective of this paper is to fill this gap by developing a generalized Ricard...
Adaptation of a general circulation model to ocean dynamics
Turner, R. E.; Rees, T. H.; Woodbury, G. E.
1976-01-01
A primitive-variable general circulation model of the ocean was formulated in which fast external gravity waves are suppressed with rigid-lid surface constraint pressires which also provide a means for simulating the effects of large-scale free-surface topography. The surface pressure method is simpler to apply than the conventional stream function models, and the resulting model can be applied to both global ocean and limited region situations. Strengths and weaknesses of the model are also presented.
A generalized statistical model for the size distribution of wealth
International Nuclear Information System (INIS)
Clementi, F; Gallegati, M; Kaniadakis, G
2012-01-01
In a recent paper in this journal (Clementi et al 2009 J. Stat. Mech. P02037), we proposed a new, physically motivated, distribution function for modeling individual incomes, having its roots in the framework of the κ-generalized statistical mechanics. The performance of the κ-generalized distribution was checked against real data on personal income for the United States in 2003. In this paper we extend our previous model so as to be able to account for the distribution of wealth. Probabilistic functions and inequality measures of this generalized model for wealth distribution are obtained in closed form. In order to check the validity of the proposed model, we analyze the US household wealth distributions from 1984 to 2009 and conclude an excellent agreement with the data that is superior to any other model already known in the literature. (paper)
A generalized statistical model for the size distribution of wealth
Clementi, F.; Gallegati, M.; Kaniadakis, G.
2012-12-01
In a recent paper in this journal (Clementi et al 2009 J. Stat. Mech. P02037), we proposed a new, physically motivated, distribution function for modeling individual incomes, having its roots in the framework of the κ-generalized statistical mechanics. The performance of the κ-generalized distribution was checked against real data on personal income for the United States in 2003. In this paper we extend our previous model so as to be able to account for the distribution of wealth. Probabilistic functions and inequality measures of this generalized model for wealth distribution are obtained in closed form. In order to check the validity of the proposed model, we analyze the US household wealth distributions from 1984 to 2009 and conclude an excellent agreement with the data that is superior to any other model already known in the literature.
Directory of Open Access Journals (Sweden)
Niklas Berliner
Full Text Available Advances in sequencing have led to a rapid accumulation of mutations, some of which are associated with diseases. However, to draw mechanistic conclusions, a biochemical understanding of these mutations is necessary. For coding mutations, accurate prediction of significant changes in either the stability of proteins or their affinity to their binding partners is required. Traditional methods have used semi-empirical force fields, while newer methods employ machine learning of sequence and structural features. Here, we show how combining both of these approaches leads to a marked boost in accuracy. We introduce ELASPIC, a novel ensemble machine learning approach that is able to predict stability effects upon mutation in both, domain cores and domain-domain interfaces. We combine semi-empirical energy terms, sequence conservation, and a wide variety of molecular details with a Stochastic Gradient Boosting of Decision Trees (SGB-DT algorithm. The accuracy of our predictions surpasses existing methods by a considerable margin, achieving correlation coefficients of 0.77 for stability, and 0.75 for affinity predictions. Notably, we integrated homology modeling to enable proteome-wide prediction and show that accurate prediction on modeled structures is possible. Lastly, ELASPIC showed significant differences between various types of disease-associated mutations, as well as between disease and common neutral mutations. Unlike pure sequence-based prediction methods that try to predict phenotypic effects of mutations, our predictions unravel the molecular details governing the protein instability, and help us better understand the molecular causes of diseases.
Modeling of chemical exergy of agricultural biomass using improved general regression neural network
International Nuclear Information System (INIS)
Huang, Y.W.; Chen, M.Q.; Li, Y.; Guo, J.
2016-01-01
A comprehensive evaluation for energy potential contained in agricultural biomass was a vital step for energy utilization of agricultural biomass. The chemical exergy of typical agricultural biomass was evaluated based on the second law of thermodynamics. The chemical exergy was significantly influenced by C and O elements rather than H element. The standard entropy of the samples also was examined based on their element compositions. Two predicted models of the chemical exergy were developed, which referred to a general regression neural network model based upon the element composition, and a linear model based upon the high heat value. An auto-refinement algorithm was firstly developed to improve the performance of regression neural network model. The developed general regression neural network model with K-fold cross-validation had a better ability for predicting the chemical exergy than the linear model, which had lower predicted errors (±1.5%). - Highlights: • Chemical exergies of agricultural biomass were evaluated based upon fifty samples. • Values for the standard entropy of agricultural biomass samples were calculated. • A linear relationship between chemical exergy and HHV of samples was detected. • An improved GRNN prediction model for the chemical exergy of biomass was developed.
Generalized entropy formalism and a new holographic dark energy model
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.
A generalized model via random walks for information filtering
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.
Quantification of Porcine Vocal Fold Geometry.
Stevens, Kimberly A; Thomson, Scott L; Jetté, Marie E; Thibeault, Susan L
2016-07-01
The aim of this study was to quantify porcine vocal fold medial surface geometry and three-dimensional geometric distortion induced by freezing the larynx, especially in the region of the vocal folds. The medial surface geometries of five excised porcine larynges were quantified and reported. Five porcine larynges were imaged in a micro-CT scanner, frozen, and rescanned. Segmentations and three-dimensional reconstructions were used to quantify and characterize geometric features. Comparisons were made with geometry data previously obtained using canine and human vocal folds as well as geometries of selected synthetic vocal fold models. Freezing induced an overall expansion of approximately 5% in the transverse plane and comparable levels of nonuniform distortion in sagittal and coronal planes. The medial surface of the porcine vocal folds was found to compare reasonably well with other geometries, although the compared geometries exhibited a notable discrepancy with one set of published human female vocal fold geometry. Porcine vocal folds are qualitatively geometrically similar to data available for canine and human vocal folds, as well as commonly used models. Freezing of tissue in the larynx causes distortion of around 5%. The data can provide direction in estimating uncertainty due to bulk distortion of tissue caused by freezing, as well as quantitative geometric data that can be directly used in developing vocal fold models. Copyright © 2016 The Voice Foundation. Published by Elsevier Inc. All rights reserved.
Merons in a generally covariant model with Gursey term
International Nuclear Information System (INIS)
Akdeniz, K.G.; Smailagic, A.
1982-10-01
We study meron solutions of the generally covariant and Weyl invariant fermionic model with Gursey term. We find that, due to the presence of this term, merons can exist even without the cosmological constant. This is a new feature compared to previously studied models. (author)
Simulation modelling in agriculture: General considerations. | R.I. ...
African Journals Online (AJOL)
A computer simulation model is a detailed working hypothesis about a given system. 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 pragmatic approach to model building is discussed; techniques are ...
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.
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).
Simplicial models for trace spaces II: General higher dimensional automata
DEFF Research Database (Denmark)
Raussen, Martin
of directed paths with given end points in a pre-cubical complex as the nerve of a particular category. The paper generalizes the results from Raussen [19, 18] in which we had to assume that the HDA in question arises from a semaphore model. In particular, important for applications, it allows for models...
Generalized algebra-valued models of set theory
Löwe, B.; Tarafder, S.
2015-01-01
We generalize the construction of lattice-valued models of set theory due to Takeuti, Titani, Kozawa and Ozawa to a wider class of algebras and show that this yields a model of a paraconsistent logic that validates all axioms of the negation-free fragment of Zermelo-Fraenkel set theory.
Efficient probabilistic model checking on general purpose graphic processors
Bosnacki, D.; Edelkamp, S.; Sulewski, D.; Pasareanu, C.S.
2009-01-01
We present algorithms for parallel probabilistic model checking on general purpose graphic processing units (GPGPUs). For this purpose we exploit the fact that some of the basic algorithms for probabilistic model checking rely on matrix vector multiplication. Since this kind of linear algebraic
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
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 distr...
A General Microscopic Traffic Model Yielding Dissipative Shocks
DEFF Research Database (Denmark)
Gaididei, Yuri Borisovich; Caputo, Jean Guy; Christiansen, Peter Leth
2018-01-01
We consider a general microscopic traffic model with a delay. An algebraic traffic function reduces the equation to the Aw-Rascle microscopic model while a sigmoid function gives the standard “follow the leader”. For zero delay we prove that the homogeneous solution is globally stable...
Nature of dynamical suppressions in the generalized Veneziano model
International Nuclear Information System (INIS)
Odorico, R.
1976-05-01
It is shown by explicit numerical calculations that of a class of coupling suppressions existing in the generalized Veneziano model, which have been recently used to interpret the psi data and other related phenomena, only a part can be attributed to the exponential growth with energy of the number of levels in the model. The remaining suppressions have a more direct dual origin
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.
Bayesian Subset Modeling for High-Dimensional Generalized Linear Models
Liang, Faming; Song, Qifan; Yu, Kai
2013-01-01
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
Infrared problems in two-dimensional generalized σ-models
International Nuclear Information System (INIS)
Curci, G.; Paffuti, G.
1989-01-01
We study the correlations of the energy-momentum tensor for classically conformally invariant generalized σ-models in the Wilson operator-product-expansion approach. We find that these correlations are, in general, infrared divergent. The absence of infrared divergences is obtained, as one can expect, for σ-models on a group manifold or for σ-models with a string-like interpretation. Moreover, the infrared divergences spoil the naive scaling arguments used by Zamolodchikov in the demonstration of the C-theorem. (orig.)
Calibration and validation of a general infiltration model
Mishra, Surendra Kumar; Ranjan Kumar, Shashi; Singh, Vijay P.
1999-08-01
A general infiltration model proposed by Singh and Yu (1990) was calibrated and validated using a split sampling approach for 191 sets of infiltration data observed in the states of Minnesota and Georgia in the USA. Of the five model parameters, fc (the final infiltration rate), So (the available storage space) and exponent n were found to be more predictable than the other two parameters: m (exponent) and a (proportionality factor). A critical examination of the general model revealed that it is related to the Soil Conservation Service (1956) curve number (SCS-CN) method and its parameter So is equivalent to the potential maximum retention of the SCS-CN method and is, in turn, found to be a function of soil sorptivity and hydraulic conductivity. The general model was found to describe infiltration rate with time varying curve number.
Spherical images and inextensible curved folding
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.
Partially Observed Mixtures of IRT Models: An Extension of the Generalized Partial-Credit Model
Von Davier, Matthias; Yamamoto, Kentaro
2004-01-01
The generalized partial-credit model (GPCM) is used frequently in educational testing and in large-scale assessments for analyzing polytomous data. Special cases of the generalized partial-credit model are the partial-credit model--or Rasch model for ordinal data--and the two parameter logistic (2PL) model. This article extends the GPCM to the…
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...
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)
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…
Generalized Tavis-Cummings models and quantum networks
Gorokhov, A. V.
2018-04-01
The properties of quantum networks based on generalized Tavis-Cummings models are theoretically investigated. We have calculated the information transfer success rate from one node to another in a simple model of a quantum network realized with two-level atoms placed in the cavities and interacting with an external laser field and cavity photons. The method of dynamical group of the Hamiltonian and technique of corresponding coherent states were used for investigation of the temporal dynamics of the two nodes model.
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.)
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.)
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.
Generalized heat-transport equations: parabolic and hyperbolic models
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.
Approaching climate-adaptive facades with foldings
DEFF Research Database (Denmark)
Sack-Nielsen, Torsten
2014-01-01
envelopes based on folding principles such as origami. Three major aspects cover the project’s interest in this topic: Shape, kinetics and the application of new multi-functional materials form the interdisciplinary framework of this research. Shape// Initially small paper sketch models demonstrate folding...
Generalized semi-Markovian dividend discount model: risk and return
D'Amico, Guglielmo
2016-01-01
The article presents a general discrete time dividend valuation model when the dividend growth rate is a general continuous variable. The main assumption is that the dividend growth rate follows a discrete time semi-Markov chain with measurable space. The paper furnishes sufficient conditions that assure finiteness of fundamental prices and risks and new equations that describe the first and second order price-dividend ratios. Approximation methods to solve equations are provided and some new...
Practical likelihood analysis for spatial generalized linear mixed models
DEFF Research Database (Denmark)
Bonat, W. H.; Ribeiro, Paulo Justiniano
2016-01-01
We investigate an algorithm for maximum likelihood estimation of spatial generalized linear mixed models based on the Laplace approximation. We compare our algorithm with a set of alternative approaches for two datasets from the literature. The Rhizoctonia root rot and the Rongelap are......, 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...... of Laplace approximation include the computation of the maximized log-likelihood value, which can be used for model selection and tests, and the possibility to obtain realistic confidence intervals for model parameters based on profile likelihoods. The Laplace approximation also avoids the tuning...
Modeling the brain morphology distribution in the general aging population
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.
A general diagnostic model applied to language testing data.
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.
Generalized additive model of air pollution to daily mortality
International Nuclear Information System (INIS)
Kim, J.; Yang, H.E.
2005-01-01
The association of air pollution with daily mortality due to cardiovascular disease, respiratory disease, and old age (65 or older) in Seoul, Korea was investigated in 1999 using daily values of TSP, PM10, O 3 , SO 2 , NO 2 , and CO. Generalized additive Poisson models were applied to allow for the highly flexible fitting of daily trends in air pollution as well as nonlinear association with meteorological variables such as temperature, humidity, and wind speed. To estimate the effect of air pollution and weather on mortality, LOESS smoothing was used in generalized additive models. The findings suggest that air pollution levels affect significantly the daily mortality. (orig.)
Kinematics of large scale asymmetric folds and associated smaller ...
Indian Academy of Sciences (India)
The present work reiterates the importance of analysis of ... these models is the assumption that the folds are passive folds ... applicability of these models is thus limited in the case of ...... with contrasted rheological properties, a theory for the.
Generalized memory associativity in a network model for the neuroses
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.
Seekhao, Nuttiiya; Shung, Caroline; JaJa, Joseph; Mongeau, Luc; Li-Jessen, Nicole Y K
2016-05-01
We present an efficient and scalable scheme for implementing agent-based modeling (ABM) simulation with In Situ visualization of large complex systems on heterogeneous computing platforms. The scheme is designed to make optimal use of the resources available on a heterogeneous platform consisting of a multicore CPU and a GPU, resulting in minimal to no resource idle time. Furthermore, the scheme was implemented under a client-server paradigm that enables remote users to visualize and analyze simulation data as it is being generated at each time step of the model. Performance of a simulation case study of vocal fold inflammation and wound healing with 3.8 million agents shows 35× and 7× speedup in execution time over single-core and multi-core CPU respectively. Each iteration of the model took less than 200 ms to simulate, visualize and send the results to the client. This enables users to monitor the simulation in real-time and modify its course as needed.
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.
Seasonal predictability of Kiremt rainfall in coupled general circulation models
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.
Interacting holographic dark energy models: a general approach
Som, S.; Sil, A.
2014-08-01
Dark energy models inspired by the cosmological holographic principle are studied in homogeneous isotropic spacetime with a general choice for the dark energy density . Special choices of the parameters enable us to obtain three different holographic models, including the holographic Ricci dark energy (RDE) model. Effect of interaction between dark matter and dark energy on the dynamics of those models are investigated for different popular forms of interaction. It is found that crossing of phantom divide can be avoided in RDE models for β>0.5 irrespective of the presence of interaction. A choice of α=1 and β=2/3 leads to a varying Λ-like model introducing an IR cutoff length Λ -1/2. It is concluded that among the popular choices an interaction of the form Q∝ Hρ m suits the best in avoiding the coincidence problem in this model.
A comparison of RNA folding measures
Directory of Open Access Journals (Sweden)
Gardner Paul P
2005-10-01
Full Text Available Abstract 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. Conclusion Due to the correlations between the different measures we find that it is sufficient to use only two of them in RNA folding studies, one to test if the sequence in question has lower energy than a random sequence with the same dinucleotide frequency (the Z-score and the other to see if the sequence has a unique fold (the average base-pair distance, D.
a Model Study of Small-Scale World Map Generalization
Cheng, Y.; Yin, Y.; Li, C. M.; Wu, W.; Guo, P. P.; Ma, X. L.; Hu, F. M.
2018-04-01
With the globalization and rapid development every filed is taking an increasing interest in physical geography and human economics. There is a surging demand for small scale world map in large formats all over the world. Further study of automated mapping technology, especially the realization of small scale production on a large scale global map, is the key of the cartographic field need to solve. In light of this, this paper adopts the improved model (with the map and data separated) in the field of the mapmaking generalization, which can separate geographic data from mapping data from maps, mainly including cross-platform symbols and automatic map-making knowledge engine. With respect to the cross-platform symbol library, the symbol and the physical symbol in the geographic information are configured at all scale levels. With respect to automatic map-making knowledge engine consists 97 types, 1086 subtypes, 21845 basic algorithm and over 2500 relevant functional modules.In order to evaluate the accuracy and visual effect of our model towards topographic maps and thematic maps, we take the world map generalization in small scale as an example. After mapping generalization process, combining and simplifying the scattered islands make the map more explicit at 1 : 2.1 billion scale, and the map features more complete and accurate. Not only it enhance the map generalization of various scales significantly, but achieve the integration among map-makings of various scales, suggesting that this model provide a reference in cartographic generalization for various scales.
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
Optimisation of a parallel ocean general circulation model
M. I. Beare; D. P. Stevens
1997-01-01
International audience; This paper presents the development of a general-purpose parallel ocean circulation model, for use on a wide range of computer platforms, from traditional scalar machines to workstation clusters and massively parallel processors. Parallelism is provided, as a modular option, via high-level message-passing routines, thus hiding the technical intricacies from the user. An initial implementation highlights that the parallel efficiency of the model is adversely affected by...
A general graphical user interface for automatic reliability modeling
Liceaga, Carlos A.; Siewiorek, Daniel P.
1991-01-01
Reported here is a general Graphical User Interface (GUI) for automatic reliability modeling of Processor Memory Switch (PMS) structures using a Markov model. This GUI is based on a hierarchy of windows. One window has graphical editing capabilities for specifying the system's communication structure, hierarchy, reconfiguration capabilities, and requirements. Other windows have field texts, popup menus, and buttons for specifying parameters and selecting actions. An example application of the GUI is given.
Optimal Designs for the Generalized Partial Credit Model
Bürkner, Paul-Christian; Schwabe, Rainer; Holling, Heinz
2018-01-01
Analyzing ordinal data becomes increasingly important in psychology, especially in the context of item response theory. The generalized partial credit model (GPCM) is probably the most widely used ordinal model and finds application in many large scale educational assessment studies such as PISA. In the present paper, optimal test designs are investigated for estimating persons' abilities with the GPCM for calibrated tests when item parameters are known from previous studies. We will derive t...
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
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
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 ...
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 ...
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.
Confidence Intervals for Assessing Heterogeneity in Generalized Linear Mixed Models
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…
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...
An applied general equilibrium model for Dutch agribusiness policy analysis
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
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
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
A generalized development model for testing GPS user equipment
Hemesath, N.
1978-01-01
The generalized development model (GDM) program, which was intended to establish how well GPS user equipment can perform under a combination of jamming and dynamics, is described. The systems design and the characteristics of the GDM are discussed. The performance aspects of the GDM are listed and the application of the GDM to civil aviation is examined.
Salehin, Z.; Woobaidullah, A. S. M.; Snigdha, S. S.
2015-12-01
Bengal Basin with its prolific gas rich province provides needed energy to Bangladesh. Present energy situation demands more Hydrocarbon explorations. Only 'Semutang' is discovered in the high amplitude structures, where rest of are in the gentle to moderate structures of western part of Chittagong-Tripura Fold Belt. But it has some major thrust faults which have strongly breached the reservoir zone. The major objectives of this research are interpretation of gas horizons and faults, then to perform velocity model, structural and property modeling to obtain reservoir properties. It is needed to properly identify the faults and reservoir heterogeneities. 3D modeling is widely used to reveal the subsurface structure in faulted zone where planning and development drilling is major challenge. Thirteen 2D seismic and six well logs have been used to identify six gas bearing horizons and a network of faults and to map the structure at reservoir level. Variance attributes were used to identify faults. Velocity model is performed for domain conversion. Synthetics were prepared from two wells where sonic and density logs are available. Well to seismic tie at reservoir zone shows good match with Direct Hydrocarbon Indicator on seismic section. Vsh, porosity, water saturation and permeability have been calculated and various cross plots among porosity logs have been shown. Structural modeling is used to make zone and layering accordance with minimum sand thickness. Fault model shows the possible fault network, those liable for several dry wells. Facies model have been constrained with Sequential Indicator Simulation method to show the facies distribution along the depth surfaces. Petrophysical models have been prepared with Sequential Gaussian Simulation to estimate petrophysical parameters away from the existing wells to other parts of the field and to observe heterogeneities in reservoir. Average porosity map for each gas zone were constructed. The outcomes of the research
Solitons and protein folding: An In Silico experiment
International Nuclear Information System (INIS)
Ilieva, N.; Dai, J.; Sieradzan, A.; Niemi, A.
2015-01-01
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
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.
A General Model for Testing Mediation and Moderation Effects
MacKinnon, David P.
2010-01-01
This paper describes methods for testing mediation and moderation effects in a dataset, both together and separately. Investigations of this kind are especially valuable in prevention research to obtain information on the process by which a program achieves its effects and whether the program is effective for subgroups of individuals. A general model that simultaneously estimates mediation and moderation effects is presented, and the utility of combining the effects into a single model is described. Possible effects of interest in the model are explained, as are statistical methods to assess these effects. The methods are further illustrated in a hypothetical prevention program example. PMID:19003535
Generalized Jaynes-Cummings model as a quantum search algorithm
International Nuclear Information System (INIS)
Romanelli, A.
2009-01-01
We propose a continuous time quantum search algorithm using a generalization of the Jaynes-Cummings model. In this model the states of the atom are the elements among which the algorithm realizes the search, exciting resonances between the initial and the searched states. This algorithm behaves like Grover's algorithm; the optimal search time is proportional to the square root of the size of the search set and the probability to find the searched state oscillates periodically in time. In this frame, it is possible to reinterpret the usual Jaynes-Cummings model as a trivial case of the quantum search algorithm.
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,
Zeros of the partition function for some generalized Ising models
International Nuclear Information System (INIS)
Dunlop, F.
1981-01-01
The author considers generalized Ising Models with two and four body interactions in a complex external field h such that Re h>=mod(Im h) + C, where C is an explicit function of the interaction parameters. The partition function Z(h) is then shown to satisfy mod(Z(h))>=Z(c), so that the pressure is analytic in h inside the given region. The method is applied to specific examples: the gauge invariant Ising Model, and the Widom Rowlinson model on the lattice. (Auth.)
A Graphical User Interface to Generalized Linear Models in MATLAB
Directory of Open Access Journals (Sweden)
Peter Dunn
1999-07-01
Full Text Available Generalized linear models unite a wide variety of statistical models in a common theoretical framework. This paper discusses GLMLAB-software that enables such models to be fitted in the popular mathematical package MATLAB. It provides a graphical user interface to the powerful MATLAB computational engine to produce a program that is easy to use but with many features, including offsets, prior weights and user-defined distributions and link functions. MATLAB's graphical capacities are also utilized in providing a number of simple residual diagnostic plots.
A General Accelerated Degradation Model Based on the Wiener Process.
Liu, Le; Li, Xiaoyang; Sun, Fuqiang; Wang, Ning
2016-12-06
Accelerated degradation testing (ADT) is an efficient tool to conduct material service reliability and safety evaluations by analyzing performance degradation data. Traditional stochastic process models are mainly for linear or linearization degradation paths. However, those methods are not applicable for the situations where the degradation processes cannot be linearized. Hence, in this paper, a general ADT model based on the Wiener process is proposed to solve the problem for accelerated degradation data analysis. The general model can consider the unit-to-unit variation and temporal variation of the degradation process, and is suitable for both linear and nonlinear ADT analyses with single or multiple acceleration variables. The statistical inference is given to estimate the unknown parameters in both constant stress and step stress ADT. The simulation example and two real applications demonstrate that the proposed method can yield reliable lifetime evaluation results compared with the existing linear and time-scale transformation Wiener processes in both linear and nonlinear ADT analyses.
Generalized Landau-Lifshitz models on the interval
International Nuclear Information System (INIS)
Doikou, Anastasia; Karaiskos, Nikos
2011-01-01
We study the classical generalized gl n Landau-Lifshitz (L-L) model with special boundary conditions that preserve integrability. We explicitly derive the first non-trivial local integral of motion, which corresponds to the boundary Hamiltonian for the sl 2 L-L model. Novel expressions of the modified Lax pairs associated to the integrals of motion are also extracted. The relevant equations of motion with the corresponding boundary conditions are determined. Dynamical integrable boundary conditions are also examined within this spirit. Then the generalized isotropic and anisotropic gl n Landau-Lifshitz models are considered, and novel expressions of the boundary Hamiltonians and the relevant equations of motion and boundary conditions are derived.
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
A generalized conditional heteroscedastic model for temperature downscaling
Modarres, R.; Ouarda, T. B. M. J.
2014-11-01
This study describes a method for deriving the time varying second order moment, or heteroscedasticity, of local daily temperature and its association to large Coupled Canadian General Circulation Models predictors. This is carried out by applying a multivariate generalized autoregressive conditional heteroscedasticity (MGARCH) approach to construct the conditional variance-covariance structure between General Circulation Models (GCMs) predictors and maximum and minimum temperature time series during 1980-2000. Two MGARCH specifications namely diagonal VECH and dynamic conditional correlation (DCC) are applied and 25 GCM predictors were selected for a bivariate temperature heteroscedastic modeling. It is observed that the conditional covariance between predictors and temperature is not very strong and mostly depends on the interaction between the random process governing temporal variation of predictors and predictants. The DCC model reveals a time varying conditional correlation between GCM predictors and temperature time series. No remarkable increasing or decreasing change is observed for correlation coefficients between GCM predictors and observed temperature during 1980-2000 while weak winter-summer seasonality is clear for both conditional covariance and correlation. Furthermore, the stationarity and nonlinearity Kwiatkowski-Phillips-Schmidt-Shin (KPSS) and Brock-Dechert-Scheinkman (BDS) tests showed that GCM predictors, temperature and their conditional correlation time series are nonlinear but stationary during 1980-2000 according to BDS and KPSS test results. However, the degree of nonlinearity of temperature time series is higher than most of the GCM predictors.
Muscular anatomy of the human ventricular folds.
Moon, Jerald; Alipour, Fariborz
2013-09-01
Our purpose in this study was to better understand the muscular anatomy of the ventricular folds in order to help improve biomechanical modeling of phonation and to better understand the role of these muscles during phonatory and nonphonatory tasks. Four human larynges were decalcified, sectioned coronally from posterior to anterior by a CryoJane tape transfer system, and stained with Masson's trichrome. The total and relative areas of muscles observed in each section were calculated and used for characterizing the muscle distribution within the ventricular folds. The ventricular folds contained anteriorly coursing thyroarytenoid and ventricularis muscle fibers that were in the lower half of the ventricular fold posteriorly, and some ventricularis muscle was evident in the upper and lateral portions of the fold more anteriorly. Very little muscle tissue was observed in the medial half of the fold, and the anterior half of the ventricular fold was largely devoid of any muscle tissue. All 4 larynges contained muscle bundles that coursed superiorly and medially through the upper half of the fold, toward the lateral margin of the epiglottis. Although variability of expression was evident, a well-defined thyroarytenoid muscle was readily apparent lateral to the arytenoid cartilage in all specimens.
Generalized Modeling of the Human Lower Limb Assembly
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
Frustration in Condensed Matter and Protein Folding
Li, Z.; Tanner, S.; Conroy, B.; Owens, F.; Tran, M. M.; Boekema, C.
2014-03-01
By means of computer modeling, we are studying frustration in condensed matter and protein folding, including the influence of temperature and Thomson-figure formation. Frustration is due to competing interactions in a disordered state. The key issue is how the particles interact to reach the lowest frustration. The relaxation for frustration is mostly a power function (randomly assigned pattern) or an exponential function (regular patterns like Thomson figures). For the atomic Thomson model, frustration is predicted to decrease with the formation of Thomson figures at zero kelvin. We attempt to apply our frustration modeling to protein folding and dynamics. We investigate the homogeneous protein frustration that would cause the speed of the protein folding to increase. Increase of protein frustration (where frustration and hydrophobicity interplay with protein folding) may lead to a protein mutation. Research is supported by WiSE@SJSU and AFC San Jose.
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
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.
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.
A Non-Gaussian Spatial Generalized Linear Latent Variable Model
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.
A Non-Gaussian Spatial Generalized Linear Latent Variable Model
Irincheeva, Irina; Cantoni, Eva; Genton, Marc G.
2012-01-01
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.
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...... and eradication programmes based on changes in PRRS sero-prevalence was explored. Results showed a declining trend in PRRS sero-prevalence between 2007 and 2014 suggesting that Danish herds are slowly eradicating PRRS. The simulation study demonstrated the flexibility of DGLMs in adapting to changes intrends...... 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...
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.
A General Model for Repeated Audit Controls Using Monotone Subsampling
Raats, V.M.; van der Genugten, B.B.; Moors, J.J.A.
2002-01-01
In categorical repeated audit controls, fallible auditors classify sample elements in order to estimate the population fraction of elements in certain categories.To take possible misclassifications into account, subsequent checks are performed with a decreasing number of observations.In this paper a model is presented for a general repeated audit control system, where k subsequent auditors classify elements into r categories.Two different sub-sampling procedures will be discussed, named 'stra...
Electromagnetic axial anomaly in a generalized linear sigma model
Fariborz, Amir H.; Jora, Renata
2017-06-01
We construct the electromagnetic anomaly effective term for a generalized linear sigma model with two chiral nonets, one with a quark-antiquark structure, the other one with a four-quark content. We compute in the leading order of this framework the decays into two photons of six pseudoscalars: π0(137 ), π0(1300 ), η (547 ), η (958 ), η (1295 ) and η (1760 ). Our results agree well with the available experimental data.
Nuclear inertia for fission in a generalized cranking model
International Nuclear Information System (INIS)
Kunz, J.; Nix, J.R.
1984-01-01
A time dependent formalism which is appropriate for β vibrations and fission is developed for a generalized cranking model. The formalism leads to additional terms in the density matrix which affect the nuclear inertia. The case of a harmonic oscillator potential is used to demonstrate the contribution of the pairing gap term on the β vibrational inertia for Pu 240. The inertia remains finite and close to the limiting irrotational value
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 ...
Generalized Calogero-Sutherland systems from many-matrix models
International Nuclear Information System (INIS)
Polychronakos, Alexios P.
1999-01-01
We construct generalizations of the Calogero-Sutherland-Moser system by appropriately reducing a model involving many unitary matrices. The resulting systems consist of particles on the circle with internal degrees of freedom, coupled through modifications of the inverse-square potential. The coupling involves SU(M) non-invariant (anti) ferromagnetic interactions of the internal degrees of freedom. The systems are shown to be integrable and the spectrum and wavefunctions of the quantum version are derived
Generalized Bogoliubov Polariton Model: An Application to Stock Exchange Market
International Nuclear Information System (INIS)
Anh, Chu Thuy; Anh, Truong Thi Ngoc; Lan, Nguyen Tri; Viet, Nguyen Ai
2016-01-01
A generalized Bogoliubov method for investigation non-simple and complex systems was developed. We take two branch polariton Hamiltonian model in second quantization representation and replace the energies of quasi-particles by two distribution functions of research objects. Application to stock exchange market was taken as an example, where the changing the form of return distribution functions from Boltzmann-like to Gaussian-like was studied. (paper)
Structural dynamic analysis with generalized damping models analysis
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
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)
Optimisation of a parallel ocean general circulation model
Beare, M. I.; Stevens, D. P.
1997-10-01
This paper presents the development of a general-purpose parallel ocean circulation model, for use on a wide range of computer platforms, from traditional scalar machines to workstation clusters and massively parallel processors. Parallelism is provided, as a modular option, via high-level message-passing routines, thus hiding the technical intricacies from the user. An initial implementation highlights that the parallel efficiency of the model is adversely affected by a number of factors, for which optimisations are discussed and implemented. The resulting ocean code is portable and, in particular, allows science to be achieved on local workstations that could otherwise only be undertaken on state-of-the-art supercomputers.
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.
Generalized model for Memristor-based Wien family oscillators
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.
General dosimetry model for internal contamination with radioisotopes
International Nuclear Information System (INIS)
Nino, L.
1989-01-01
Radiation dose by inner contamination with radioisotopes is not measured directly but evaluated by the application of mathematical models of fixation and elimination, taken into account biological activity of each organ with respect to the incorporated material. Models proposed by ICRP for the respiratory and gastrointestinal tracts (30) seems that they should not be applied independently because of the evident correlation between them. In this paper both models are integrated in a more general one with neither modification nor limitation of the starting models. It has been applied to some patients in the Instituto Nacional de Cancerologia, who received some I-131 dose via oral and results are quite similar to dose experimentally obtained via urine spectrograms. Based on this results the method was formalized and applied to professional exposed personnel of the medical staff at the same Institute; due to high doses found in some of the urine samples, probable I-131 air contamination could be supposed
Working covariance model selection for generalized estimating equations.
Carey, Vincent J; Wang, You-Gan
2011-11-20
We investigate methods for data-based selection of working covariance models in the analysis of correlated data with generalized estimating equations. We study two selection criteria: Gaussian pseudolikelihood and a geodesic distance based on discrepancy between model-sensitive and model-robust regression parameter covariance estimators. The Gaussian pseudolikelihood is found in simulation to be reasonably sensitive for several response distributions and noncanonical mean-variance relations for longitudinal data. Application is also made to a clinical dataset. Assessment of adequacy of both correlation and variance models for longitudinal data should be routine in applications, and we describe open-source software supporting this practice. Copyright © 2011 John Wiley & Sons, Ltd.
Pharmaceutical industry and trade liberalization using computable general equilibrium model.
Barouni, M; Ghaderi, H; Banouei, Aa
2012-01-01
Computable general equilibrium models are known as a powerful instrument in economic analyses and widely have been used in order to evaluate trade liberalization effects. The purpose of this study was to provide the impacts of trade openness on pharmaceutical industry using CGE model. Using a computable general equilibrium model in this study, the effects of decrease in tariffs as a symbol of trade liberalization on key variables of Iranian pharmaceutical products were studied. Simulation was performed via two scenarios in this study. The first scenario was the effect of decrease in tariffs of pharmaceutical products as 10, 30, 50, and 100 on key drug variables, and the second was the effect of decrease in other sectors except pharmaceutical products on vital and economic variables of pharmaceutical products. The required data were obtained and the model parameters were calibrated according to the social accounting matrix of Iran in 2006. The results associated with simulation demonstrated that the first scenario has increased import, export, drug supply to markets and household consumption, while import, export, supply of product to market, and household consumption of pharmaceutical products would averagely decrease in the second scenario. Ultimately, society welfare would improve in all scenarios. We presents and synthesizes the CGE model which could be used to analyze trade liberalization policy issue in developing countries (like Iran), and thus provides information that policymakers can use to improve the pharmacy economics.
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.
International Nuclear Information System (INIS)
Niehaus, T A; Suhai, S; March, N H
2008-01-01
Holas, Howard and March (2003 Phys. Lett. A 310 451) have obtained analytic solutions for ground-state properties of a whole family of two-electron spin-compensated harmonically confined model atoms whose different members are characterized by a specific interparticle potential energy u(r 12 ). Here, we make a start on the dynamic generalization of the harmonic external potential, the motivation being the serious criticism levelled recently against the foundations of time-dependent density-functional theory (e.g., Schirmer and Dreuw 2007 Phys. Rev. A 75 022513). In this context, we derive a simplified expression for the time-dependent electron density for arbitrary interparticle interaction, which is fully determined by a one-dimensional non-interacting Hamiltonian. Moreover, a closed solution for the momentum space density in the Moshinsky model is obtained
Nuclear inertia for fission in a generalized cranking model
International Nuclear Information System (INIS)
Kunz, J.; Nix, J.R.
1984-01-01
The Inglis cranking model has been widely used to calculate the nuclear inertia associated with collective degrees of freedom. After the inclusion of pairing correlations, theoretical results obtained with the cranking model for nuclear rotations and γ-vibrations were in relatively good agreement with experimental data. Calculations of β-vibrational inertias were also performed in the cranking model for fission deformations. Theoretical results were several times the irrotational values and gave reasonable agreement with experimental spontaneous-fission lifetimes, although in one study a renormalization factor of 0.8 was required. However, as pointed out by many authors, the Inglis cranking model possesses two serious deficiencies. First, problems arise when the single-particle potential contains momentum-dependence terms. Second, in the limit of large pairing strength the inertia approaches zero instead of a finite (irrotational) limit. Alternative approaches to the cranking model which did not lead to such unacceptable results were developed by Migdal, Belyaev and Thouless and Valatin. They showed that these deficiencies of the cranking model are due to a lack of self-consistency, since the reaction of the mean field to the collective motion is neglected in the Inglis model. Previously we used their arguments and developed a generalized cranking model for stationary collective motion. Here it is shown how to develop a time-dependent formalism appropriate to β-vibrations and fission. 10 references
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.
A general modeling framework for describing spatially structured population dynamics
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
General Potential-Current Model and Validation for Electrocoagulation
International Nuclear Information System (INIS)
Dubrawski, Kristian L.; Du, Codey; Mohseni, Madjid
2014-01-01
A model relating potential and current in continuous parallel plate iron electrocoagulation (EC) was developed for application in drinking water treatment. The general model can be applied to any EC parallel plate system relying only on geometric and tabulated input variables without the need of system-specific experimentally derived constants. For the theoretical model, the anode and cathode were vertically divided into n equipotential segments in a single pass, upflow, and adiabatic EC reactor. Potential and energy balances were simultaneously solved at each vertical segment, which included the contribution of ionic concentrations, solution temperature and conductivity, cathodic hydrogen flux, and gas/liquid ratio. We experimentally validated the numerical model with a vertical upflow EC reactor using a 24 cm height 99.99% pure iron anode divided into twelve 2 cm segments. Individual experimental currents from each segment were summed to determine total current, and compared with the theoretically derived value. Several key variables were studied to determine their impact on model accuracy: solute type, solute concentration, current density, flow rate, inter-electrode gap, and electrode surface condition. Model results were in good agreement with experimental values at cell potentials of 2-20 V (corresponding to a current density range of approximately 50-800 A/m 2 ), with mean relative deviation of 9% for low flow rate, narrow electrode gap, polished electrodes, and 150 mg/L NaCl. Highest deviation occurred with a large electrode gap, unpolished electrodes, and Na 2 SO 4 electrolyte, due to parasitic H 2 O oxidation and less than unity current efficiency. This is the first general model which can be applied to any parallel plate EC system for accurate electrochemical voltage or current prediction
A Generalized Dynamic Model of Geared System: Establishment and Application
Directory of Open Access Journals (Sweden)
Hui Liu
2011-12-01
Full Text Available In order to make the dynamic characteristic simulation of the ordinary and planetary gears drive more accurate and more efficient , a generalized dynamic model of geared system is established including internal and external mesh gears in this paper. It is used to build a mathematical model, which achieves the auto judgment of the gear mesh state. We do not need to concern about active or passive gears any more, and the complicated power flow analysis can be avoided. With the numerical integration computation, the axis orbits diagram and dynamic gear mesh force characteristic are acquired and the results show that the dynamic response of translational displacement is greater when contacting line direction change is considered, and with the quickly change of direction of contacting line, the amplitude of mesh force would be increased, which easily causes the damage to the gear tooth. Moreover, compared with ordinary gear, dynamic responses of planetary gear would be affected greater by the gear backlash. Simulation results show the effectiveness of the generalized dynamic model and the mathematical model.
Reshocks, rarefactions, and the generalized Layzer model for hydrodynamic instabilities
International Nuclear Information System (INIS)
Mikaelian, K.O.
2008-01-01
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 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
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.
Consensus-based training and assessment model for general surgery.
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.
Analog quantum simulation of generalized Dicke models in trapped ions
Aedo, Ibai; Lamata, Lucas
2018-04-01
We propose the analog quantum simulation of generalized Dicke models in trapped ions. By combining bicromatic laser interactions on multiple ions we can generate all regimes of light-matter coupling in these models, where here the light mode is mimicked by a motional mode. We present numerical simulations of the three-qubit Dicke model both in the weak field (WF) regime, where the Jaynes-Cummings behavior arises, and the ultrastrong coupling (USC) regime, where a rotating-wave approximation cannot be considered. We also simulate the two-qubit biased Dicke model in the WF and USC regimes and the two-qubit anisotropic Dicke model in the USC regime and the deep-strong coupling regime. The agreement between the mathematical models and the ion system convinces us that these quantum simulations can be implemented in the laboratory with current or near-future technology. This formalism establishes an avenue for the quantum simulation of many-spin Dicke models in trapped ions.
Varandas, A J C; Sarkar, B
2011-05-14
Generalized Born-Oppenheimer equations including the geometrical phase effect are derived for three- and four-fold electronic manifolds in Jahn-Teller systems near the degeneracy seam. The method is readily extendable to N-fold systems of arbitrary dimension. An application is reported for a model threefold system, and the results are compared with Born-Oppenheimer (geometrical phase ignored), extended Born-Oppenheimer, and coupled three-state calculations. The theory shows unprecedented simplicity while depicting all features of more elaborated ones.
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
A Model Independent General Search for new physics in ATLAS
Amoroso, S; The ATLAS collaboration
2016-01-01
We present results of a model-independent general search for new phenomena in proton-proton collisions at a centre-of-mass energy of 8 TeV with the ATLAS detector at the LHC. The data set corresponds to a total integrated luminosity of 20.3~\\ifb. Event topologies involving isolated electrons, photons and muons, as well as jets, including those identified as originating from \\textit{b}-quarks (\\textit{b}-jets) and missing transverse momentum are investigated. The events are subdivided according to their final states into exclusive event classes. For the 697 classes with a Standard Model expectation greater than 0.1 events, a search algorithm tests the compatibility of data against the Monte Carlo simulated background in three kinematic variables sensitive to new physics effects. No significant deviation is found in data. The number and size of the observed deviations follow the Standard Model expectation obtained from simulated pseudo-experiments.
A Model Independent General Search for new physics in ATLAS
Amoroso, S.; ATLAS Collaboration
2016-04-01
We present results of a model-independent general search for new phenomena in proton-proton collisions at a centre-of-mass energy of 8 TeV with the ATLAS detector at the LHC. The data set corresponds to a total integrated luminosity of 20.3 fb-1. Event topologies involving isolated electrons, photons and muons, as well as jets, including those identified as originating from b-quarks (b-jets) and missing transverse momentum are investigated. The events are subdivided according to their final states into exclusive event classes. For the 697 classes with a Standard Model expectation greater than 0.1 events, a search algorithm tests the compatibility of data against the Monte Carlo simulated background in three kinematic variables sensitive to new physics effects. No significant deviation is found in data. The number and size of the observed deviations follow the Standard Model expectation obtained from simulated pseudo-experiments.
Statistical mechanics of sparse generalization and graphical model selection
International Nuclear Information System (INIS)
Lage-Castellanos, Alejandro; Pagnani, Andrea; Weigt, Martin
2009-01-01
One of the crucial tasks in many inference problems is the extraction of an underlying sparse graphical model from a given number of high-dimensional measurements. In machine learning, this is frequently achieved using, as a penalty term, the L p norm of the model parameters, with p≤1 for efficient dilution. Here we propose a statistical mechanics analysis of the problem in the setting of perceptron memorization and generalization. Using a replica approach, we are able to evaluate the relative performance of naive dilution (obtained by learning without dilution, following by applying a threshold to the model parameters), L 1 dilution (which is frequently used in convex optimization) and L 0 dilution (which is optimal but computationally hard to implement). Whereas both L p diluted approaches clearly outperform the naive approach, we find a small region where L 0 works almost perfectly and strongly outperforms the simpler to implement L 1 dilution
Dimensional Reduction for the General Markov Model on Phylogenetic Trees.
Sumner, Jeremy G
2017-03-01
We present a method of dimensional reduction for the general Markov model of sequence evolution on a phylogenetic tree. We show that taking certain linear combinations of the associated random variables (site pattern counts) reduces the dimensionality of the model from exponential in the number of extant taxa, to quadratic in the number of taxa, while retaining the ability to statistically identify phylogenetic divergence events. A key feature is the identification of an invariant subspace which depends only bilinearly on the model parameters, in contrast to the usual multi-linear dependence in the full space. We discuss potential applications including the computation of split (edge) weights on phylogenetic trees from observed sequence data.
The Michigan Titan Thermospheric General Circulation Model (TTGCM)
Bell, J. M.; Bougher, S. W.; de Lahaye, V.; Waite, J. H.
2005-12-01
The Cassini flybys of Titan since late October, 2004 have provided data critical to better understanding its chemical and thermal structures. With this in mind, a 3-D TGCM of Titan's atmosphere from 600km to the exobase (~1450km) has been developed. This paper presents the first results from the partially operational code. Currently, the TTGCM includes static background chemistry (Lebonnois et al 2001, Vervack et al 2004) coupled with thermal conduction routines. The thermosphere remains dominated by solar EUV forcing and HCN rotational cooling, which is calculated by a full line-by-line radiative transfer routine along the lines of Yelle (1991) and Mueller-Wodarg (2000, 2002). In addition, an approximate treatment of magnetospheric heating is explored. This paper illustrates the model's capabilities as well as some initial results from the Titan Thermospheric General Circulation model that will be compared with both the Cassini INMS data and the model of Mueller-Wodarg (2000,2002).
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.
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.
Toward a general psychological model of tension and suspense.
Lehne, Moritz; Koelsch, Stefan
2015-01-01
Tension and suspense are powerful emotional experiences that occur in a wide variety of contexts (e.g., in music, film, literature, and everyday life). The omnipresence of tension and suspense suggests that they build on very basic cognitive and affective mechanisms. However, the psychological underpinnings of tension experiences remain largely unexplained, and tension and suspense are rarely discussed from a general, domain-independent perspective. In this paper, we argue that tension experiences in different contexts (e.g., musical tension or suspense in a movie) build on the same underlying psychological processes. We discuss key components of tension experiences and propose a domain-independent model of tension and suspense. According to this model, tension experiences originate from states of conflict, instability, dissonance, or uncertainty that trigger predictive processes directed at future events of emotional significance. We also discuss possible neural mechanisms underlying tension and suspense. The model provides a theoretical framework that can inform future empirical research on tension phenomena.
A generalized and parameterized interference model for cognitive radio networks
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.
Wen, Fu-Lai; Wang, Yu-Chiun; Shibata, Tatsuo
2017-06-20
During embryonic development, epithelial sheets fold into complex structures required for tissue and organ functions. Although substantial efforts have been devoted to identifying molecular mechanisms underlying epithelial folding, far less is understood about how forces deform individual cells to sculpt the overall sheet morphology. Here we describe a simple and general theoretical model for the autonomous folding of monolayered epithelial sheets. We show that active modulation of intracellular mechanics along the basal-lateral as well as the apical surfaces is capable of inducing fold formation in the absence of buckling instability. Apical modulation sculpts epithelia into shallow and V-shaped folds, whereas basal-lateral modulation generates deep and U-shaped folds. These characteristic tissue shapes remain unchanged when subject to mechanical perturbations from the surroundings, illustrating that the autonomous folding is robust against environmental variabilities. At the cellular scale, how cells change shape depends on their initial aspect ratios and the modulation mechanisms. Such cell deformation characteristics are verified via experimental measurements for a canonical folding process driven by apical modulation, indicating that our theory could be used to infer the underlying folding mechanisms based on experimental data. The mechanical principles revealed in our model could potentially guide future studies on epithelial folding in diverse systems. Copyright © 2017. Published by Elsevier Inc.
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.
The generalized hedgehog and the projected chiral soliton model
International Nuclear Information System (INIS)
Fiolhais, M.; Kernforschungsanlage Juelich G.m.b.H.; Goeke, K.; Bochum Univ.; Gruemmer, F.; Urbano, J.N.
1988-01-01
The linear chiral soliton model with quark fields and elementary pion and sigma fields is solved in order to describe static properties of the nucleon and the delta resonance. To this end a Fock state of the system is constructed which consists of three valence quarks in a 1s orbit with a generalized hedgehog spin-flavour configuration cosηvertical strokeu↓> - sin ηvertical stroked↑>. Coherent states are used to provide a quantum description for the mesonic parts of the total wave function. The corresponding classical pion field also exhibits a generalized hedgehog structure. Various nucleon properties are calculated. These include proton and neutron charge raii, and the mangnetic moment of the proton for which experiment is obtained. (orig./HSI)
General Business Model Patterns for Local Energy Management Concepts
Energy Technology Data Exchange (ETDEWEB)
Facchinetti, Emanuele, E-mail: emanuele.facchinetti@hslu.ch; Sulzer, Sabine [Lucerne Competence Center for Energy Research, Lucerne University of Applied Science and Arts, Horw (Switzerland)
2016-03-03
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.
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.
General circulation model study of atmospheric carbon monoxide
International Nuclear Information System (INIS)
Pinto, J.P.; Yung, Y.L.; Rind, D.; Russell, G.L.; Lerner, J.A.; Hansen, J.E.; Hameed, S.
1983-01-01
The carbon monoxide cycle is studied by incorporating the known and hypothetical sources and sinks in a tracer model that uses the winds generated by a general circulation model. Photochemical production and loss terms, which depend on OH radical concentrations, are calculated in an interactive fashion. The computed global distribution and seasonal variations of CO are compared with observations to obtain constraints on the distribution and magnitude of the sources and sinks of CO, and on the tropospheric abundance of OH. The simplest model that accounts for available observations requires a low latitude plant source of about 1.3 x 10 15 g yr -1 , in addition to sources from incomplete combustion of fossil fuels and oxidation of methane. The globally averaged OH concentration calculated in the model is 7 x 10 5 cm -3 . Models that calculate globally averaged OH concentrations much lower than our nominal value are not consistent with the observed variability of CO. Such models are also inconsistent with measurements of CO isotopic abundances, which imply the existence of plant sources
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.
A General Accelerated Degradation Model Based on the Wiener Process
Directory of Open Access Journals (Sweden)
Le Liu
2016-12-01
Full Text Available Accelerated degradation testing (ADT is an efficient tool to conduct material service reliability and safety evaluations by analyzing performance degradation data. Traditional stochastic process models are mainly for linear or linearization degradation paths. However, those methods are not applicable for the situations where the degradation processes cannot be linearized. Hence, in this paper, a general ADT model based on the Wiener process is proposed to solve the problem for accelerated degradation data analysis. The general model can consider the unit-to-unit variation and temporal variation of the degradation process, and is suitable for both linear and nonlinear ADT analyses with single or multiple acceleration variables. The statistical inference is given to estimate the unknown parameters in both constant stress and step stress ADT. The simulation example and two real applications demonstrate that the proposed method can yield reliable lifetime evaluation results compared with the existing linear and time-scale transformation Wiener processes in both linear and nonlinear ADT analyses.
Generalized fish life-cycle poplulation model and computer program
International Nuclear Information System (INIS)
DeAngelis, D.L.; Van Winkle, W.; Christensen, S.W.; Blum, S.R.; Kirk, B.L.; Rust, B.W.; Ross, C.
1978-03-01
A generalized fish life-cycle population model and computer program have been prepared to evaluate the long-term effect of changes in mortality in age class 0. The general question concerns what happens to a fishery when density-independent sources of mortality are introduced that act on age class 0, particularly entrainment and impingement at power plants. This paper discusses the model formulation and computer program, including sample results. The population model consists of a system of difference equations involving age-dependent fecundity and survival. The fecundity for each age class is assumed to be a function of both the fraction of females sexually mature and the weight of females as they enter each age class. Natural mortality for age classes 1 and older is assumed to be independent of population size. Fishing mortality is assumed to vary with the number and weight of fish available to the fishery. Age class 0 is divided into six life stages. The probability of survival for age class 0 is estimated considering both density-independent mortality (natural and power plant) and density-dependent mortality for each life stage. Two types of density-dependent mortality are included. These are cannibalism of each life stage by older age classes and intra-life-stage competition
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
A generalized logarithmic image processing model based on the gigavision sensor model.
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.
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
Estimation and variable selection for generalized additive partial linear models
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.
Vocal fold hemorrhage: factors predicting recurrence.
Lennon, Christen J; Murry, Thomas; Sulica, Lucian
2014-01-01
Vocal fold hemorrhage is an acute phonotraumatic injury treated with voice rest; recurrence is a generally accepted indication for surgical intervention. This study aims to identify factors predictive of recurrence based on outcomes of a large clinical series. Retrospective cohort. Retrospective review of cases of vocal fold hemorrhage presenting to a university laryngology service. Demographic information was compiled. Videostroboscopic exams were evaluated for hemorrhage extent, presence of varix, mucosal lesion, and/or vocal fold paresis. Vocal fold hemorrhage recurrence was the main outcome measure. Follow-up telephone survey was used to complement clinical data. Forty-seven instances of vocal fold hemorrhage were evaluated (25M:22F; 32 professional voice users). Twelve of the 47 (26%) patients experienced recurrence. Only the presence of varix demonstrated significant association with recurrence (P = 0.0089) on multivariate logistic regression. Vocal fold hemorrhage recurred in approximately 26% of patients. Varix was a predictor of recurrence, with 48% of those with varix experiencing recurrence. Monitoring, behavioral management and/or surgical intervention may be indicated to treat patients with such characteristics. © 2013 The American Laryngological, Rhinological and Otological Society, Inc.
Water tracers in the general circulation model ECHAM
International Nuclear Information System (INIS)
Hoffmann, G.; Heimann, M.
1993-01-01
We have installed a water tracer model into the ECHAM General Circulation Model (GCM) parameterizing all fractionation processes of the stable water isotopes ( 1 H 2 18 O and 1 H 2 H 16 O). A five year simulation was performed under present day conditions. We focus on the applicability of such a water tracer model to obtain information about the quality of the hydrological cycle of the GCM. The analysis of the simulated 1 H 2 18 O composition of the precipitation indicates too weak fractionated precipitation over the Antarctic and Greenland ice sheets and too strong fractionated precipitation over large areas of the tropical and subtropical land masses. We can show that these deficiencies are connected with problems of model quantities such as the precipitation and the resolution of the orography. The linear relationship between temperature and the δ 18 O value, i.e. the Dansgaard slope, is reproduced quite well in the model. The slope is slightly too flat and the strong correlation between temperature and δ 18 O vanishes at very low temperatures compared to the observations. (orig.)
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.
Scaling of Precipitation Extremes Modelled by Generalized Pareto Distribution
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.
General mirror pairs for gauged linear sigma models
Energy Technology Data Exchange (ETDEWEB)
Aspinwall, Paul S.; Plesser, M. Ronen [Departments of Mathematics and Physics, Duke University,Box 90320, Durham, NC 27708-0320 (United States)
2015-11-05
We carefully analyze the conditions for an abelian gauged linear σ-model to exhibit nontrivial IR behavior described by a nonsingular superconformal field theory determining a superstring vacuum. This is done without reference to a geometric phase, by associating singular behavior to a noncompact space of (semi-)classical vacua. We find that models determined by reflexive combinatorial data are nonsingular for generic values of their parameters. This condition has the pleasant feature that the mirror of a nonsingular gauged linear σ-model is another such model, but it is clearly too strong and we provide an example of a non-reflexive mirror pair. We discuss a weaker condition inspired by considering extremal transitions, which is also mirror symmetric and which we conjecture to be sufficient. We apply these ideas to extremal transitions and to understanding the way in which both Berglund-Hübsch mirror symmetry and the Vafa-Witten mirror orbifold with discrete torsion can be seen as special cases of the general combinatorial duality of gauged linear σ-models. In the former case we encounter an example showing that our weaker condition is still not necessary.
General mirror pairs for gauged linear sigma models
International Nuclear Information System (INIS)
Aspinwall, Paul S.; Plesser, M. Ronen
2015-01-01
We carefully analyze the conditions for an abelian gauged linear σ-model to exhibit nontrivial IR behavior described by a nonsingular superconformal field theory determining a superstring vacuum. This is done without reference to a geometric phase, by associating singular behavior to a noncompact space of (semi-)classical vacua. We find that models determined by reflexive combinatorial data are nonsingular for generic values of their parameters. This condition has the pleasant feature that the mirror of a nonsingular gauged linear σ-model is another such model, but it is clearly too strong and we provide an example of a non-reflexive mirror pair. We discuss a weaker condition inspired by considering extremal transitions, which is also mirror symmetric and which we conjecture to be sufficient. We apply these ideas to extremal transitions and to understanding the way in which both Berglund-Hübsch mirror symmetry and the Vafa-Witten mirror orbifold with discrete torsion can be seen as special cases of the general combinatorial duality of gauged linear σ-models. In the former case we encounter an example showing that our weaker condition is still not necessary.
A Bayesian, generalized frailty model for comet assays.
Ghebretinsae, Aklilu Habteab; Faes, Christel; Molenberghs, Geert; De Boeck, Marlies; Geys, Helena
2013-05-01
This paper proposes a flexible modeling approach for so-called comet assay data regularly encountered in preclinical research. While such data consist of non-Gaussian outcomes in a multilevel hierarchical structure, traditional analyses typically completely or partly ignore this hierarchical nature by summarizing measurements within a cluster. Non-Gaussian outcomes are often modeled using exponential family models. This is true not only for binary and count data, but also for, example, time-to-event outcomes. Two important reasons for extending this family are for (1) the possible occurrence of overdispersion, meaning that the variability in the data may not be adequately described by the models, which often exhibit a prescribed mean-variance link, and (2) the accommodation of a hierarchical structure in the data, owing to clustering in the data. The first issue is dealt with through so-called overdispersion models. Clustering is often accommodated through the inclusion of random subject-specific effects. Though not always, one conventionally assumes such random effects to be normally distributed. In the case of time-to-event data, one encounters, for example, the gamma frailty model (Duchateau and Janssen, 2007 ). While both of these issues may occur simultaneously, models combining both are uncommon. Molenberghs et al. ( 2010 ) proposed a broad class of generalized linear models accommodating overdispersion and clustering through two separate sets of random effects. Here, we use this method to model data from a comet assay with a three-level hierarchical structure. Although a conjugate gamma random effect is used for the overdispersion random effect, both gamma and normal random effects are considered for the hierarchical random effect. Apart from model formulation, we place emphasis on Bayesian estimation. Our proposed method has an upper hand over the traditional analysis in that it (1) uses the appropriate distribution stipulated in the literature; (2) deals
On Optimal Data Split for Generalization Estimation and Model Selection
DEFF Research Database (Denmark)
Larsen, Jan; Goutte, Cyril
1999-01-01
The paper is concerned with studying the very different behavior of the two data splits using hold-out cross-validation, K-fold cross-validation and randomized permutation cross-validation. First we describe the theoretical basics of various cross-validation techniques with the purpose of reliably...
Generalized Skyrme model with the loosely bound potential
Gudnason, Sven Bjarke; Zhang, Baiyang; Ma, Nana
2016-12-01
We study a generalization of the loosely bound Skyrme model which consists of the Skyrme model with a sixth-order derivative term—motivated by its fluidlike properties—and the second-order loosely bound potential—motivated by lowering the classical binding energies of higher-charged Skyrmions. We use the rational map approximation for the Skyrmion of topological charge B =4 , calculate the binding energy of the latter, and estimate the systematic error in using this approximation. In the parameter space that we can explore within the rational map approximation, we find classical binding energies as low as 1.8%, and once taking into account the contribution from spin-isospin quantization, we obtain binding energies as low as 5.3%. We also calculate the contribution from the sixth-order derivative term to the electric charge density and axial coupling.
General informatics teaching with B-Learning teaching model
Directory of Open Access Journals (Sweden)
Nguyen The Dung
2018-03-01
Full Text Available Blended learning (B-learning, a combination of face-to-face teaching and E-learning-supported-teaching in an online course, and Information and Communication Technology (ICT tools have been studied in recent years. In addition, the use of this teaching model is effective in teaching and learning conditions in which some certain subjects are appropriate for the specific teaching context. As it has been a matter of concern of the universities in Vietnam today, deep studies related to this topic is crucial to be conducted. In this article, the process of developing online courses and organizing teaching for the General Informatics subject for first-year students at the Hue University of Education with B-learning teaching model will be presented. The combination of 60% face-to-face and 40% online learning.
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
Optimisation of a parallel ocean general circulation model
Directory of Open Access Journals (Sweden)
M. I. Beare
1997-10-01
Full Text Available This paper presents the development of a general-purpose parallel ocean circulation model, for use on a wide range of computer platforms, from traditional scalar machines to workstation clusters and massively parallel processors. Parallelism is provided, as a modular option, via high-level message-passing routines, thus hiding the technical intricacies from the user. An initial implementation highlights that the parallel efficiency of the model is adversely affected by a number of factors, for which optimisations are discussed and implemented. The resulting ocean code is portable and, in particular, allows science to be achieved on local workstations that could otherwise only be undertaken on state-of-the-art supercomputers.
Optimisation of a parallel ocean general circulation model
Directory of Open Access Journals (Sweden)
M. I. Beare
Full Text Available This paper presents the development of a general-purpose parallel ocean circulation model, for use on a wide range of computer platforms, from traditional scalar machines to workstation clusters and massively parallel processors. Parallelism is provided, as a modular option, via high-level message-passing routines, thus hiding the technical intricacies from the user. An initial implementation highlights that the parallel efficiency of the model is adversely affected by a number of factors, for which optimisations are discussed and implemented. The resulting ocean code is portable and, in particular, allows science to be achieved on local workstations that could otherwise only be undertaken on state-of-the-art supercomputers.
[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
Explicit estimating equations for semiparametric generalized linear latent variable models
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.
Generalized one-loop neutrino mass model with charged particles
Cheung, Kingman; Okada, Hiroshi
2018-04-01
We propose a radiative neutrino-mass model by introducing 3 generations of fermion pairs E-(N +1 )/2E+(N +1 )/2 and a couple of multicharged bosonic doublet fields ΦN /2,ΦN /2 +1, where N =1 , 3, 5, 7, 9. We show that the models can satisfy the neutrino masses and oscillation data, and are consistent with lepton-flavor violations, the muon anomalous magnetic moment, the oblique parameters, and the beta function of the U (1 )Y hypercharge gauge coupling. We also discuss the collider signals for various N , namely, multicharged leptons in the final state from the Drell-Yan production of E-(N +1 )/2E+(N +1 )/2. In general, the larger the N the more charged leptons will appear in the final state.
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
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
On the thermodynamic properties of the generalized Gaussian core model
Directory of Open Access Journals (Sweden)
B.M.Mladek
2005-01-01
Full Text Available We present results of a systematic investigation of the properties of the generalized Gaussian core model of index n. The potential of this system interpolates via the index n between the potential of the Gaussian core model and the penetrable sphere system, thereby varying the steepness of the repulsion. We have used both conventional and self-consistent liquid state theories to calculate the structural and thermodynamic properties of the system; reference data are provided by computer simulations. The results indicate that the concept of self-consistency becomes indispensable to guarantee excellent agreement with simulation data; in particular, structural consistency (in our approach taken into account via the zero separation theorem is obviously a very important requirement. Simulation results for the dimensionless equation of state, β P / ρ, indicate that for an index-value of 4, a clustering transition, possibly into a structurally ordered phase might set in as the system is compressed.
Convex Relaxations for a Generalized Chan-Vese Model
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.
The generalized chiral Schwinger model on the two-sphere
International Nuclear Information System (INIS)
Bassetto, A.
1995-01-01
A family of theories which interpolate between vector and chiral Schwinger models is studied on the two-sphere S 2 . The conflict between the loss of gauge invariance and global geometrical properties is solved by introducing a fixed background connection. In this way the generalized Dirac-Weyl operator can be globally defined on S 2 . The generating functional of the Green functions is obtained by taking carefully into account the contribution of gauge fields with non-trivial topological charge and of the related zero-modes of the Dirac determinant. In the decompactification limit, the Green functions of the flat case are recovered; in particular the fermionic condensate in the vacuum vanishes, at variance with its behaviour in the vector Schwinger model. ((orig.))
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.
Minkel, Donald Howe
Effects of gravity on buckle folding are studied using a Newtonian fluid finite element model of a single layer embedded between two thicker less viscous layers. The methods allow arbitrary density jumps, surface tension coefficients, resistance to slip at the interfaces, and tracking of fold growth to a large amplitudes. When density increases downward in two equal jumps, a layer buckles less and thickens more than with uniform density. When density increases upward in two equal jumps, it buckles more and thickens less. A low density layer with periodic thickness variations buckles more, sometimes explosively. Thickness variations form, even if not present initially. These effects are greater with; smaller viscosities, larger density jump, larger length scale, and slower shortening rate. They also depend on wavelength and amplitude, and these dependencies are described in detail. The model is applied to the explosive growth of the salt anticlines of the Paradox Basin, Colorado and Utah. There, shale (higher density) overlies salt (lower density). Methods for simulating realistic earth surface erosion and deposition conditions are introduced. Growth rates increase both with ease of slip at the salt-shale interface, and when earth surface relief stays low due to erosion and deposition. Model anticlines grow explosively, attaining growth rates and amplitudes close to those of the field examples. Fastest growing wavelengths are the same as seen in the field. It is concluded that a combination of partial-slip at the salt-shale interface, with reasonable earth surface conditions, promotes sufficiently fast buckling of the salt-shale interface due to density inversion alone. Neither basement faulting, nor tectonic shortening is required to account for the observed structures. Of fundamental importance is the strong tendency of gravity to promote buckling in low density layers with thickness variations. These develop, even if not present initially.
Diabatic models with transferrable parameters for generalized chemical reactions
International Nuclear Information System (INIS)
Reimers, Jeffrey R; McKemmish, Laura K; McKenzie, Ross H; Hush, Noel S
2017-01-01
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
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
A general evolving model for growing bipartite networks
International Nuclear Information System (INIS)
Tian, Lixin; He, Yinghuan; Liu, Haijun; Du, Ruijin
2012-01-01
In this Letter, we propose and study an inner evolving bipartite network model. Significantly, we prove that the degree distribution of two different kinds of nodes both obey power-law form with adjustable exponents. Furthermore, the joint degree distribution of any two nodes for bipartite networks model is calculated analytically by the mean-field method. The result displays that such bipartite networks are nearly uncorrelated networks, which is different from one-mode networks. Numerical simulations and empirical results are given to verify the theoretical results. -- Highlights: ► We proposed a general evolving bipartite network model which was based on priority connection, reconnection and breaking edges. ► We prove that the degree distribution of two different kinds of nodes both obey power-law form with adjustable exponents. ► The joint degree distribution of any two nodes for bipartite networks model is calculated analytically by the mean-field method. ► The result displays that such bipartite networks are nearly uncorrelated networks, which is different from one-mode networks.
Generalized model for k -core percolation and interdependent networks
Panduranga, Nagendra K.; Gao, Jianxi; Yuan, Xin; Stanley, H. Eugene; Havlin, Shlomo
2017-09-01
Cascading failures in complex systems have been studied extensively using two different models: k -core percolation and interdependent networks. We combine the two models into a general model, solve it analytically, and validate our theoretical results through extensive simulations. We also study the complete phase diagram of the percolation transition as we tune the average local k -core threshold and the coupling between networks. We find that the phase diagram of the combined processes is very rich and includes novel features that do not appear in the models studying each of the processes separately. For example, the phase diagram consists of first- and second-order transition regions separated by two tricritical lines that merge and enclose a two-stage transition region. In the two-stage transition, the size of the giant component undergoes a first-order jump at a certain occupation probability followed by a continuous second-order transition at a lower occupation probability. Furthermore, at certain fixed interdependencies, the percolation transition changes from first-order → second-order → two-stage → first-order as the k -core threshold is increased. The analytic equations describing the phase boundaries of the two-stage transition region are set up, and the critical exponents for each type of transition are derived analytically.
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)
Modeling containment of large wildfires using generalized linear mixed-model analysis
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...
Modeling Answer Change Behavior: An Application of a Generalized Item Response Tree Model
Jeon, Minjeong; De Boeck, Paul; van der Linden, Wim
2017-01-01
We present a novel application of a generalized item response tree model to investigate test takers' answer change behavior. The model allows us to simultaneously model the observed patterns of the initial and final responses after an answer change as a function of a set of latent traits and item parameters. The proposed application is illustrated…
Generalized PSF modeling for optimized quantitation in PET imaging.
Ashrafinia, Saeed; Mohy-Ud-Din, Hassan; Karakatsanis, Nicolas A; Jha, Abhinav K; Casey, Michael E; Kadrmas, Dan J; Rahmim, Arman
2017-06-21
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.
Complex Environmental Data Modelling Using Adaptive General Regression Neural Networks
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
General Methods for Evolutionary Quantitative Genetic Inference from Generalized Mixed Models.
de Villemereuil, Pierre; Schielzeth, Holger; Nakagawa, Shinichi; Morrissey, Michael
2016-11-01
Methods for inference and interpretation of evolutionary quantitative genetic parameters, and for prediction of the response to selection, are best developed for traits with normal distributions. Many traits of evolutionary interest, including many life history and behavioral traits, have inherently nonnormal distributions. The generalized linear mixed model (GLMM) framework has become a widely used tool for estimating quantitative genetic parameters for nonnormal traits. However, whereas GLMMs provide inference on a statistically convenient latent scale, it is often desirable to express quantitative genetic parameters on the scale upon which traits are measured. The parameters of fitted GLMMs, despite being on a latent scale, fully determine all quantities of potential interest on the scale on which traits are expressed. We provide expressions for deriving each of such quantities, including population means, phenotypic (co)variances, variance components including additive genetic (co)variances, and parameters such as heritability. We demonstrate that fixed effects have a strong impact on those parameters and show how to deal with this by averaging or integrating over fixed effects. The expressions require integration of quantities determined by the link function, over distributions of latent values. In general cases, the required integrals must be solved numerically, but efficient methods are available and we provide an implementation in an R package, QGglmm. We show that known formulas for quantities such as heritability of traits with binomial and Poisson distributions are special cases of our expressions. Additionally, we show how fitted GLMM can be incorporated into existing methods for predicting evolutionary trajectories. We demonstrate the accuracy of the resulting method for evolutionary prediction by simulation and apply our approach to data from a wild pedigreed vertebrate population. Copyright © 2016 de Villemereuil et al.
Non-cylindrical fold growth in the Zagros fold and thrust belt (Kurdistan, NE-Iraq)
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
Modeling of space environment impact on nanostructured materials. General principles
Voronina, Ekaterina; Novikov, Lev
2016-07-01
In accordance with the resolution of ISO TC20/SC14 WG4/WG6 joint meeting, Technical Specification (TS) 'Modeling of space environment impact on nanostructured materials. General principles' which describes computer simulation methods of space environment impact on nanostructured materials is being prepared. Nanomaterials surpass traditional materials for space applications in many aspects due to their unique properties associated with nanoscale size of their constituents. This superiority in mechanical, thermal, electrical and optical properties will evidently inspire a wide range of applications in the next generation spacecraft intended for the long-term (~15-20 years) operation in near-Earth orbits and the automatic and manned interplanetary missions. Currently, ISO activity on developing standards concerning different issues of nanomaterials manufacturing and applications is high enough. Most such standards are related to production and characterization of nanostructures, however there is no ISO documents concerning nanomaterials behavior in different environmental conditions, including the space environment. The given TS deals with the peculiarities of the space environment impact on nanostructured materials (i.e. materials with structured objects which size in at least one dimension lies within 1-100 nm). The basic purpose of the document is the general description of the methodology of applying computer simulation methods which relate to different space and time scale to modeling processes occurring in nanostructured materials under the space environment impact. This document will emphasize the necessity of applying multiscale simulation approach and present the recommendations for the choice of the most appropriate methods (or a group of methods) for computer modeling of various processes that can occur in nanostructured materials under the influence of different space environment components. In addition, TS includes the description of possible
Do downscaled general circulation models reliably simulate historical climatic conditions?
Bock, Andrew R.; Hay, Lauren E.; McCabe, Gregory J.; Markstrom, Steven L.; Atkinson, R. Dwight
2018-01-01
The accuracy of statistically downscaled (SD) general circulation model (GCM) simulations of monthly surface climate for historical conditions (1950–2005) was assessed for the conterminous United States (CONUS). The SD monthly precipitation (PPT) and temperature (TAVE) from 95 GCMs from phases 3 and 5 of the Coupled Model Intercomparison Project (CMIP3 and CMIP5) were used as inputs to a monthly water balance model (MWBM). Distributions of MWBM input (PPT and TAVE) and output [runoff (RUN)] variables derived from gridded station data (GSD) and historical SD climate were compared using the Kolmogorov–Smirnov (KS) test For all three variables considered, the KS test results showed that variables simulated using CMIP5 generally are more reliable than those derived from CMIP3, likely due to improvements in PPT simulations. At most locations across the CONUS, the largest differences between GSD and SD PPT and RUN occurred in the lowest part of the distributions (i.e., low-flow RUN and low-magnitude PPT). Results indicate that for the majority of the CONUS, there are downscaled GCMs that can reliably simulate historical climatic conditions. But, in some geographic locations, none of the SD GCMs replicated historical conditions for two of the three variables (PPT and RUN) based on the KS test, with a significance level of 0.05. In these locations, improved GCM simulations of PPT are needed to more reliably estimate components of the hydrologic cycle. Simple metrics and statistical tests, such as those described here, can provide an initial set of criteria to help simplify GCM selection.
A generalized model for estimating the energy density of invertebrates
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.
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
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 ...
Vocal fold injection medialization laryngoplasty.
Modi, Vikash K
2012-01-01
Unilateral vocal fold paralysis (UVFP) can cause glottic insufficiency that can result in hoarseness, chronic cough, dysphagia, and/or aspiration. In rare circumstances, UVFP can cause airway obstruction necessitating a tracheostomy. The treatment options for UVFP include observation, speech therapy, vocal fold injection medialization laryngoplasty, thyroplasty, and laryngeal reinnervation. In this chapter, the author will discuss the technique of vocal fold injection for medialization of a UVFP. Copyright © 2012 S. Karger AG, Basel.
Gauge Theory and Calibrated Geometry for Calabi-Yau 4-folds
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
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
Generalized Swept Mid-structure for Polygonal Models
Martin, Tobias; Chen, Guoning; Musuvathy, Suraj; Cohen, Elaine; Hansen, Charles
2012-01-01
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.
Generalized Swept Mid-structure for Polygonal Models
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.
Heterochiral Knottin Protein: Folding and Solution Structure.
Mong, Surin K; Cochran, Frank V; Yu, Hongtao; Graziano, Zachary; Lin, Yu-Shan; Cochran, Jennifer R; Pentelute, Bradley L
2017-10-31
Homochirality is a general feature of biological macromolecules, and Nature includes few examples of heterochiral proteins. Herein, we report on the design, chemical synthesis, and structural characterization of heterochiral proteins possessing loops of amino acids of chirality opposite to that of the rest of a protein scaffold. Using the protein Ecballium elaterium trypsin inhibitor II, we discover that selective β-alanine substitution favors the efficient folding of our heterochiral constructs. Solution nuclear magnetic resonance spectroscopy of one such heterochiral protein reveals a homogeneous global fold. Additionally, steered molecular dynamics simulation indicate β-alanine reduces the free energy required to fold the protein. We also find these heterochiral proteins to be more resistant to proteolysis than homochiral l-proteins. This work informs the design of heterochiral protein architectures containing stretches of both d- and l-amino acids.
The review on tessellation origami inspired folded structure
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.
Digital terrain model generalization incorporating scale, semantic and cognitive constraints
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
Experimental investigation of protein folding and misfolding.
Dobson, Christopher M
2004-09-01
Newly synthesised proteins need to fold, often to intricate and close-packed structures, in order to function. The underlying mechanism by which this complex process takes place both in vitro and in vivo is now becoming understood, at least in general terms, as a result of the application of a wide range of biophysical and computational methods used in combination with the techniques of biochemistry and protein engineering. It is increasingly apparent, however, that folding is not only crucial for generating biological activity, but that it is also coupled to a wide range of processes within the cell, ranging from the trafficking of proteins to specific organelles to the regulation of cell growth and differentiation. Not surprisingly, therefore, the failure of proteins to fold appropriately, or to remain correctly folded, is associated with a large number of cellular malfunctions that give rise to disease. Misfolding, and its consequences such as aggregation, can be investigated by extending the types of techniques used to study the normal folding process. Application of these techniques is enabling the development of a unified description of the interconversion and regulation of the different conformational states available to proteins in living systems. Such a description proves a generic basis for understanding the fundamental links between protein misfolding and its associated clinical disorders, such as Alzheimer's disease and Type II diabetes, and for exploring novel therapeutic strategies directed at their prevention and treatment on a rational basis.
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
Generalized Functional Linear Models With Semiparametric Single-Index Interactions
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.
CHAIN-WISE GENERALIZATION OF ROAD NETWORKS USING MODEL SELECTION
Directory of Open Access Journals (Sweden)
D. Bulatov
2017-05-01
Full Text Available Streets are essential entities of urban terrain and their automatized extraction from airborne sensor data is cumbersome because of a complex interplay of geometric, topological and semantic aspects. Given a binary image, representing the road class, centerlines of road segments are extracted by means of skeletonization. The focus of this paper lies in a well-reasoned representation of these segments by means of geometric primitives, such as straight line segments as well as circle and ellipse arcs. We propose the fusion of raw segments based on similarity criteria; the output of this process are the so-called chains which better match to the intuitive perception of what a street is. Further, we propose a two-step approach for chain-wise generalization. First, the chain is pre-segmented using circlePeucker and finally, model selection is used to decide whether two neighboring segments should be fused to a new geometric entity. Thereby, we consider both variance-covariance analysis of residuals and model complexity. The results on a complex data-set with many traffic roundabouts indicate the benefits of the proposed procedure.
Cognitive performance modeling based on general systems performance theory.
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).
Critical rotation of general-relativistic polytropic models revisited
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.
Generalized Functional Linear Models With Semiparametric Single-Index Interactions
Li, Yehua; Wang, Naisyin; Carroll, Raymond J.
2010-01-01
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.
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
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
Solvent Effects on Protein Folding/Unfolding
García, A. E.; Hillson, N.; Onuchic, J. N.
Pressure effects on the hydrophobic potential of mean force led Hummer et al. to postulate a model for pressure denaturation of proteins in which denaturation occurs by means of water penetration into the protein interior, rather than by exposing the protein hydrophobic core to the solvent --- commonly used to describe temperature denaturation. We study the effects of pressure in protein folding/unfolding kinetics in an off-lattice minimalist model of a protein in which pressure effects have been incorporated by means of the pair-wise potential of mean force of hydrophobic groups in water. We show that pressure slows down the kinetics of folding by decreasing the reconfigurational diffusion coefficient and moves the location of the folding transition state.
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