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Sample records for 3-state potts model

  1. Simulation of the 3-state Potts model with chemical potential

    SciTech Connect

    Mercado, Ydalia Delgado; Gattringer, Christof; Evertz, Hans Gerd

    2011-05-23

    The 3-state Potts model with chemical potential is mapped to a flux representation where the complex action problem is resolved. We perform a Monte Carlo simulation based on a worm algorithm to study the phase diagram of the model. Our results shed light on the role which center symmetry and its breaking play for the QCD phase diagram.

  2. BTF Potts compound texture model

    NASA Astrophysics Data System (ADS)

    Haindl, Michal; Reměs, Václav; Havlíček, Vojtěch

    2015-03-01

    This paper introduces a method for modeling mosaic-like textures using a multispectral parametric Bidirectional Texture Function (BTF) compound Markov random field model (CMRF). The primary purpose of our synthetic texture approach is to reproduce, compress, and enlarge a given measured texture image so that ideally both natural and synthetic texture will be visually indiscernible, but the model can be easily applied for BFT material editing. The CMRF model consist of several sub-models each having different characteristics along with an underlying structure model which controls transitions between these sub models. The proposed model uses the Potts random field for distributing local texture models in the form of analytically solvable wide-sense BTF Markovian representation for single regions among the fields of a mosaic approximated by the Voronoi diagram. The control field of the BTF-CMRF is generated by the Potts random field model build on top of the adjacency graph of a measured mosaic. The compound random field synthesis combines the modified fast Swendsen- Wang Markov Chain Monte Carlo sampling of the hierarchical Potts MRF part with the fast and analytical synthesis of single regional BTF MRFs. The local texture regions (not necessarily continuous) are represented by an analytical BTF model which consists of single factors modeled by the adaptive 3D causal auto-regressive (3DCAR) random field model which can be analytically estimated as well as synthesized. The visual quality of the resulting complex synthetic textures generally surpasses the outputs of the previously published simpler non-compound BTF-MRF models.

  3. Dilute Potts model in two dimensions.

    PubMed

    Qian, Xiaofeng; Deng, Youjin; Blöte, Henk W J

    2005-11-01

    We study the two-dimensional dilute q-state Potts model by means of transfer-matrix and Monte Carlo methods. Using the random-cluster representation, we include noninteger values of q. We locate phase transitions in the three-dimensional parameter space of q, the Potts coupling K>0, and the chemical potential of the vacancies. The critical plane is found to contain a line of fixed points that divides into a critical branch and a tricritical one, just as predicted by the renormalization scenario formulated by Nienhuis et al for the dilute Potts model. The universal properties along the line of fixed points agree with the theoretical predictions. We also determine the density of the vacancies along these branches. For q=2-squareroot of 2 we obtain the phase diagram in a three-dimensional parameter space that also includes a coupling V> or = 0 between the vacancies. For q=2, the latter space contains the Blume-Capel model as a special case. We include a determination of the tricritical point of this model, as well as an analysis of percolation clusters constructed on tricritical Potts configurations for noninteger q. This percolation study is based on Monte Carlo algorithms that include local updates flipping between Potts sites and vacancies. The bond updates are performed locally for and by means of a cluster algorithm for q>1. The updates for q>1 use a number of operations per site independent of the system size. PMID:16383713

  4. Dilute Potts model in two dimensions

    NASA Astrophysics Data System (ADS)

    Qian, Xiaofeng; Deng, Youjin; Blöte, Henk W. J.

    2005-11-01

    We study the two-dimensional dilute q -state Potts model by means of transfer-matrix and Monte Carlo methods. Using the random-cluster representation, we include noninteger values of q . We locate phase transitions in the three-dimensional parameter space of q , the Potts coupling K⩾0 , and the chemical potential of the vacancies. The critical plane is found to contain a line of fixed points that divides into a critical branch and a tricritical one, just as predicted by the renormalization scenario formulated by Nienhuis for the dilute Potts model. The universal properties along the line of fixed points agree with the theoretical predictions. We also determine the density of the vacancies along these branches. For q=2-2 we obtain the phase diagram in a three-dimensional parameter space that also includes a coupling V⩾0 between the vacancies. For q=2 , the latter space contains the Blume-Capel model as a special case. We include a determination of the tricritical point of this model, as well as an analysis of percolation clusters constructed on tricritical Potts configurations for noninteger q . This percolation study is based on Monte Carlo algorithms that include local updates flipping between Potts sites and vacancies. The bond updates are performed locally for q<1 and by means of a cluster algorithm for q>1 . The updates for q>1 use a number of operations per site independent of the system size.

  5. Potts-model critical manifolds revisited

    NASA Astrophysics Data System (ADS)

    Scullard, Christian R.; Lykke Jacobsen, Jesper

    2016-03-01

    We compute critical polynomials for the q-state Potts model on the Archimedean lattices, using a parallel implementation of the algorithm of Jacobsen (2014 J. Phys. A: Math. Theor 47 135001) that gives us access to larger sizes than previously possible. The exact polynomials are computed for bases of size 6 × 6 unit cells, and the root in the temperature variable v={{{e}}}K-1 is determined numerically at q = 1 for bases of size 8 × 8. This leads to improved results for bond percolation thresholds, and for the Potts-model critical manifolds in the real (q, v) plane. In the two most favourable cases, we find now the kagome-lattice threshold to eleven digits and that of the (3,{12}2) lattice to thirteen. Our critical manifolds reveal many interesting features in the antiferromagnetic region of the Potts model, and determine accurately the extent of the Berker-Kadanoff phase for the lattices studied.

  6. Phase Transitions in Delaunay Potts Models

    NASA Astrophysics Data System (ADS)

    Adams, Stefan; Eyers, Michael

    2016-01-01

    We establish phase transitions for certain classes of continuum Delaunay multi-type particle systems (continuum Potts models) with infinite range repulsive interaction between particles of different type. In one class of the Delaunay Potts models studied the repulsive interaction is a triangle (multi-body) interaction whereas in the second class the interaction is between pairs (edges) of the Delaunay graph. The result for the edge model is an extension of finite range results in Bertin et al. (J Stat Phys 114(1-2):79-100, 2004) for the Delaunay graph and in Georgii and Häggström (Commun Math Phys 181:507-528, 1996) for continuum Potts models to an infinite range repulsion decaying with the edge length. This is a proof of an old conjecture of Lebowitz and Lieb. The repulsive triangle interactions have infinite range as well and depend on the underlying geometry and thus are a first step towards studying phase transitions for geometry-dependent multi-body systems. Our approach involves a Delaunay random-cluster representation analogous to the Fortuin-Kasteleyn representation of the Potts model. The phase transitions manifest themselves in the percolation of the corresponding random-cluster model. Our proofs rely on recent studies (Dereudre et al. in Probab Theory Relat Fields 153:643-670, 2012) of Gibbs measures for geometry-dependent interactions.

  7. Interplay between sign problem and Z3 symmetry in three-dimensional Potts models

    NASA Astrophysics Data System (ADS)

    Hirakida, Takehiro; Kouno, Hiroaki; Takahashi, Junichi; Yahiro, Masanobu

    2016-07-01

    We construct four kinds of Z3 -symmetric three-dimensional (3D) Potts models, each with a different number of states at each site on a 3D lattice, by extending the 3D 3-state Potts model. Comparing the ordinary Potts model with the four Z3-symmetric Potts models, we investigate how Z3 symmetry affects the sign problem and see how the deconfinement transition line changes in the μ -κ plane as the number of states increases, where μ (κ ) plays a role of chemical potential (temperature) in the models. We find that the sign problem is almost cured by imposing Z3 symmetry. This mechanism may happen in Z3-symmetric QCD-like theory. We also show that the deconfinement transition line has stronger μ dependence with respect to increasing the number of states.

  8. Non compact continuum limit of two coupled Potts models

    NASA Astrophysics Data System (ADS)

    Vernier, Éric; Lykke Jacobsen, Jesper; Saleur, Hubert

    2014-10-01

    We study two Q-state Potts models coupled by the product of their energy operators, in the regime 2 < Q ⩽ 4 where the coupling is relevant. A particular choice of weights for the square lattice is shown to be equivalent to the integrable a_3(2) vertex model. It corresponds to a selfdual system of two antiferromagnetic Potts models, coupled ferromagnetically. We derive the Bethe ansatz equations and study them numerically for two arbitrary twist angles. The continuum limit is shown to involve two compact bosons and one non compact boson, with discrete states emerging from the continuum at appropriate twists. The non compact boson entails strong logarithmic corrections to the finite-size behaviour of the scaling levels, an understanding of which allows us to correct an earlier proposal for some of the critical exponents. In particular, we infer the full set of magnetic scaling dimensions (watermelon operators) of the Potts model.

  9. Series analysis of Q-state checkerboard Potts models

    SciTech Connect

    Hansel, D.; Maillard, J.M.

    1988-12-01

    The series analysis of the low temperature expansion of the checkerboard q-state Potts model in a magnetic field initiated in two previous papers is continued. In particular algebraic varieties of the parameter space (corresponding or generalizing the so-called disorder solutions), the checkerboard Potts model and its Bethe approximation are indistinguishable as far as one is concerned with the partition function and its first order derivatives. The difference between the two models occurs for higher order derivatives. In particular one gives the exact expression of the (low temperature expansion of the) susceptibility of the checkerboard Ising model in zero magnetic field on one of these varieties.

  10. Phenomenological theory of the Potts model evaporation-condensation transition

    NASA Astrophysics Data System (ADS)

    Ibáñez-Berganza, M.

    2016-01-01

    We present a phenomenological theory describing the finite-size evaporation-condensation transition of the q-state Potts model in the microcanonical ensemble. Our arguments rely on the existence of an exponent σ, relating the surface and the volume of the condensed phase droplet. The evaporation-condensation transition temperature and energy converge to their infinite-size values with the same power, a=(1-σ)/(2-σ) , of the inverse of the system size. For the 2D Potts model we show, by means of efficient simulations up to q = 24 and 10242 sites, that the exponent a is compatible with 1/4, assuming assymptotic finite-size convergence. While this value cannot be addressed by the evaporation-condensation theory developed for the Ising model, it is obtained in the present scheme if σ=2/3 , in agreement with previous theoretical guesses. The connection with the phenomenon of metastability in the canonical ensemble is also discussed.

  11. The Potts model on a Bethe lattice with nonmagnetic impurities

    SciTech Connect

    Semkin, S. V. Smagin, V. P.

    2015-10-15

    We have obtained a solution for the Potts model on a Bethe lattice with mobile nonmagnetic impurities. A method is proposed for constructing a “pseudochaotic” impurity distribution by a vanishing correlation in the arrangement of impurity atoms for the nearest sites. For a pseudochaotic impurity distribution, we obtained the phase-transition temperature, magnetization, and spontaneous magnetization jumps at the phase-transition temperature.

  12. A hybrid parallel framework for the cellular Potts model simulations

    SciTech Connect

    Jiang, Yi; He, Kejing; Dong, Shoubin

    2009-01-01

    The Cellular Potts Model (CPM) has been widely used for biological simulations. However, most current implementations are either sequential or approximated, which can't be used for large scale complex 3D simulation. In this paper we present a hybrid parallel framework for CPM simulations. The time-consuming POE solving, cell division, and cell reaction operation are distributed to clusters using the Message Passing Interface (MPI). The Monte Carlo lattice update is parallelized on shared-memory SMP system using OpenMP. Because the Monte Carlo lattice update is much faster than the POE solving and SMP systems are more and more common, this hybrid approach achieves good performance and high accuracy at the same time. Based on the parallel Cellular Potts Model, we studied the avascular tumor growth using a multiscale model. The application and performance analysis show that the hybrid parallel framework is quite efficient. The hybrid parallel CPM can be used for the large scale simulation ({approx}10{sup 8} sites) of complex collective behavior of numerous cells ({approx}10{sup 6}).

  13. Exact Potts model partition functions on ladder graphs

    NASA Astrophysics Data System (ADS)

    Shrock, Robert

    2000-08-01

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

  14. Hexagon and pentagon identities for the Z sub 3 Potts model

    SciTech Connect

    Ryang, S. )

    1991-04-15

    Investigating the transformation properties of the conformal blocks in the {ital Z}{sub 3} Potts model we derive some braid matrices. From the obtained braid matrices we explicitly show how the hexagon and pentagon identities are satisfied.

  15. Multiscale Model of Colorectal Cancer Using the Cellular Potts Framework

    PubMed Central

    Osborne, James M

    2015-01-01

    Colorectal cancer (CRC) is one of the major causes of death in the developed world and forms a canonical example of tumorigenesis. CRC arises from a string of mutations of individual cells in the colorectal crypt, making it particularly suited for multiscale multicellular modeling, where mutations of individual cells can be clearly represented and their effects readily tracked. In this paper, we present a multicellular model of the onset of colorectal cancer, utilizing the cellular Potts model (CPM). We use the model to investigate how, through the modification of their mechanical properties, mutant cells colonize the crypt. Moreover, we study the influence of mutations on the shape of cells in the crypt, suggesting possible cell- and tissue-level indicators for identifying early-stage cancerous crypts. Crucially, we discuss the effect that the motility parameters of the model (key factors in the behavior of the CPM) have on the distribution of cells within a homeostatic crypt, resulting in an optimal parameter regime that accurately reflects biological assumptions. In summary, the key results of this paper are 1) how to couple the CPM with processes occurring on other spatial scales, using the example of the crypt to motivate suitable motility parameters; 2) modeling mutant cells with the CPM; 3) and investigating how mutations influence the shape of cells in the crypt. PMID:26461973

  16. A node-based version of the cellular Potts model.

    PubMed

    Scianna, Marco; Preziosi, Luigi

    2016-09-01

    The cellular Potts model (CPM) is a lattice-based Monte Carlo method that uses an energetic formalism to describe the phenomenological mechanisms underlying the biophysical problem of interest. We here propose a CPM-derived framework that relies on a node-based representation of cell-scale elements. This feature has relevant consequences on the overall simulation environment. First, our model can be implemented on any given domain, provided a proper discretization (which can be regular or irregular, fixed or time evolving). Then, it allowed an explicit representation of cell membranes, whose displacements realistically result in cell movement. Finally, our node-based approach can be easily interfaced with continuous mechanics or fluid dynamics models. The proposed computational environment is here applied to some simple biological phenomena, such as cell sorting and chemotactic migration, also in order to achieve an analysis of the performance of the underlying algorithm. This work is finally equipped with a critical comparison between the advantages and disadvantages of our model with respect to the traditional CPM and to some similar vertex-based approaches. PMID:27416549

  17. Potts models with magnetic field: Arithmetic, geometry, and computation

    NASA Astrophysics Data System (ADS)

    Dasu, Shival; Marcolli, Matilde

    2015-11-01

    We give a sheaf theoretic interpretation of Potts models with external magnetic field, in terms of constructible sheaves and their Euler characteristics. We show that the polynomial countability question for the hypersurfaces defined by the vanishing of the partition function is affected by changes in the magnetic field: elementary examples suffice to see non-polynomially countable cases that become polynomially countable after a perturbation of the magnetic field. The same recursive formula for the Grothendieck classes, under edge-doubling operations, holds as in the case without magnetic field, but the closed formulae for specific examples like banana graphs differ in the presence of magnetic field. We give examples of computation of the Euler characteristic with compact support, for the set of real zeros, and find a similar exponential growth with the size of the graph. This can be viewed as a measure of topological and algorithmic complexity. We also consider the computational complexity question for evaluations of the polynomial, and show both tractable and NP-hard examples, using dynamic programming.

  18. Verification and Validation Strategy for Implementation of Hybrid Potts-Phase Field Hydride Modeling Capability in MBM

    SciTech Connect

    Jason D. Hales; Veena Tikare

    2014-04-01

    The Used Fuel Disposition (UFD) program has initiated a project to develop a hydride formation modeling tool using a hybrid Potts­phase field approach. The Potts model is incorporated in the SPPARKS code from Sandia National Laboratories. The phase field model is provided through MARMOT from Idaho National Laboratory.

  19. Marginal dimensions of the Potts model with invisible states

    NASA Astrophysics Data System (ADS)

    Krasnytska, M.; Sarkanych, P.; Berche, B.; Holovatch, Yu; Kenna, R.

    2016-06-01

    We reconsider the mean-field Potts model with q interacting and r non-interacting (invisible) states. The model was recently introduced to explain discrepancies between theoretical predictions and experimental observations of phase transitions in some systems where the Z q -symmetry is spontaneously broken. We analyse the marginal dimensions of the model, i.e., the value of r at which the order of the phase transition changes. In the q = 2 case, we determine that value to be {r}{{c}}=3.65(5); there is a second-order phase transition there when r\\lt {r}{{c}} and a first-order one at r\\gt {r}{{c}}. We also analyse the region 1≤slant q\\lt 2 and show that the change from second to first order there is manifest through a new mechanism involving two marginal values of r. The q = 1 limit gives bond percolation. Above the lower value r c1, the order parameters exhibit discontinuities at temperature \\tilde{t} below a critical value t c. The larger value r c2 marks the point at which the phase transition at t c changes from second to first order. Thus, for {r}{{c}1}\\lt r\\lt {r}{{c}2}, the transition at t c remains second order while at \\tilde{t} the system undergoes a first order phase transition. As r increases further, \\tilde{t} increases, bringing the discontinuity closer to t c. Finally, when r exceeds r c2 \\tilde{t} coincides with t c and the phase transition becomes first order. This new mechanism indicates how the discontinuity characteristic of first order phase transitions emerges.

  20. Cyclic period-3 window in antiferromagnetic potts and Ising models on recursive lattices

    NASA Astrophysics Data System (ADS)

    Ananikian, N. S.; Ananikyan, L. N.; Chakhmakhchyan, L. A.

    2011-09-01

    The magnetic properties of the antiferromagnetic Potts model with two-site interaction and the antiferromagnetic Ising model with three-site interaction on recursive lattices have been studied. A cyclic period-3 window has been revealed by the recurrence relation method in the antiferromagnetic Q-state Potts model on the Bethe lattice (at Q < 2) and in the antiferromagnetic Ising model with three-site interaction on the Husimi cactus. The Lyapunov exponents have been calculated, modulated phases and a chaotic regime in the cyclic period-3 window have been found for one-dimensional rational mappings determined the properties of these systems.

  1. Duality and Fisher zeros in the two-dimensional Potts model on a square lattice

    NASA Astrophysics Data System (ADS)

    Astorino, Marco; Canfora, Fabrizio

    2010-05-01

    A phenomenological approach to the ferromagnetic two-dimensional (2D) Potts model on square lattice is proposed. Our goal is to present a simple functional form that obeys the known properties possessed by the free energy of the q -state Potts model. The duality symmetry of the 2D Potts model together with the known results on its critical exponent α allows us to fix consistently the details of the proposed expression for the free energy. The agreement of the analytic ansatz with numerical data in the q=3 case is very good at high and low temperatures as well as at the critical point. It is shown that the q>4 cases naturally fit into the same scheme and that one should also expect a good agreement with numerical data. The limiting q=4 case is shortly discussed.

  2. A Bayesian non-parametric Potts model with application to pre-surgical FMRI data.

    PubMed

    Johnson, Timothy D; Liu, Zhuqing; Bartsch, Andreas J; Nichols, Thomas E

    2013-08-01

    The Potts model has enjoyed much success as a prior model for image segmentation. Given the individual classes in the model, the data are typically modeled as Gaussian random variates or as random variates from some other parametric distribution. In this article, we present a non-parametric Potts model and apply it to a functional magnetic resonance imaging study for the pre-surgical assessment of peritumoral brain activation. In our model, we assume that the Z-score image from a patient can be segmented into activated, deactivated, and null classes, or states. Conditional on the class, or state, the Z-scores are assumed to come from some generic distribution which we model non-parametrically using a mixture of Dirichlet process priors within the Bayesian framework. The posterior distribution of the model parameters is estimated with a Markov chain Monte Carlo algorithm, and Bayesian decision theory is used to make the final classifications. Our Potts prior model includes two parameters, the standard spatial regularization parameter and a parameter that can be interpreted as the a priori probability that each voxel belongs to the null, or background state, conditional on the lack of spatial regularization. We assume that both of these parameters are unknown, and jointly estimate them along with other model parameters. We show through simulation studies that our model performs on par, in terms of posterior expected loss, with parametric Potts models when the parametric model is correctly specified and outperforms parametric models when the parametric model in misspecified. PMID:22627277

  3. Critical behavior of the q = 3 , 4-Potts model on quasiperiodic decagonal lattices

    NASA Astrophysics Data System (ADS)

    Ferraz, Carlos Handrey Araujo

    2015-12-01

    In this study, we performed Monte Carlo simulations of the q = 3 , 4-Potts model on quasiperiodic decagonal lattices (QDL) to assess the critical behavior of these systems. Using the single histogram technique in conjunction with the finite-size scaling analysis, we estimate the infinite lattice critical temperatures and the leading critical exponents for q = 3 and q = 4 states. Our estimates for the critical exponents on QDL are in good agreement with the exact values on 2D periodic lattices, supporting the claim that both the q = 3 and q = 4 Potts model on quasiperiodic lattices belong to the same universality class as those on 2D periodic lattices.

  4. Potts model on directed small-world Voronoi-Delaunay lattices

    NASA Astrophysics Data System (ADS)

    Marques, R. M.; Lima, F. W. S.; Costa Filho, Raimundo N.

    2016-06-01

    The critical properties of the Potts model with q = 3 and 4 states in two-dimensions on directed small-world Voronoi-Delaunay random lattices with quenched connectivity disorder are investigated. This disordered system is simulated by applying the Monte Carlo update heat bath algorithm. The Potts model on these directed small-world random lattices presents in fact a second-order phase transition with new critical exponents for q = 3 and value of the rewiring probability p = 0.01, but for q = 4 the system exhibits only a first-order phase transition independent of p (0 < p < 1).

  5. Parallel family trees for transfer matrices in the Potts model

    NASA Astrophysics Data System (ADS)

    Navarro, Cristobal A.; Canfora, Fabrizio; Hitschfeld, Nancy; Navarro, Gonzalo

    2015-02-01

    The computational cost of transfer matrix methods for the Potts model is related to the question in how many ways can two layers of a lattice be connected? Answering the question leads to the generation of a combinatorial set of lattice configurations. This set defines the configuration space of the problem, and the smaller it is, the faster the transfer matrix can be computed. The configuration space of generic (q , v) transfer matrix methods for strips is in the order of the Catalan numbers, which grows asymptotically as O(4m) where m is the width of the strip. Other transfer matrix methods with a smaller configuration space indeed exist but they make assumptions on the temperature, number of spin states, or restrict the structure of the lattice. In this paper we propose a parallel algorithm that uses a sub-Catalan configuration space of O(3m) to build the generic (q , v) transfer matrix in a compressed form. The improvement is achieved by grouping the original set of Catalan configurations into a forest of family trees, in such a way that the solution to the problem is now computed by solving the root node of each family. As a result, the algorithm becomes exponentially faster than the Catalan approach while still highly parallel. The resulting matrix is stored in a compressed form using O(3m ×4m) of space, making numerical evaluation and decompression to be faster than evaluating the matrix in its O(4m ×4m) uncompressed form. Experimental results for different sizes of strip lattices show that the parallel family trees (PFT) strategy indeed runs exponentially faster than the Catalan Parallel Method (CPM), especially when dealing with dense transfer matrices. In terms of parallel performance, we report strong-scaling speedups of up to 5.7 × when running on an 8-core shared memory machine and 28 × for a 32-core cluster. The best balance of speedup and efficiency for the multi-core machine was achieved when using p = 4 processors, while for the cluster

  6. An improvement of extremality regions for Gibbs measures of the Potts model on a Cayley tree

    NASA Astrophysics Data System (ADS)

    Haydarov, Farhod; Khakimov, Rustam

    2016-03-01

    We give a condition of extemelity for translation-invariant Gibbs measures of q—state Potts model on a Cayley tree. We'll improve the regions of extremality for some measures considered in [14]. Moreover, some results in [14] are generalized.

  7. Phase transitions of the q-state Potts model on multiply-laced Sierpinski gaskets

    NASA Astrophysics Data System (ADS)

    Tian, Liang; Ma, Hui; Guo, Wenan; Tang, Lei-Han

    2013-05-01

    We present an exact solution of the q-state Potts model on a class of generalized Sierpinski fractal lattices. The model is shown to possess an ordered phase at low temperatures and a continuous transition to the high temperature disordered phase at any q ≥ 1. Multicriticality is observed in the presence of a symmetry-breaking field. Exact renormalization group analysis yields the phase diagram of the model and a complete set of critical exponents at various transitions.

  8. Fluctuation complexity of agent-based financial time series model by stochastic Potts system

    NASA Astrophysics Data System (ADS)

    Hong, Weijia; Wang, Jun

    2015-03-01

    Financial market is a complex evolved dynamic system with high volatilities and noises, and the modeling and analyzing of financial time series are regarded as the rather challenging tasks in financial research. In this work, by applying the Potts dynamic system, a random agent-based financial time series model is developed in an attempt to uncover the empirical laws in finance, where the Potts model is introduced to imitate the trading interactions among the investing agents. Based on the computer simulation in conjunction with the statistical analysis and the nonlinear analysis, we present numerical research to investigate the fluctuation behaviors of the proposed time series model. Furthermore, in order to get a robust conclusion, we consider the daily returns of Shanghai Composite Index and Shenzhen Component Index, and the comparison analysis of return behaviors between the simulation data and the actual data is exhibited.

  9. Graphical Representations for Ising and Potts Models in General External Fields

    NASA Astrophysics Data System (ADS)

    Cioletti, Leandro; Vila, Roberto

    2016-01-01

    This work is concerned with the theory of graphical representation for the Ising and Potts models over general lattices with non-translation invariant external field. We explicitly describe in terms of the random-cluster representation the distribution function and, consequently, the expected value of a single spin for the Ising and q-state Potts models with general external fields. We also consider the Gibbs states for the Edwards-Sokal representation of the Potts model with non-translation invariant magnetic field and prove a version of the FKG inequality for the so called general random-cluster model (GRC model) with free and wired boundary conditions in the non-translation invariant case. Adding the amenability hypothesis on the lattice, we obtain the uniqueness of the infinite connected component and the almost sure quasilocality of the Gibbs measures for the GRC model with such general magnetic fields. As a final application of the theory developed, we show the uniqueness of the Gibbs measures for the ferromagnetic Ising model with a positive power-law decay magnetic field with small enough power, as conjectured in Bissacot et al. (Commun Math Phys 337: 41-53, 2015).

  10. Lattice models of glasses and Potts models for community detection

    NASA Astrophysics Data System (ADS)

    Darst, Richard K.

    In Part I, we construct a configurationally constrained lattice glass model following the example of Biroli and Mézard (Phys. Rev. Lett., 82, 025501 (2001)), which we denote t154. By examining the relaxation, atomic motion, Stokes-Einstein relationship violation, time-dependent displacement (van Hove function), wavevector-dependent relaxation, and multi-point correlations S4 and χ4 , we can show that this new model satisfies all minimal requirements set by the observed phenomena of dynamical heterogeneity of supercooled liquids, though with a drastically different theoretical basis from existing lattice models of glasses based on kinetic facilitation. We then proceed to perform a more detailed comparison between lattice glass models, including t154 and a model by Ciamarra et. al. (Phys. Rev. E 68 066111 (2003)), with traditional facilitated models. We study two forms of dynamical sensitivity: sensitivity to boundary conditions, and a sensitivity to initial conditions. By comparison to atomistic computer simulation, we find evidence that the lattice glass models better describe glassy behavior. We conclude by discussing the implications of our findings for contrasting theories of the glass transition. In Part II, we change our focus and examine community detection in graphs from a theoretical standpoint. Many disparate community definitions have been proposed, however except for one, few have been analyzed in any great detail. In this work, we, for the first time, formally study a definition based on internal edge density. Using the concept that internal edge density is the fraction of intra-community edges relative to the maximal number of intra-community edges, we produce a rich framework to use as the basis of community detection. We discuss its use in local and global community detection algorithms, and how our methods can extend to overlapping and hierarchical communities, and weighted, directed, and multi-graphs. In order to validate our definition, we use

  11. CSOS models descending from chiral Potts models: degeneracy of the eigenspace and loop algebra

    NASA Astrophysics Data System (ADS)

    Au-Yang, Helen; Perk, Jacques H. H.

    2016-04-01

    Monodromy matrices of the {{\\boldsymbol{τ }}}2\\phantom{^{\\prime }} model are known to satisfy a Yang-Baxter equation with a six-vertex R-matrix as the intertwiner. The commutation relations of the elements of the monodromy matrices are completely determined by this R-matrix. We show the reason why in the superintegrable case the eigenspace is degenerate, but not in the general case. We then show that the eigenspaces of special CSOS models descending from the chiral Potts model are also degenerate. The existence of an L({{sl}}2) quantum loop algebra (or subalgebra) in these models is established by showing that the Serre relations hold for the generators. The highest weight polynomial (or the Drinfeld polynomial) of the representation is obtained by using the method of Baxter for the superintegrable case. As a byproduct, the eigenvalues of all such CSOS models are given explicitly.

  12. Sums of random matrices and the Potts model on random planar maps

    NASA Astrophysics Data System (ADS)

    Atkin, Max R.; Niedner, Benjamin; Wheater, John F.

    2016-05-01

    We compute the partition function of the q-states Potts model on a random planar lattice with p≤slant q allowed, equally weighted colours on a connected boundary. To this end, we employ its matrix model representation in the planar limit, generalising a result by Voiculescu for the addition of random matrices to a situation beyond free probability theory. We show that the partition functions with p and q - p colours on the boundary are related algebraically. Finally, we investigate the phase diagram of the model when 0≤slant q≤slant 4 and comment on the conformal field theory description of the critical points.

  13. Shaken, but not stirred—Potts model coupled to quantum gravity

    NASA Astrophysics Data System (ADS)

    Ambjørn, J. A.; Anagnostopoulos, K. N.; Loll, R.; Pushkina, I.

    2009-01-01

    We investigate the critical behaviour of both matter and geometry of the three-state Potts model coupled to two-dimensional Lorentzian quantum gravity in the framework of causal dynamical triangulations. Contrary to what general arguments on the effects of disorder suggest, we find strong numerical evidence that the critical exponents of the matter are not changed under the influence of quantum fluctuations in the geometry, compared to their values on fixed, regular lattices. This lends further support to previous findings that quantum gravity models based on causal dynamical triangulations are in many ways better behaved than their Euclidean counterparts.

  14. The early history of the integrable chiral Potts model and the odd-even problem

    NASA Astrophysics Data System (ADS)

    Perk, Jacques H. H.

    2016-04-01

    In the first part of this paper I shall discuss the round-about way of how the integrable chiral Potts model was discovered about 30 years ago. As there should be more higher-genus models to be discovered, this might be of interest. In the second part I shall discuss some quantum group aspects, especially issues of odd versus even N related to the Serre relations conjecture in our quantum loop subalgebra paper of 5 years ago and how we can make good use of coproducts, also borrowing ideas of Drinfeld, Jimbo, Deguchi, Fabricius, McCoy and Nishino.

  15. Potts model simulation of grain size distributions during final stage sintering

    SciTech Connect

    Zeng, P.; Tikare, V.

    1998-09-01

    The Potts Monte Carlo model was used to simulate microstructural evolution and characterize grain size distribution during the final stages of sintering. Simultaneous grain growth, pore migration and pore shrinkage were simulated in a system with an initial porosity of 10% with varying ratios of grain boundary mobility to pore shrinkage rates. This investigation shows that the presence of pores changes the grain size distribution and the topological characteristics due to pinning of grains by pores. As pores shrink away, their pinning effect decreases. Once pore shrinkage is complete, normal grain growth is achieved.

  16. Dynamics of Cell Shape and Forces on Micropatterned Substrates Predicted by a Cellular Potts Model

    PubMed Central

    Albert, Philipp J.; Schwarz, Ulrich S.

    2014-01-01

    Micropatterned substrates are often used to standardize cell experiments and to quantitatively study the relation between cell shape and function. Moreover, they are increasingly used in combination with traction force microscopy on soft elastic substrates. To predict the dynamics and steady states of cell shape and forces without any a priori knowledge of how the cell will spread on a given micropattern, here we extend earlier formulations of the two-dimensional cellular Potts model. The third dimension is treated as an area reservoir for spreading. To account for local contour reinforcement by peripheral bundles, we augment the cellular Potts model by elements of the tension-elasticity model. We first parameterize our model and show that it accounts for momentum conservation. We then demonstrate that it is in good agreement with experimental data for shape, spreading dynamics, and traction force patterns of cells on micropatterned substrates. We finally predict shapes and forces for micropatterns that have not yet been experimentally studied. PMID:24896113

  17. The Star Square in the Baxter-Bazhanov Model and the Star-Triangle Relation in the Chiral Potts Model

    NASA Astrophysics Data System (ADS)

    Hu, Zhan-Ning

    In this letter, the connection is found between the "star-square" relation in the Baxter-Bazhanov model and the "star-triangle" relation in the chiral Potts model, which means that the tetrahedron equation of the Baxter-Bazhanov model is a consequence of the latter. The four additional constraints in the tetrahedron equation given by Kashaev et al. hold naturally in respect to the spherical trigonometry parametrizations.

  18. Structural propensities of kinase family proteins from a Potts model of residue co-variation.

    PubMed

    Haldane, Allan; Flynn, William F; He, Peng; Vijayan, R S K; Levy, Ronald M

    2016-08-01

    Understanding the conformational propensities of proteins is key to solving many problems in structural biology and biophysics. The co-variation of pairs of mutations contained in multiple sequence alignments of protein families can be used to build a Potts Hamiltonian model of the sequence patterns which accurately predicts structural contacts. This observation paves the way to develop deeper connections between evolutionary fitness landscapes of entire protein families and the corresponding free energy landscapes which determine the conformational propensities of individual proteins. Using statistical energies determined from the Potts model and an alignment of 2896 PDB structures, we predict the propensity for particular kinase family proteins to assume a "DFG-out" conformation implicated in the susceptibility of some kinases to type-II inhibitors, and validate the predictions by comparison with the observed structural propensities of the corresponding proteins and experimental binding affinity data. We decompose the statistical energies to investigate which interactions contribute the most to the conformational preference for particular sequences and the corresponding proteins. We find that interactions involving the activation loop and the C-helix and HRD motif are primarily responsible for stabilizing the DFG-in state. This work illustrates how structural free energy landscapes and fitness landscapes of proteins can be used in an integrated way, and in the context of kinase family proteins, can potentially impact therapeutic design strategies. PMID:27241634

  19. Multi-Scale Modeling in Morphogenesis: A Critical Analysis of the Cellular Potts Model

    PubMed Central

    Voss-Böhme, Anja

    2012-01-01

    Cellular Potts models (CPMs) are used as a modeling framework to elucidate mechanisms of biological development. They allow a spatial resolution below the cellular scale and are applied particularly when problems are studied where multiple spatial and temporal scales are involved. Despite the increasing usage of CPMs in theoretical biology, this model class has received little attention from mathematical theory. To narrow this gap, the CPMs are subjected to a theoretical study here. It is asked to which extent the updating rules establish an appropriate dynamical model of intercellular interactions and what the principal behavior at different time scales characterizes. It is shown that the longtime behavior of a CPM is degenerate in the sense that the cells consecutively die out, independent of the specific interdependence structure that characterizes the model. While CPMs are naturally defined on finite, spatially bounded lattices, possible extensions to spatially unbounded systems are explored to assess to which extent spatio-temporal limit procedures can be applied to describe the emergent behavior at the tissue scale. To elucidate the mechanistic structure of CPMs, the model class is integrated into a general multiscale framework. It is shown that the central role of the surface fluctuations, which subsume several cellular and intercellular factors, entails substantial limitations for a CPM's exploitation both as a mechanistic and as a phenomenological model. PMID:22984409

  20. A study of perfect wetting for Potts and Blume-Capel models with correlation inequalities

    SciTech Connect

    De Coninck, J.; Messager, A.; Miracle-Sole, S.; Ruiz, J. )

    1988-07-01

    The so-called perfect wetting phenomenon is studied for the q-state, d {>=} 2 Potts model. Using a new correlation inequality, a general inequality is established for the surface tension between ordered phases ({sigma}{sup a,b}) and the surface tension between an ordered and the disordered phases ({sigma}{sup a,f}) for any even value of q. This result implies in particular {sigma}{sub {beta}{sub t}}{sup a,b} {>=} {sigma}{sub {beta}{sub t}}{sup a,f} + {sigma}{sub {beta}{sub t}}{sup b,f} > 0 at the transition point {beta}{sub t} where the previous phases coexist for q large. This inequality is connected to perfect wetting at the transition point using thermodynamic considerations. The same kinds of results are derived for the Blume-Capel model.

  1. High-precision percolation thresholds and Potts-model critical manifolds from graph polynomials

    NASA Astrophysics Data System (ADS)

    >Jesper Lykke Jacobsen,

    2014-04-01

    The critical curves of the q-state Potts model can be determined exactly for regular two-dimensional lattices G that are of the three-terminal type. This comprises the square, triangular, hexagonal and bow-tie lattices. Jacobsen and Scullard have defined a graph polynomial PB(q, v) that gives access to the critical manifold for general lattices. It depends on a finite repeating part of the lattice, called the basis B, and its real roots in the temperature variable v = eK - 1 provide increasingly accurate approximations to the critical manifolds upon increasing the size of B. Using transfer matrix techniques, these authors computed PB(q, v) for large bases (up to 243 edges), obtaining determinations of the ferromagnetic critical point vc > 0 for the (4, 82), kagome, and (3, 122) lattices to a precision (of the order 10-8) slightly superior to that of the best available Monte Carlo simulations. In this paper we describe a more efficient transfer matrix approach to the computation of PB(q, v) that relies on a formulation within the periodic Temperley-Lieb algebra. This makes possible computations for substantially larger bases (up to 882 edges), and the precision on vc is hence taken to the range 10-13. We further show that a large variety of regular lattices can be cast in a form suitable for this approach. This includes all Archimedean lattices, their duals and their medials. For all these lattices we tabulate high-precision estimates of the bond percolation thresholds pc and Potts critical points vc. We also trace and discuss the full Potts critical manifold in the (q, v) plane, paying special attention to the antiferromagnetic region v < 0. Finally, we adapt the technique to site percolation as well, and compute the polynomials PB(p) for certain Archimedean and dual lattices (those having only cubic and quartic vertices), using very large bases (up to 243 vertices). This produces the site percolation thresholds pc to a precision of the order of 10-9.

  2. Spanning Forests and the q-State Potts Model in the Limit q →0

    NASA Astrophysics Data System (ADS)

    Jacobsen, Jesper Lykke; Salas, Jesús; Sokal, Alan D.

    2005-06-01

    We study the q-state Potts model with nearest-neighbor coupling v=eβJ-1 in the limit q,v → 0 with the ratio w = v/q held fixed. Combinatorially, this limit gives rise to the generating polynomial of spanning forests; physically, it provides information about the Potts-model phase diagram in the neighborhood of (q,v) = (0,0). We have studied this model on the square and triangular lattices, using a transfer-matrix approach at both real and complex values of w. For both lattices, we have computed the symbolic transfer matrices for cylindrical strips of widths 2≤ L ≤ 10, as well as the limiting curves B of partition-function zeros in the complex w-plane. For real w, we find two distinct phases separated by a transition point w= w 0, where w0 =-1/4 (resp. w0=-0.1753 ± 0.0002) for the square (resp. triangular) lattice. For w>w0 we find a non-critical disordered phase that is compatible with the predicted asymptotic freedom as w → +∞. For w

  3. FAST TRACK COMMUNICATION Critical exponents of domain walls in the two-dimensional Potts model

    NASA Astrophysics Data System (ADS)

    Dubail, Jérôme; Lykke Jacobsen, Jesper; Saleur, Hubert

    2010-12-01

    We address the geometrical critical behavior of the two-dimensional Q-state Potts model in terms of the spin clusters (i.e. connected domains where the spin takes a constant value). These clusters are different from the usual Fortuin-Kasteleyn clusters, and are separated by domain walls that can cross and branch. We develop a transfer matrix technique enabling the formulation and numerical study of spin clusters even when Q is not an integer. We further identify geometrically the crossing events which give rise to conformal correlation functions. This leads to an infinite series of fundamental critical exponents h_{\\ell _1-\\ell _2,2\\ell _1}, valid for 0 <= Q <= 4, that describe the insertion of ell1 thin and ell2 thick domain walls.

  4. A parallel implementation of the Cellular Potts Model for simulation of cell-based morphogenesis

    PubMed Central

    Chen, Nan; Glazier, James A.; Izaguirre, Jesús A.; Alber, Mark S.

    2007-01-01

    The Cellular Potts Model (CPM) has been used in a wide variety of biological simulations. However, most current CPM implementations use a sequential modified Metropolis algorithm which restricts the size of simulations. In this paper we present a parallel CPM algorithm for simulations of morphogenesis, which includes cell–cell adhesion, a cell volume constraint, and cell haptotaxis. The algorithm uses appropriate data structures and checkerboard subgrids for parallelization. Communication and updating algorithms synchronize properties of cells simulated on different processor nodes. Tests show that the parallel algorithm has good scalability, permitting large-scale simulations of cell morphogenesis (107 or more cells) and broadening the scope of CPM applications. The new algorithm satisfies the balance condition, which is sufficient for convergence of the underlying Markov chain. PMID:18084624

  5. A Cellular Potts Model of single cell migration in presence of durotaxis.

    PubMed

    Allena, R; Scianna, M; Preziosi, L

    2016-05-01

    Cell migration is a fundamental biological phenomenon during which cells sense their surroundings and respond to different types of signals. In presence of durotaxis, cells preferentially crawl from soft to stiff substrates by reorganizing their cytoskeleton from an isotropic to an anisotropic distribution of actin filaments. In the present paper, we propose a Cellular Potts Model to simulate single cell migration over flat substrates with variable stiffness. We have tested five configurations: (i) a substrate including a soft and a stiff region, (ii) a soft substrate including two parallel stiff stripes, (iii) a substrate made of successive stripes with increasing stiffness to create a gradient and (iv) a stiff substrate with four embedded soft squares. For each simulation, we have evaluated the morphology of the cell, the distance covered, the spreading area and the migration speed. We have then compared the numerical results to specific experimental observations showing a consistent agreement. PMID:26968932

  6. Transfer matrix computation of critical polynomials for two-dimensional Potts models

    DOE PAGESBeta

    Jacobsen, Jesper Lykke; Scullard, Christian R.

    2013-02-04

    We showed, In our previous work, that critical manifolds of the q-state Potts model can be studied by means of a graph polynomial PB(q, v), henceforth referred to as the critical polynomial. This polynomial may be defined on any periodic two-dimensional lattice. It depends on a finite subgraph B, called the basis, and the manner in which B is tiled to construct the lattice. The real roots v = eK — 1 of PB(q, v) either give the exact critical points for the lattice, or provide approximations that, in principle, can be made arbitrarily accurate by increasing the size ofmore » B in an appropriate way. In earlier work, PB(q, v) was defined by a contraction-deletion identity, similar to that satisfied by the Tutte polynomial. Here, we give a probabilistic definition of PB(q, v), which facilitates its computation, using the transfer matrix, on much larger B than was previously possible.We present results for the critical polynomial on the (4, 82), kagome, and (3, 122) lattices for bases of up to respectively 96, 162, and 243 edges, compared to the limit of 36 edges with contraction-deletion. We discuss in detail the role of the symmetries and the embedding of B. The critical temperatures vc obtained for ferromagnetic (v > 0) Potts models are at least as precise as the best available results from Monte Carlo simulations or series expansions. For instance, with q = 3 we obtain vc(4, 82) = 3.742 489 (4), vc(kagome) = 1.876 459 7 (2), and vc(3, 122) = 5.033 078 49 (4), the precision being comparable or superior to the best simulation results. More generally, we trace the critical manifolds in the real (q, v) plane and discuss the intricate structure of the phase diagram in the antiferromagnetic (v < 0) region.« less

  7. Structural phase transition in perovskite metal-formate frameworks: a Potts-type model with dipolar interactions.

    PubMed

    Šimėnas, Mantas; Balčiūnas, Sergejus; Ma Combining Cedilla Czka, Mirosław; Banys, Jūras; Tornau, Evaldas E

    2016-07-21

    We propose a combined experimental and numerical study to describe an order-disorder structural phase transition in perovskite-based [(CH3)2NH2][M(HCOO)3] (M = Zn(2+), Mn(2+), Fe(2+), Co(2+) and Ni(2+)) dense metal-organic frameworks (MOFs). The three-fold degenerate orientation of the molecular (CH3)2NH2(+) (DMA(+)) cation implies a selection of the statistical three-state model of the Potts type. It is constructed on a simple cubic lattice where each lattice point can be occupied by a DMA(+) cation in one of the available states. In our model the main interaction is the nearest-neighbor Potts-type interaction, which effectively accounts for the H-bonding between DMA(+) cations and M(HCOO)3(-) cages. The model is modified by accounting for the dipolar interactions which are evaluated for the real monoclinic lattice using density functional theory. We employ the Monte Carlo method to numerically study the model. The calculations are supplemented with the experimental measurements of electric polarization. The obtained results indicate that the three-state Potts model correctly describes the phase transition order in these MOFs, while dipolar interactions are necessary to obtain better agreement with the experimental polarization. We show that in our model with substantial dipolar interactions the ground state changes from uniform to the layers with alternating polarization directions. PMID:27341447

  8. Trigonometrical sums connected with the chiral Potts model, Verlinde dimension formula, two-dimensional resistor network, and number theory

    SciTech Connect

    Chair, Noureddine

    2014-02-15

    We have recently developed methods for obtaining exact two-point resistance of the complete graph minus N edges. We use these methods to obtain closed formulas of certain trigonometrical sums that arise in connection with one-dimensional lattice, in proving Scott’s conjecture on permanent of Cauchy matrix, and in the perturbative chiral Potts model. The generalized trigonometrical sums of the chiral Potts model are shown to satisfy recursion formulas that are transparent and direct, and differ from those of Gervois and Mehta. By making a change of variables in these recursion formulas, the dimension of the space of conformal blocks of SU(2) and SO(3) WZW models may be computed recursively. Our methods are then extended to compute the corner-to-corner resistance, and the Kirchhoff index of the first non-trivial two-dimensional resistor network, 2×N. Finally, we obtain new closed formulas for variant of trigonometrical sums, some of which appear in connection with number theory. -- Highlights: • Alternative derivation of certain trigonometrical sums of the chiral Potts model are given. • Generalization of these trigonometrical sums satisfy recursion formulas. • The dimension of the space of conformal blocks may be computed from these recursions. • Exact corner-to-corner resistance, the Kirchhoff index of 2×N are given.

  9. Fraction of uninfected walkers in the one-dimensional Potts model

    NASA Astrophysics Data System (ADS)

    O'Donoghue, S. J.; Bray, A. J.

    2002-05-01

    The dynamics of the one-dimensional q-state Potts model, in the zero-temperature limit, can be formulated through the motion of random walkers which either annihilate (A+A-->∅) or coalesce (A+A-->A) with a q-dependent probability. We consider all of the walkers in this model to be mutually infectious. Whenever two walkers meet, they experience mutual contamination. Walkers which avoid an encounter with another random walker up to time t remain uninfected. The fraction of uninfected walkers is known to obey a power-law decay U(t)~t-φ(q), with a nontrivial exponent φ(q) [C. Monthus, Phys. Rev. E 54, 4844 (1996); S. N. Majumdar and S. J. Cornell, ibid. 57, 3757 (1998)]. We probe the numerical values of φ(q) to a higher degree of accuracy than previous simulations and relate the exponent φ(q) to the persistence exponent θ(q) [B. Derrida, V. Hakim, and V. Pasquier, Phys. Rev. Lett. 75, 751 (1995)], through the relation φ(q)=γ(q)θ(q) where γ is an exponent introduced in [S. J. O'Donoghue and A. J. Bray, preceding paper, Phys. Rev. E 65, XXXX (2002)]. Our study is extended to include the coupled diffusion-limited reaction A+A-->B, B+B-->A in one dimension with equal initial densities of A and B particles. We find that the density of walkers decays in this model as ρ(t)~t-1/2. The fraction of sites unvisited by either an A or a B particle is found to obey a power law, P(t)~t-θ with θ~=1.33. We discuss these exponents within the context of the q-state Potts model and present numerical evidence that the fraction of walkers which remain uninfected decays as U(t)~t-φ, where φ~=1.13 when infection occurs between like particles only, and φ~=1.93 when we also include cross-species contamination. We find that the relation between φ and θ in this model can also be characterized by an exponent γ, where similarly, φ=γθ.

  10. Nature of phase transitions in Axelrod-like coupled Potts models in two dimensions

    NASA Astrophysics Data System (ADS)

    Gandica, Yerali; Chiacchiera, Silvia

    2016-03-01

    We study F coupled q -state Potts models in a two-dimensional square lattice. The interaction between the different layers is attractive to favor a simultaneous alignment in all of them, and its strength is fixed. The nature of the phase transition for zero field is numerically determined for F =2 ,3 . Using the Lee-Kosterlitz method, we find that it is continuous for F =2 and q =2 , whereas it is abrupt for higher values of q and/or F . When a continuous or a weakly first-order phase transition takes place, we also analyze the properties of the geometrical clusters. This allows us to determine the fractal dimension D of the incipient infinite cluster and to examine the finite-size scaling of the cluster number density via data collapse. A mean-field approximation of the model, from which some general trends can be determined, is presented too. Finally, since this lattice model has been recently considered as a thermodynamic counterpart of the Axelrod model of social dynamics, we discuss our results in connection with this one.

  11. Cluster-size distribution and the magnetic property of a Potts model

    NASA Astrophysics Data System (ADS)

    Hu, Chin-Kun

    1986-11-01

    Based on the connection between a q-state Potts model (QPM) and a q-state bond-correlated percolation model (QBCPM), we propose that in the calculation of the free energy and a physical quantity, e.g., the magnetic susceptibility, we need only to retain the terms of the most probable cluster-size distribution (MPCSD) defined in the text. For the one-dimensional model, the MPCSD may be calculated exactly. The free energy and the magnetic susceptibility determined by such MPCSD are the same as those calculated exactly by the transfer-matrix method. For the QPM on the lattice with dimensions d>=2, the above assumption about the MPCSD implies that the magnetic susceptibility of the QPM is proportional to the mean cluster sizes of the QBCPM for both T>Tc and Tmodels. The implication of this work on the theory of the scaling laws of the critical exponents is also discussed.

  12. Transfer matrix computation of critical polynomials for two-dimensional Potts models

    SciTech Connect

    Jacobsen, Jesper Lykke; Scullard, Christian R.

    2013-02-04

    We showed, In our previous work, that critical manifolds of the q-state Potts model can be studied by means of a graph polynomial PB(q, v), henceforth referred to as the critical polynomial. This polynomial may be defined on any periodic two-dimensional lattice. It depends on a finite subgraph B, called the basis, and the manner in which B is tiled to construct the lattice. The real roots v = eK — 1 of PB(q, v) either give the exact critical points for the lattice, or provide approximations that, in principle, can be made arbitrarily accurate by increasing the size of B in an appropriate way. In earlier work, PB(q, v) was defined by a contraction-deletion identity, similar to that satisfied by the Tutte polynomial. Here, we give a probabilistic definition of PB(q, v), which facilitates its computation, using the transfer matrix, on much larger B than was previously possible.We present results for the critical polynomial on the (4, 82), kagome, and (3, 122) lattices for bases of up to respectively 96, 162, and 243 edges, compared to the limit of 36 edges with contraction-deletion. We discuss in detail the role of the symmetries and the embedding of B. The critical temperatures vc obtained for ferromagnetic (v > 0) Potts models are at least as precise as the best available results from Monte Carlo simulations or series expansions. For instance, with q = 3 we obtain vc(4, 82) = 3.742 489 (4), vc(kagome) = 1.876 459 7 (2), and vc(3, 122) = 5.033 078 49 (4), the precision being comparable or superior to the best simulation results. More generally, we trace the critical manifolds in the real (q, v) plane and discuss the intricate structure of the phase diagram in the antiferromagnetic (v < 0) region.

  13. Structural properties of Potts model partition functions and chromatic polynomials for lattice strips

    NASA Astrophysics Data System (ADS)

    Chang, Shu-Chiuan; Shrock, Robert

    2001-07-01

    The q-state Potts model partition function (equivalent to the Tutte polynomial) for a lattice strip of fixed width Ly and arbitrary length Lx has the form Z(G,q,v)=∑ j=1N Z,G,λ c Z,G,j(λ Z,G,j) L x, where v is a temperature-dependent variable. The special case of the zero-temperature antiferromagnet ( v=-1) is the chromatic polynomial P( G, q). Using coloring and transfer matrix methods, we give general formulas for C X,G=∑ j=1N X,G,λ c X,G,j for X= Z, P on cyclic and Möbius strip graphs of the square and triangular lattice. Combining these with a general expression for the (unique) coefficient cZ, G, j of degree d in q: c (d)=U 2d( q/2) , where Un( x) is the Chebyshev polynomial of the second kind, we determine the number of λZ, G, j's with coefficient c( d) in Z( G, q, v) for these cyclic strips of width Ly to be n Z(L y,d)=(2d+1)(L y+d+1) -1{2L y}/{L y-d } for 0⩽ d⩽ Ly and zero otherwise. For both cyclic and Möbius strips of these lattices, the total number of distinct eigenvalues λZ, G, j is calculated to be N Z,L y,λ = {2L y}/{L y}. Results are also presented for the analogous numbers nP( Ly, d) and NP, Ly, λ for P( G, q). We find that nP( Ly,0)= nP( Ly-1,1)= MLy-1 (Motzkin number), nZ( Ly,0)= CLy (the Catalan number), and give an exact expression for NP, Ly, λ. Our results for NZ, Ly, λ and NP, Ly, λ apply for both the cyclic and Möbius strips of both the square and triangular lattices; we also point out the interesting relations NZ, Ly, λ=2 NDA, tri, Ly and NP, Ly, λ=2 NDA, sq, Ly, where NDA, Λ, n denotes the number of directed lattice animals on the lattice Λ. We find the asymptotic growths NZ, Ly, λ∼ Ly-1/24 Ly and NP, Ly, λ∼ Ly-1/23 Ly as Ly→∞. Some general geometric identities for Potts model partition functions are also presented.

  14. Reconstruction of a Real World Social Network using the Potts Model and Loopy Belief Propagation

    PubMed Central

    Bisconti, Cristian; Corallo, Angelo; Fortunato, Laura; Gentile, Antonio A.; Massafra, Andrea; Pellè, Piergiuseppe

    2015-01-01

    The scope of this paper is to test the adoption of a statistical model derived from Condensed Matter Physics, for the reconstruction of the structure of a social network. The inverse Potts model, traditionally applied to recursive observations of quantum states in an ensemble of particles, is here addressed to observations of the members' states in an organization and their (anti)correlations, thus inferring interactions as links among the members. Adopting proper (Bethe) approximations, such an inverse problem is showed to be tractable. Within an operational framework, this network-reconstruction method is tested for a small real-world social network, the Italian parliament. In this study case, it is easy to track statuses of the parliament members, using (co)sponsorships of law proposals as the initial dataset. In previous studies of similar activity-based networks, the graph structure was inferred directly from activity co-occurrences: here we compare our statistical reconstruction with such standard methods, outlining discrepancies and advantages. PMID:26617539

  15. Improved contact prediction in proteins: using pseudolikelihoods to infer Potts models.

    PubMed

    Ekeberg, Magnus; Lövkvist, Cecilia; Lan, Yueheng; Weigt, Martin; Aurell, Erik

    2013-01-01

    Spatially proximate amino acids in a protein tend to coevolve. A protein's three-dimensional (3D) structure hence leaves an echo of correlations in the evolutionary record. Reverse engineering 3D structures from such correlations is an open problem in structural biology, pursued with increasing vigor as more and more protein sequences continue to fill the data banks. Within this task lies a statistical inference problem, rooted in the following: correlation between two sites in a protein sequence can arise from firsthand interaction but can also be network-propagated via intermediate sites; observed correlation is not enough to guarantee proximity. To separate direct from indirect interactions is an instance of the general problem of inverse statistical mechanics, where the task is to learn model parameters (fields, couplings) from observables (magnetizations, correlations, samples) in large systems. In the context of protein sequences, the approach has been referred to as direct-coupling analysis. Here we show that the pseudolikelihood method, applied to 21-state Potts models describing the statistical properties of families of evolutionarily related proteins, significantly outperforms existing approaches to the direct-coupling analysis, the latter being based on standard mean-field techniques. This improved performance also relies on a modified score for the coupling strength. The results are verified using known crystal structures of specific sequence instances of various protein families. Code implementing the new method can be found at http://plmdca.csc.kth.se/. PMID:23410359

  16. Improved contact prediction in proteins: Using pseudolikelihoods to infer Potts models

    NASA Astrophysics Data System (ADS)

    Ekeberg, Magnus; Lövkvist, Cecilia; Lan, Yueheng; Weigt, Martin; Aurell, Erik

    2013-01-01

    Spatially proximate amino acids in a protein tend to coevolve. A protein's three-dimensional (3D) structure hence leaves an echo of correlations in the evolutionary record. Reverse engineering 3D structures from such correlations is an open problem in structural biology, pursued with increasing vigor as more and more protein sequences continue to fill the data banks. Within this task lies a statistical inference problem, rooted in the following: correlation between two sites in a protein sequence can arise from firsthand interaction but can also be network-propagated via intermediate sites; observed correlation is not enough to guarantee proximity. To separate direct from indirect interactions is an instance of the general problem of inverse statistical mechanics, where the task is to learn model parameters (fields, couplings) from observables (magnetizations, correlations, samples) in large systems. In the context of protein sequences, the approach has been referred to as direct-coupling analysis. Here we show that the pseudolikelihood method, applied to 21-state Potts models describing the statistical properties of families of evolutionarily related proteins, significantly outperforms existing approaches to the direct-coupling analysis, the latter being based on standard mean-field techniques. This improved performance also relies on a modified score for the coupling strength. The results are verified using known crystal structures of specific sequence instances of various protein families. Code implementing the new method can be found at http://plmdca.csc.kth.se/.

  17. Cellular Potts Modeling of Tumor Growth, Tumor Invasion, and Tumor Evolution

    PubMed Central

    Szabó, András; Merks, Roeland M. H.

    2013-01-01

    Despite a growing wealth of available molecular data, the growth of tumors, invasion of tumors into healthy tissue, and response of tumors to therapies are still poorly understood. Although genetic mutations are in general the first step in the development of a cancer, for the mutated cell to persist in a tissue, it must compete against the other, healthy or diseased cells, for example by becoming more motile, adhesive, or multiplying faster. Thus, the cellular phenotype determines the success of a cancer cell in competition with its neighbors, irrespective of the genetic mutations or physiological alterations that gave rise to the altered phenotype. What phenotypes can make a cell “successful” in an environment of healthy and cancerous cells, and how? A widely used tool for getting more insight into that question is cell-based modeling. Cell-based models constitute a class of computational, agent-based models that mimic biophysical and molecular interactions between cells. One of the most widely used cell-based modeling formalisms is the cellular Potts model (CPM), a lattice-based, multi particle cell-based modeling approach. The CPM has become a popular and accessible method for modeling mechanisms of multicellular processes including cell sorting, gastrulation, or angiogenesis. The CPM accounts for biophysical cellular properties, including cell proliferation, cell motility, and cell adhesion, which play a key role in cancer. Multiscale models are constructed by extending the agents with intracellular processes including metabolism, growth, and signaling. Here we review the use of the CPM for modeling tumor growth, tumor invasion, and tumor progression. We argue that the accessibility and flexibility of the CPM, and its accurate, yet coarse-grained and computationally efficient representation of cell and tissue biophysics, make the CPM the method of choice for modeling cellular processes in tumor development. PMID:23596570

  18. Competitive heterogeneous nucleation onto a microscopic impurity in a Potts model

    NASA Astrophysics Data System (ADS)

    Asuquo, Cletus C.; McArthur, Danielle; Bowles, Richard K.

    2016-08-01

    Many metastable systems can nucleate to multiple competing stable or intermediate metastable states. In this work, a Potts model, subject to external fields, is used to study the competitive nucleation of two phases attempting to grow on a microscopic impurity. Monte Carlo simulations are used to calculate the free energy surfaces for the system under different conditions, where the relative stability of the phases is adjusted by changing the interaction parameters, and the nucleation rates obtained using multicomponent transition state theory (TST) are compared with the rates measured using the survival probability method. We find that the two methods predict similar nucleation rates when the free energy barrier used in the transition state theory is defined as the work required to form a critical embryo from the metastable phase. An analysis of the free energy surfaces also reveals that the competition between the nucleating phases leads to an effective drying of the impurity which slows down the nucleation rate compared to the single phase case.

  19. Implications of lack-of-ergodicity in 2D Potts model

    NASA Astrophysics Data System (ADS)

    Ota, Smita

    2015-03-01

    Microcanonical Monte Carlo simulation is used to study two dimensional (2D) q state Potts model. We consider a 2D square lattice having NxN spins with periodic boundary condition and simulated the system with N =15 and q =10. The demon energy distribution is found to be exponential for high system energy and large system size. For smaller system size and above the first order transition the demon energy distribution is found to deviate from exp(- βED) and has the form exp(- βED + γ ED2). Here β = 1/kBT and kB is the Boltzmann constant. It is found that γ is finite at higher temperatures. As the system energy is reduced γ becomes zero near the first order transition. It is found that during cooling γ changes sign from negative to positive and then to negative again near the 1st order transition. Therefore the demon energy distribution becomes exp(- βED) (or ergodic) at two values of system energy near the 1st order transition. Further cooling or at still lower temperatures the system shows lack of ergodicity. However, difference in heating cooling curves are apparent in E vs γ. The system energies for which γ is zero during cooling can represent the 'ergodic' states. This can be related to the two-level systems observed in glasses at low temperatures.

  20. Potts model partition functions for self-dual families of strip graphs

    NASA Astrophysics Data System (ADS)

    Chang, Shu-Chiuan; Shrock, Robert

    2001-12-01

    We consider the q-state Potts model on families of self-dual strip graphs GD of the square lattice of width Ly and arbitrarily great length Lx, with periodic longitudinal boundary conditions. The general partition function Z and the T=0 antiferromagnetic special case P (chromatic polynomial) have the respective forms ∑ j=1 NF, Ly, λcF, Ly, j( λF, Ly, j) Lx, with F= Z, P. For arbitrary Ly, we determine (i) the general coefficient cF, Ly, j in terms of Chebyshev polynomials, (ii) the number nF( Ly, d) of terms with each type of coefficient, and (iii) the total number of terms NF, Ly, λ. We point out interesting connections between the nZ( Ly, d) and Temperley-Lieb algebras, and between the NF, Ly, λ and enumerations of directed lattice animals. Exact calculations of P are presented for 2⩽ Ly⩽4. In the limit of infinite length, we calculate the ground state degeneracy per site (exponent of the ground state entropy), W( q). Generalizing q from Z+ to C, we determine the continuous locus B in the complex q plane where W( q) is singular. We find the interesting result that for all Ly values considered, the maximal point at which B crosses the real q-axis, denoted qc, is the same, and is equal to the value for the infinite square lattice, qc=3. This is the first family of strip graphs of which we are aware that exhibits this type of universality of qc.

  1. Exact valence bond entanglement entropy and probability distribution in the XXX spin chain and the potts model.

    PubMed

    Jacobsen, J L; Saleur, H

    2008-02-29

    We determine exactly the probability distribution of the number N_(c) of valence bonds connecting a subsystem of length L>1 to the rest of the system in the ground state of the XXX antiferromagnetic spin chain. This provides, in particular, the asymptotic behavior of the valence-bond entanglement entropy S_(VB)=N_(c)ln2=4ln2/pi(2)lnL disproving a recent conjecture that this should be related with the von Neumann entropy, and thus equal to 1/3lnL. Our results generalize to the Q-state Potts model. PMID:18352661

  2. Effect of quenched-in nonmagnetic impurities on phase transitions in a two-dimensional antiferromagnetic three-vertex Potts model on a triangular lattice

    NASA Astrophysics Data System (ADS)

    Murtazaev, A. K.; Babaev, A. B.; Ataeva, G. Ya.

    2015-07-01

    The effect of quenched-in nonmagnetic impurities on phase transitions in a two-dimensional diluted antiferromagnetic three-vertex Potts model on a triangular lattice has been investigated using the Monte Carlo method. The systems with linear dimensions L × L = N and L = 9-144 have been considered. It has been shown using the fourth-order Binder cumulant method that the introduction of a quenched-in disorder into a spin system described by the two-dimensional antiferromagnetic Potts model leads to a change from the first-order phase transition to the second-order phase transition.

  3. Phase transitions in a two-dimensional antiferromagnetic Potts model on a triangular lattice with next-nearest neighbor interactions

    NASA Astrophysics Data System (ADS)

    Babaev, A. B.; Magomedov, M. A.; Murtazaev, A. K.; Kassan-Ogly, F. A.; Proshkin, A. I.

    2016-02-01

    Phase transitions (PTs) and frustrations in two-dimensional structures described by a three-vertex antiferromagnetic Potts model on a triangular lattice are investigated by the Monte Carlo method with regard to nearest and next-nearest neighbors with interaction constants J 1 and J 2, respectively. PTs in these models are analyzed for the ratio r = J 2/ J 1 of next-nearest to nearest exchange interaction constants in the interval | r| = 0-1.0. On the basis of the analysis of the low-temperature entropy, the density of states function of the system, and the fourth-order Binder cumulants, it is shown that a Potts model with interaction constants J 1 < 0 and J 2 < 0 exhibits a first-order PT in the range of 0 ⩽ r < 0.2, whereas, in the interval 0.2 ⩽ r ⩽ 1.0, frustrations arise in the system. At the same time, for J 1 > 0 and J 2 < 0, frustrations arise in the range 0.5 < | r| < 1.0, while, in the interval 0 ⩽ | r| ⩽ 1/3, the model exhibits a second-order PT.

  4. Large pseudocounts and L2-norm penalties are necessary for the mean-field inference of Ising and Potts models

    NASA Astrophysics Data System (ADS)

    Barton, J. P.; Cocco, S.; De Leonardis, E.; Monasson, R.

    2014-07-01

    The mean-field (MF) approximation offers a simple, fast way to infer direct interactions between elements in a network of correlated variables, a common, computationally challenging problem with practical applications in fields ranging from physics and biology to the social sciences. However, MF methods achieve their best performance with strong regularization, well beyond Bayesian expectations, an empirical fact that is poorly understood. In this work, we study the influence of pseudocount and L2-norm regularization schemes on the quality of inferred Ising or Potts interaction networks from correlation data within the MF approximation. We argue, based on the analysis of small systems, that the optimal value of the regularization strength remains finite even if the sampling noise tends to zero, in order to correct for systematic biases introduced by the MF approximation. Our claim is corroborated by extensive numerical studies of diverse model systems and by the analytical study of the m-component spin model for large but finite m. Additionally, we find that pseudocount regularization is robust against sampling noise and often outperforms L2-norm regularization, particularly when the underlying network of interactions is strongly heterogeneous. Much better performances are generally obtained for the Ising model than for the Potts model, for which only couplings incoming onto medium-frequency symbols are reliably inferred.

  5. Quasi-Long-Range Order and Vortex Lattice in the Three-State Potts Model

    NASA Astrophysics Data System (ADS)

    Bhattacharya, Soumyadeep; Ray, Purusattam

    2016-03-01

    We show that the order-disorder phase transition in the three-state Potts ferromagnet on a square lattice is driven by a coupled proliferation of domain walls and vortices. Raising the vortex core energy above a threshold value decouples the proliferation and splits the transition into two. The phase between the two transitions exhibits an emergent U(1) symmetry and quasi-long-range order. Lowering the core energy below a threshold value also splits the order-disorder transition but the system forms a vortex lattice in the intermediate phase.

  6. Critical frontier of the Potts and percolation models on triangular-type and kagome-type lattices. II. Numerical analysis.

    PubMed

    Ding, Chengxiang; Fu, Zhe; Guo, Wenan; Wu, F Y

    2010-06-01

    In the preceding paper, one of us (F. Y. Wu) considered the Potts model and bond and site percolation on two general classes of two-dimensional lattices, the triangular-type and kagome-type lattices, and obtained closed-form expressions for the critical frontier with applications to various lattice models. For the triangular-type lattices Wu's result is exact, and for the kagome-type lattices Wu's expression is under a homogeneity assumption. The purpose of the present paper is twofold: First, an essential step in Wu's analysis is the derivation of lattice-dependent constants A,B,C for various lattice models, a process which can be tedious. We present here a derivation of these constants for subnet networks using a computer algorithm. Second, by means of a finite-size scaling analysis based on numerical transfer matrix calculations, we deduce critical properties and critical thresholds of various models and assess the accuracy of the homogeneity assumption. Specifically, we analyze the q -state Potts model and the bond percolation on the 3-12 and kagome-type subnet lattices (n×n):(n×n) , n≤4 , for which the exact solution is not known. Our numerical determination of critical properties such as conformal anomaly and magnetic correlation length verifies that the universality principle holds. To calibrate the accuracy of the finite-size procedure, we apply the same numerical analysis to models for which the exact critical frontiers are known. The comparison of numerical and exact results shows that our numerical values are correct within errors of our finite-size analysis, which correspond to 7 or 8 significant digits. This in turn infers that the homogeneity assumption determines critical frontiers with an accuracy of 5 decimal places or higher. Finally, we also obtained the exact percolation thresholds for site percolation on kagome-type subnet lattices (1×1):(n×n) for 1≤n≤6 . PMID:20866382

  7. Kauffman knot invariant from SO(N) or Sp(N) Chern-Simons theory and the Potts model

    SciTech Connect

    Astorino, Marco

    2010-06-15

    The expectation value of Wilson loop operators in three-dimensional SO(N) Chern-Simons gauge theory gives a known knot invariant: the Kauffman polynomial. Here this result is derived, at the first order, via a simple variational method. With the same procedure the skein relation for Sp(N) are also obtained. Jones polynomial arises as special cases: Sp(2), SO(-2), and SL(2,R). These results are confirmed and extended up to the second order, by means of perturbation theory, which moreover let us establish a duality relation between SO({+-}N) and Sp({+-}N) invariants. A correspondence between the first orders in perturbation theory of SO(-2), Sp(2) or SU(2) Chern-Simons quantum holonomy's traces and the partition function of the Q=4 Potts model is built.

  8. Transfer Matrices and Partition-Function Zeros for Antiferromagnetic Potts Models VI. Square Lattice with Extra-Vertex Boundary Conditions

    NASA Astrophysics Data System (ADS)

    Salas, Jesús; Sokal, Alan D.

    2011-09-01

    We study, using transfer-matrix methods, the partition-function zeros of the square-lattice q-state Potts antiferromagnet at zero temperature (= square-lattice chromatic polynomial) for the boundary conditions that are obtained from an m× n grid with free boundary conditions by adjoining one new vertex adjacent to all the sites in the leftmost column and a second new vertex adjacent to all the sites in the rightmost column. We provide numerical evidence that the partition-function zeros are becoming dense everywhere in the complex q-plane outside the limiting curve {B}_{infty}(sq) for this model with ordinary (e.g. free or cylindrical) boundary conditions. Despite this, the infinite-volume free energy is perfectly analytic in this region.

  9. On Descriptions of All Translation Invariant p-adic Gibbs Measures for the Potts Model on The Cayley Tree of Order Three

    NASA Astrophysics Data System (ADS)

    Saburov, Mansoor; Khameini Ahmad, Mohd Ali

    2015-12-01

    Unlike the real number field, a set of p-adic Gibbs measures of p-adic lattice models of statistical mechanics has a complex structure in a sense that it is strongly tied up with a Diophantine problem over p-adic fields. Recently, all translation-invariant p-adic Gibbs measures of the p-adic Potts model on the Cayley tree of order two were described by means of roots of a certain quadratic equation over some domain of the p-adic field. In this paper, we consider the same problem on the Cayley tree of order three. In this case, we show that all translation-invariant p-adic Gibbs measures of the p-adic Potts model can be described in terms of roots of some cubic equation over Zpsetminus Zp^{*}. In own its turn, we also provide a solvability criterion of a general cubic equation over Zpsetminus Zp^{*} for p > 3.

  10. Critical frontier of the Potts and percolation models on triangular-type and kagome-type lattices. II. Numerical analysis

    NASA Astrophysics Data System (ADS)

    Ding, Chengxiang; Fu, Zhe; Guo, Wenan; Wu, F. Y.

    2010-06-01

    In the preceding paper, one of us (F. Y. Wu) considered the Potts model and bond and site percolation on two general classes of two-dimensional lattices, the triangular-type and kagome-type lattices, and obtained closed-form expressions for the critical frontier with applications to various lattice models. For the triangular-type lattices Wu’s result is exact, and for the kagome-type lattices Wu’s expression is under a homogeneity assumption. The purpose of the present paper is twofold: First, an essential step in Wu’s analysis is the derivation of lattice-dependent constants A,B,C for various lattice models, a process which can be tedious. We present here a derivation of these constants for subnet networks using a computer algorithm. Second, by means of a finite-size scaling analysis based on numerical transfer matrix calculations, we deduce critical properties and critical thresholds of various models and assess the accuracy of the homogeneity assumption. Specifically, we analyze the q -state Potts model and the bond percolation on the 3-12 and kagome-type subnet lattices (n×n):(n×n) , n≤4 , for which the exact solution is not known. Our numerical determination of critical properties such as conformal anomaly and magnetic correlation length verifies that the universality principle holds. To calibrate the accuracy of the finite-size procedure, we apply the same numerical analysis to models for which the exact critical frontiers are known. The comparison of numerical and exact results shows that our numerical values are correct within errors of our finite-size analysis, which correspond to 7 or 8 significant digits. This in turn infers that the homogeneity assumption determines critical frontiers with an accuracy of 5 decimal places or higher. Finally, we also obtained the exact percolation thresholds for site percolation on kagome-type subnet lattices (1×1):(n×n) for 1≤n≤6 .

  11. Free-energy landscape and nucleation pathway of polymorphic minerals from solution in a Potts lattice-gas model.

    PubMed

    Okamoto, Atsushi; Kuwatani, Tatsu; Omori, Toshiaki; Hukushima, Koji

    2015-10-01

    Metastable minerals commonly form during reactions between water and rock. The nucleation mechanism of polymorphic phases from solution are explored here using a two-dimensional Potts model. The model system is composed of a solvent and three polymorphic solid phases. The local state and position of the solid phase are updated by Metropolis dynamics. Below the critical temperature, a large cluster of the least stable solid phase initially forms in the solution before transitioning into more-stable phases following the Ostwald step rule. The free-energy landscape as a function of the modal abundance of each solid phase clearly reveals that before cluster formation, the least stable phase has an energetic advantage because of its low interfacial energy with the solution, and after cluster formation, phase transformation occurs along the valley of the free-energy landscape, which contains several minima for the regions of three phases. Our results indicate that the solid-solid and solid-liquid interfacial energy contribute to the formation of the complex free-energy landscape and nucleation pathways following the Ostwald step rule. PMID:26565191

  12. Free-energy landscape and nucleation pathway of polymorphic minerals from solution in a Potts lattice-gas model

    NASA Astrophysics Data System (ADS)

    Okamoto, Atsushi; Kuwatani, Tatsu; Omori, Toshiaki; Hukushima, Koji

    2015-10-01

    Metastable minerals commonly form during reactions between water and rock. The nucleation mechanism of polymorphic phases from solution are explored here using a two-dimensional Potts model. The model system is composed of a solvent and three polymorphic solid phases. The local state and position of the solid phase are updated by Metropolis dynamics. Below the critical temperature, a large cluster of the least stable solid phase initially forms in the solution before transitioning into more-stable phases following the Ostwald step rule. The free-energy landscape as a function of the modal abundance of each solid phase clearly reveals that before cluster formation, the least stable phase has an energetic advantage because of its low interfacial energy with the solution, and after cluster formation, phase transformation occurs along the valley of the free-energy landscape, which contains several minima for the regions of three phases. Our results indicate that the solid-solid and solid-liquid interfacial energy contribute to the formation of the complex free-energy landscape and nucleation pathways following the Ostwald step rule.

  13. Inflection points of microcanonical entropy: Monte Carlo simulation of q state Potts model on a finite square lattice

    SciTech Connect

    Praveen, E. Satyanarayana, S. V. M.

    2014-04-24

    Traditional definition of phase transition involves an infinitely large system in thermodynamic limit. Finite systems such as biological proteins exhibit cooperative behavior similar to phase transitions. We employ recently discovered analysis of inflection points of microcanonical entropy to estimate the transition temperature of the phase transition in q state Potts model on a finite two dimensional square lattice for q=3 (second order) and q=8 (first order). The difference of energy density of states (DOS) Δ ln g(E) = ln g(E+ ΔE) −ln g(E) exhibits a point of inflexion at a value corresponding to inverse transition temperature. This feature is common to systems exhibiting both first as well as second order transitions. While the difference of DOS registers a monotonic variation around the point of inflexion for systems exhibiting second order transition, it has an S-shape with a minimum and maximum around the point of inflexion for the case of first order transition.

  14. Developing a test for random number generators using a simulation of the hierarchical Potts diamond model at the critical point

    NASA Astrophysics Data System (ADS)

    Liberty, Joshua W.

    This dissertation uses the hierarchical q-state Potts model at the critical point to develop a new random number generator test. We start with an exposition of renormalization group approach by means of which one can numerically exactly compute the free energy, specific heat and susceptibility of large, but finite lattices. We then show that generalization of these standard techniques allows one to also compute probability distributions related to the energy and the order parameter. The various computed quantities can be compared with Monte Carlo estimates of the same quantities. We demonstrate that the structure of the hierarchical lattices used allows one to perform the Monte Carlo calculations by direct sampling. This avoids the usual critical slowing down that plagues Monte Carlo calculations at the critical point. As is well known, critical behavior is highly susceptible to perturbations. We expect that flaws of the pseudo random number generator, such as correlations, will cause statistically significant discrepancies between the results of the simulations and the numerically exactly computed results. Details of the computer code generated for these tests are included.

  15. Statics and dynamics of the ten-state mean-field Potts glass model: a Monte Carlo study

    NASA Astrophysics Data System (ADS)

    Brangian, Claudio; Kob, Walter; Binder, Kurt

    2002-01-01

    We investigate by means of Monte Carlo simulations the fully connected p-state Potts model for different system sizes in order to see how the static and dynamic properties of a finite model compare with the, exactly known, behaviour of the system in the thermodynamic limit. Using p = 10 we are able to study the equilibrium dynamics for system sizes as large as N = 2560. We find that the static quantities, such as the energy, the entropy, the spin glass susceptibility as well as the distribution of the order parameter P(q) show very strong finite-size effects. From P(q) we calculate the fourth-order cumulant g4(N,T) and the Guerra parameter G(N,T) and show that these quantities cannot be used to locate the static transition temperature for the system sizes investigated. Also the spin-autocorrelation function C(t) shows strong finite-size effects in that it does not show a plateau even for temperatures around the dynamical critical temperature TD. We show that the dependence on N and T of the α-relaxation time can be understood by means of a dynamical finite-size scaling ansatz. C(t) does not obey the time-temperature superposition principle for temperatures around TD, but does so for significantly lower T. Finally we study the relaxation dynamics of the individual spins and show that their dependence on time depends strongly on the chosen spin, i.e. that the system is dynamically very heterogeneous, which explains the non-exponentiality of C(t).

  16. A cellular Potts model for the MMP-dependent and -independent cancer cell migration in matrix microtracks of different dimensions

    NASA Astrophysics Data System (ADS)

    Scianna, Marco; Preziosi, Luigi

    2014-03-01

    Cell migration is fundamental in a wide variety of physiological and pathological phenomena, among other in cancer invasion and development. In particular, the migratory/invasive capability of single metastatic cells is fundamental in determining the malignancy of a solid tumor. Specific cell migration phenotypes result for instance from the reciprocal interplay between the biophysical and biochemical properties of both the malignant cells themselves and of the surrounding environment. In particular, the extracellular matrices (ECMs) forming connective tissues can provide both loosely organized zones and densely packed barriers, which may impact cell invasion mode and efficiency. The critical processes involved in cell movement within confined spaces are (i) the proteolytic activity of matrix metalloproteinases (MMPs) and (ii) the deformation of the entire cell body, and in particular of the nucleus. We here present an extended cellular Potts model (CPM) to simulate a bio-engineered matrix system, which tests the active motile behavior of a single cancer cell into narrow channels of different widths. As distinct features of our approach, the cell is modeled as a compartmentalized discrete element, differentiated in the nucleus and in the cytosolic region, while a directional shape-dependent movement is explicitly driven by the evolution of its polarity vector. As outcomes, we find that, in a large track, the tumor cell is not able to maintain a directional movement. On the contrary, a structure of subcellular width behaves as a contact guidance sustaining cell persistent locomotion. In particular, a MMP-deprived cell is able to repolarize and follow the micropattern geometry, while a full MMP activity leads to a secondary track expansion by degrading the matrix structure. Finally, we confirm that cell movement within a subnuclear structure can be achieved either by pericellular proteolysis or by a significant deformation of cell nucleus.

  17. Percivall Pott: tuberculous spondylitis.

    PubMed

    Sternbach, G

    1996-01-01

    Tuberculous spondylitis, also known as Pott's disease, is an entity that produces a characteristic kyphotic deformity, and was described by Sir Percivall Pott in 1779 and 1782. The majority of his patients were infants and young children. Although the incidence of tuberculosis in the industrialized world has since declined dramatically, the number of cases of extrapulmonary disease, though small, has remained relatively unchanged. In developing countries, spondylitis is still generally a disease of children, but in Europe and North America, it more commonly involves older adults. Pott's spondylitis represents a reactivation of latent disease, frequently years after the initial infection. Clinical findings include complaints of back pain and symptoms of fever, chills, weight loss, malaise, and fatigue. Characteristically a late finding, paraplegia is occasionally the initial indicator of spinal involvement. There is an average delay of a year between the onset of symptoms and patient presentation. Plain spinal radiographs usually are the initial diagnostic modality utilized. Computed tomography scanning and magnetic resonance imaging can be used to further define the process. The differential diagnosis includes neoplasm, pyogenic or disseminated fungal infection, and sarcoid arthritis. PMID:8655942

  18. Critical points of Potts and O(N) models from eigenvalue identities in periodic Temperley-Lieb algebras

    NASA Astrophysics Data System (ADS)

    Lykke Jacobsen, Jesper

    2015-11-01

    In previous work with Scullard, we have defined a graph polynomial P B (q, T) that gives access to the critical temperature T c of the q-state Potts model defined on a general two-dimensional lattice {L}. It depends on a basis B, containing n × m unit cells of {L}, and the relevant root T c(n, m) of P B (q, T) was observed to converge quickly to T c in the limit n,m\\to ∞ . Moreover, in exactly solvable cases there is no finite-size dependence at all. In this paper we show how to reformulate this method as an eigenvalue problem within the periodic Temperley-Lieb (TL) algebra. This corresponds to taking m\\to ∞ first, so that the bases B are semi-infinite cylinders of circumference n. The limit implies faster convergence in n, while maintaining the n-independence in exactly solvable cases. In this setup, T c(n) is determined by equating the largest eigenvalues of two topologically distinct sectors of the transfer matrix. Crucially, these two sectors determine the same critical exponent in the continuum limit, and the observed fast convergence is thus corroborated by results of conformal field theory. We obtain similar results for the dense and dilute phases of the O(N) loop model, using now a transfer matrix within the dilute periodic TL algebra. Compared with our previous study, the eigenvalue formulation allows us to double the size n for which T c(n) can be obtained, using the same computational effort. We study in details three significant cases: (i) bond percolation on the kagome lattice, up to n max = 14; (ii) site percolation on the square lattice, to n max = 21; and (iii) self-avoiding polygons on the square lattice, to n max = 19. Convergence properties of T c(n) and extrapolation schemes are studied in details for the first two cases. This leads to rather accurate values for the percolation thresholds: p c = 0.524 404 999 167 439(4) for bond percolation on the kagome lattice, and p c = 0.592 746 050 792 10(2) for site percolation on the square lattice.

  19. Nature of ordering in Potts spin glasses

    NASA Astrophysics Data System (ADS)

    Banavar, Jayanth R.; Cieplak, Marek

    1989-09-01

    The zero-temperature scaling approach is applied to the three-state Potts spin glass. Our results suggest that the +/-J model has a lower critical dimensionality greater than 3, whereas for the Gaussian model this dimensionality is slightly less than 3. The T=0 scaling exponents are estimated in D=2 and 3. The results are based mostly on exact transfer-matrix calculations and on a Monte Carlo quenching procedure.

  20. Transfer Matrices and Partition-Function Zeros for Antiferromagnetic Potts Models. III. Triangular-Lattice Chromatic Polynomial

    NASA Astrophysics Data System (ADS)

    Jacobsen, Jesper Lykke; Salas, Jesús; Sokal, Alan D.

    2003-09-01

    We study the chromatic polynomial P G ( q) for m× n triangular-lattice strips of widths m≤12P,9F (with periodic or free transverse boundary conditions, respectively) and arbitrary lengths n (with free longitudinal boundary conditions). The chromatic polynomial gives the zero-temperature limit of the partition function for the q-state Potts antiferromagnet. We compute the transfer matrix for such strips in the Fortuin-Kasteleyn representation and obtain the corresponding accumulation sets of chromatic zeros in the complex q-plane in the limit n→∞. We recompute the limiting curve obtained by Baxter in the thermodynamic limit m, n→∞ and find new interesting features with possible physical consequences. Finally, we analyze the isolated limiting points and their relation with the Beraha numbers.

  1. CUDA programs for the GPU computing of the Swendsen-Wang multi-cluster spin flip algorithm: 2D and 3D Ising, Potts, and XY models

    NASA Astrophysics Data System (ADS)

    Komura, Yukihiro; Okabe, Yutaka

    2014-03-01

    We present sample CUDA programs for the GPU computing of the Swendsen-Wang multi-cluster spin flip algorithm. We deal with the classical spin models; the Ising model, the q-state Potts model, and the classical XY model. As for the lattice, both the 2D (square) lattice and the 3D (simple cubic) lattice are treated. We already reported the idea of the GPU implementation for 2D models (Komura and Okabe, 2012). We here explain the details of sample programs, and discuss the performance of the present GPU implementation for the 3D Ising and XY models. We also show the calculated results of the moment ratio for these models, and discuss phase transitions. Catalogue identifier: AERM_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AERM_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 5632 No. of bytes in distributed program, including test data, etc.: 14688 Distribution format: tar.gz Programming language: C, CUDA. Computer: System with an NVIDIA CUDA enabled GPU. Operating system: System with an NVIDIA CUDA enabled GPU. Classification: 23. External routines: NVIDIA CUDA Toolkit 3.0 or newer Nature of problem: Monte Carlo simulation of classical spin systems. Ising, q-state Potts model, and the classical XY model are treated for both two-dimensional and three-dimensional lattices. Solution method: GPU-based Swendsen-Wang multi-cluster spin flip Monte Carlo method. The CUDA implementation for the cluster-labeling is based on the work by Hawick et al. [1] and that by Kalentev et al. [2]. Restrictions: The system size is limited depending on the memory of a GPU. Running time: For the parameters used in the sample programs, it takes about a minute for each program. Of course, it depends on the system size, the number of Monte Carlo steps, etc. References: [1] K

  2. FAST TRACK COMMUNICATION: Ground-state fidelity and entanglement entropy for the quantum three-state Potts model in one spatial dimension

    NASA Astrophysics Data System (ADS)

    Dai, Yan-Wei; Hu, Bing-Quan; Zhao, Jian-Hui; Zhou, Huan-Qiang

    2010-09-01

    The ground-state fidelity per lattice site is computed for the quantum three-state Potts model in a transverse magnetic field on an infinite-size lattice in one spatial dimension in terms of the infinite matrix product state algorithm. It is found that, on the one hand, a pinch point is identified on the fidelity surface around the critical point, and on the other hand, the ground-state fidelity per lattice site exhibits bifurcations at pseudo critical points for different values of the truncation dimension, which in turn approach the critical point as the truncation dimension becomes large. This implies that the ground-state fidelity per lattice site enables us to capture spontaneous symmetry breaking when the control parameter crosses the critical value. In addition, a finite-entanglement scaling of the von Neumann entropy is performed with respect to the truncation dimension, resulting in a precise determination of the central charge at the critical point. Finally, we compute the transverse magnetization, from which the critical exponent β is extracted from the numerical data.

  3. Radiological evaluation of Pott puffy tumor

    SciTech Connect

    Wells, R.G.; Sty, J.R.; Landers, A.D.

    1986-03-14

    The Pott puffy tumor represents frontal osteomyelitis with subperiosteal (pericranial) abscess, secondary to frontal sinusitis. Pott puffy tumor is one of several potential complications of infection of a frontal sinus. Computed tomography (CT) and radionuclide bone imaging have proved to be invaluable tools in the diagnosis of frontal sinusitis, osteomyelitis, and intracranial infection. This article details the radionuclide bone imaging and findings on CT in three children with Pott puffy tumor, as well as the clinical features and pathophysicological mechanisms.

  4. The Effects of Cell Compressibility, Motility and Contact Inhibition on the Growth of Tumor Cell Clusters using the Cellular Potts Model

    PubMed Central

    Li, Jonathan F.; Lowengrub, John

    2014-01-01

    There are numerous biological examples where genes associated with migratory ability of cells also confer the cells with an increased fitness even though these genes may not have any known effect on the cell mitosis rates. Here, we provide insight into these observations by analyzing the effects of cell migration, compression, and contact inhibition on the growth of tumor cell clusters using the Cellular Potts Model (CPM) in a monolayer geometry. This is a follow-up of a previous study (Thalhauser et al., Biol. Direct, 2010, 5:21) in which a Moran-type model was used to study the interaction of cell proliferation, migratory potential and death on the emergence of invasive phenotypes. Here, we extend the study to include the effects of cell size and shape. In particular, we investigate the interplay between cell motility and compressibility within the CPM and find that the CPM predicts that increased cell motility leads to smaller cells. This is an artifact in the CPM. An analysis of the CPM reveals an explicit inverse-relationship between the cell stiffness and motility parameters. We use this relationship to compensate for motility-induced changes in cell size in the CPM so that in the corrected CPM, cell size is independent of the cell motility. We find that subject to comparable levels of compression, clusters of motile cells grow faster than clusters of less motile cells, in qualitative agreement with biological observations and our previous study. Increasing compression tends to reduce growth rates. Contact inhibition penalizes clumped cells by halting their growth and gives motile cells an even greater advantage. Finally, our model predicts cell size distributions that are consistent with those observed in clusters of neuroblastoma cells cultured in low and high density conditions. PMID:24211749

  5. Dynamic metastability in the two-dimensional Potts ferromagnet

    NASA Astrophysics Data System (ADS)

    Ibáñez Berganza, Miguel; Petri, Alberto; Coletti, Pietro

    2014-05-01

    We investigate the nonequilibrium dynamics of the two-dimensional (2D) Potts model on the square lattice after a quench below the discontinuous transition point. By means of numerical simulations of systems with q =12, 24, and 48, we observe the onset of a stationary regime below the temperature-driven transition, in a temperature interval decreasing with the system size and increasing with q. These results obtained dynamically agree with those obtained from the analytical continuation of the free energy [J. L. Meunier and A. Morel, Eur. Phys. J. B 13, 341 (2000), 10.1007/s100510050040], from which metastability in the 2D Potts model results to be a finite-size effect.

  6. Potts glass reflection of the decoding threshold for qudit quantum error correcting codes

    NASA Astrophysics Data System (ADS)

    Jiang, Yi; Kovalev, Alexey A.; Pryadko, Leonid P.

    We map the maximum likelihood decoding threshold for qudit quantum error correcting codes to the multicritical point in generalized Potts gauge glass models, extending the map constructed previously for qubit codes. An n-qudit quantum LDPC code, where a qudit can be involved in up to m stabilizer generators, corresponds to a ℤd Potts model with n interaction terms which can couple up to m spins each. We analyze general properties of the phase diagram of the constructed model, give several bounds on the location of the transitions, bounds on the energy density of extended defects (non-local analogs of domain walls), and discuss the correlation functions which can be used to distinguish different phases in the original and the dual models. This research was supported in part by the Grants: NSF PHY-1415600 (AAK), NSF PHY-1416578 (LPP), and ARO W911NF-14-1-0272 (LPP).

  7. Local Autoencoding for Parameter Estimation in a Hidden Potts-Markov Random Field.

    PubMed

    Song, Sanming; Si, Bailu; Herrmann, J Michael; Feng, Xisheng

    2016-05-01

    A local-autoencoding (LAE) method is proposed for the parameter estimation in a Hidden Potts-Markov random field model. Due to sampling cost, Markov chain Monte Carlo methods are rarely used in real-time applications. Like other heuristic methods, LAE is based on a conditional independence assumption. It adapts, however, the parameters in a block-by-block style with a simple Hebbian learning rule. Experiments with given label fields show that the LAE is able to converge in far less time than required for a scan. It is also possible to derive an estimate for LAE based on a Cramer–Rao bound that is similar to the classical maximum pseudolikelihood method. As a general algorithm, LAE can be used to estimate the parameters in anisotropic label fields. Furthermore, LAE is not limited to the classical Potts model and can be applied to other types of Potts models by simple label field transformations and straightforward learning rule extensions. Experimental results on image segmentations demonstrate the efficiency and generality of the LAE algorithm. PMID:27019491

  8. Chemical Equilibrium Models for the S3 State of the Oxygen-Evolving Complex of Photosystem II.

    PubMed

    Isobe, Hiroshi; Shoji, Mitsuo; Shen, Jian-Ren; Yamaguchi, Kizashi

    2016-01-19

    We have performed hybrid density functional theory (DFT) calculations to investigate how chemical equilibria can be described in the S3 state of the oxygen-evolving complex in photosystem II. For a chosen 340-atom model, 1 stable and 11 metastable intermediates have been identified within the range of 13 kcal mol(-1) that differ in protonation, charge, spin, and conformational states. The results imply that reversible interconversion of these intermediates gives rise to dynamic equilibria that involve processes with relocations of protons and electrons residing in the Mn4CaO5 cluster, as well as bound water ligands, with concomitant large changes in the cluster geometry. Such proton tautomerism and redox isomerism are responsible for reversible activation/deactivation processes of substrate oxygen species, through which Mn-O and O-O bonds are transiently ruptured and formed. These results may allow for a tentative interpretation of kinetic data on substrate water exchange on the order of seconds at room temperature, as measured by time-resolved mass spectrometry. The reliability of the hybrid DFT method for the multielectron redox reaction in such an intricate system is also addressed. PMID:26717045

  9. The Pott's puffy tumor: a dangerous sign for intracranial complications.

    PubMed

    Ketenci, Ibrahim; Unlü, Yaşar; Tucer, Bülent; Vural, Alperen

    2011-12-01

    The Pott's puffy tumor is a subperiosteal abscess of the frontal bone associated with osteomyelitis. The purpose of this article is to alert the physician to the severe complications of this entity. The records of six patients were reviewed retrospectively. There were four adults and two adolescents. Nasal endoscopy showed edematous, polypoid mucosa in middle meatus in three and nasal polyps in the rest. At initial admission, two had orbital subperiosteal abscess, but normal cranial CT findings. During hospitalization, three experienced frontal lobe abscess and one frontal cerebritis. Endoscopic sinus surgery was performed in all with external drainage of Pott's puffy tumor in addition to antibiotherapy. Three patients underwent craniotomy/craniectomy for removal of frontal lobe abscesses. One patient with frontal lobe abscess died. Pott's puffy tumor may result in potentially dangerous intracranial complications. Early diagnosis and treatment are essential to reduce morbidity and mortality. PMID:21660452

  10. Effects of Referral Bias on Estimates of Anal Intraepithelial Neoplasia Progression and Regression Rates in a 3-State Markov Model.

    PubMed

    Mathews, William Christopher; Cachay, Edward Rafael; Agmas, Wollelaw; Jackson, Christopher

    2015-09-01

    The study aim is to compare anal intraepithelial neoplasia (AIN) progression and regression rates in a cytology inception cohort to estimates based on the subcohort referred for ≥1 high-resolution anoscopies (HRAs).A cytology-based retrospective cohort was assembled including the anal cytology histories and invasive anal cancer (IAC) outcomes of all HIV-infected adults under care between 2001 and 2012. A 3-state Markov model (400, and to have HSIL at baseline and thereafter. They also had more anal cytology examinations (median 6 vs 3) and longer follow-up (median 5.5 vs 3.6 years). State transition rates were overestimated in the HRA subcohort relative to inception cohort, but the degree of discordance varied by transition: for

  11. Effects of Referral Bias on Estimates of Anal Intraepithelial Neoplasia Progression and Regression Rates in a 3-State Markov Model

    PubMed Central

    Mathews, William Christopher; Cachay, Edward Rafael; Agmas, Wollelaw; Jackson, Christopher

    2015-01-01

    Abstract The study aim is to compare anal intraepithelial neoplasia (AIN) progression and regression rates in a cytology inception cohort to estimates based on the subcohort referred for ≥1 high-resolution anoscopies (HRAs). A cytology-based retrospective cohort was assembled including the anal cytology histories and invasive anal cancer (IAC) outcomes of all HIV-infected adults under care between 2001 and 2012. A 3-state Markov model (400, and to have HSIL at baseline and thereafter. They also had more anal cytology examinations (median 6 vs 3) and longer follow-up (median 5.5 vs 3.6 years). State transition rates were overestimated in the HRA subcohort relative to inception cohort, but the degree of discordance varied by transition: for

  12. Potts ferromagnet: Transformations and critical exponents in planar hierarchical lattices

    NASA Astrophysics Data System (ADS)

    Hauser, Paulo R.; Curado, Evaldo M. F.

    1988-07-01

    We prove that the duality transformation for a Potts ferromagnet on two-rooted planar hierarchical lattices (HL) preserves the thermal eigenvalue. This leads to a relation between the correlation length critical exponents υ of a HL and its corresponding dual lattice. Using hyperscaling, we show that their specific heat critical exponents α coincide. For a smaller class of HL—namely of diamond and tress types—we prove that another transformation also preserves υ and α.

  13. Pott puffy tumor in a 4-year-old boy presenting in status epilepticus.

    PubMed

    Strony, Robert J; Dula, David

    2007-11-01

    Pott puffy tumor is an osteomyelitis of the frontal bone with the development of a subperiosteal abscess manifesting as a puffy swelling of the forehead or scalp. It is believed to occur as a complication of frontal sinusitis. The modern antibiotic era has made it a rarely encountered entity. This case describes a 4-year-old boy who presented in status epilepticus secondary to Pott puffy tumor. PMID:18007214

  14. The Pott's puffy tumor: an unusual complication of frontal sinusitis, methods for its detection.

    PubMed

    Sabatiello, M; Vanhooteghem, O; Mostinckx, S; De La Brassinne, M

    2010-01-01

    This is a case report of a Pott's puffy tumor, characterized by a subperiosteal abscess associated with frontal bone osteomyelitis, as a consequence of a frontal sinusitis, in a 15-year-old boy. Pott's puffy tumor is a rare condition usually seen as a complication of frontal sinusitis and more commonly described in children. Given that, superficial temporal artery pseudoaneurysms might be interpreted as a cyst or lipoma, it is imperative that physicians be aware of their presentation. PMID:20653869

  15. Pott's puffy tumour: the usefulness of MRI in complicated sinusitis

    PubMed Central

    Bhalla, Vishal; Khan, Nadir; Isles, Matthew

    2016-01-01

    The sinuses are common sites of infection in children, and if clinical presentation is delayed, there is a high risk of complications including intracranial spread. We present a case of a 5-year-old boy who presented with non-specific symptoms of sinusitis. He went on to develop osteomyelitis of the frontal bone and a subperiosteal abscess known as Pott's puffy tumour. Whilst computed tomography provides an excellent initial imaging, this case report emphasizes the advantages of magnetic resonance imaging, especially when there is extensive involvement of the sinuses with an absence of ionizing radiation. Prompt surgical treatment is imperative as there is a potential for significant morbidity if not quickly diagnosed and treated. PMID:27001196

  16. Miliary tuberculosis disease complicated by Pott's abscess in an infant: Seven year follow-up

    PubMed Central

    Bayhan, Gulsum Iclal; Tanir, Gonul; Gayretli Aydın, Zeynep Gokce; Yildiz, Yasemin Tasci

    2015-01-01

    A 20-month-old boy presented with 1-year history of persistent fever, cough, and progressive abdominal distention. Abdominal ultrasonography showed hepatomegaly and multiple calcifications in the liver and spleen. Thoracic computed tomography showed multiple mediastinal lymph nodes and consolidation in both lungs. Additionally, there was a 2-cm thick retroperitoneal soft tissue mass destroying the T7-8 and L1-L2 vertebral bodies. The patient was preliminarily diagnosed with miliary tuberculosis (TB) and Pott's disease, and began administering anti-TB treatment consisting of isoniazid, rifampin, ethambutol, and pyrazinamide. Acid-resistant bacilli analysis and mycobacterial culture of the biopsy specimen of Pott's abscess were positive. Mycobacterial culture and PCR of gastric aspirate were also positive. The patient's condition progressively improved with anti-TB treatment and he received 12 months of antiTB therapy. At the end of the treatment all of the patient's symptoms were relieved and he was well except for kyphosis. Miliary TB complicated by Pott's abscess is a very rare presentation of childhood TB. The presented case shows that when Pott's abscess is diagnosed and surgically corrected without delay, patients can recover without squeal. PMID:25983412

  17. A Monte Carlo Potts Investigation of Microstructural Evolution: Particle Assisted Abnormal Grain Growth

    NASA Astrophysics Data System (ADS)

    Guebels, Corentin Alain Pierre Nicolas

    The microstructural changes that occur in metals and alloys due to deformation and heat treatment are often characterized according to the macroscale deformation process (i.e. cold or hot working). The general problem of this type of characterization is that it only distinguishes the general microstructural trends. For many decades, these microstructural phenomena have been described empirically or with limited experimental verification. This shortcoming is apparent for recrystallization and abnormal grain growth processes. Understanding and characterizing the thermal and mechanical processes that compete to control grain boundary kinetics and the subsequent microstructural evolution is critical. These include but are not limited to: the input and recovery of deformation energy, the influence of deformation energy on grain boundary migration, the mechanisms controlling the nucleation of new grains, and the effect of second-phase particles. The present work introduces a new temporal scaling method and investigates the conditions in which some grain boundaries may become unpinned in an otherwise stable, pinned microstructure and extends work done by E. Holm. The temporal scaling method contributes to resolving some of the limitations of Monte Carlo Potts (MCP) simulations in the investigation of the conditions and mechanisms that distinguish recrystallization from dynamic abnormal grain growth (DAGG). Grain boundary unpinning is then investigated for the case of an idealized spherical grain and for a polycrystalline microstructure. The mechanisms of grain boundary pinning and grain growth inhibition by second-phase particles are well known. The influence of simulation temperature on grain boundary unpinning is investigated numerically using a 3D Monte Carlo Potts approach. MCP based models are commonly implemented to simulate microstructural evolution. However, the numerical implementations of recrystallization and other deformation-induced phenomena often elude

  18. Une localisation exceptionnelle de la tuberculose vertébrale Mal de Pott sous-occipital

    PubMed Central

    Yahyaoui, Sana; Majdoub, Senda; Zaghouani, Houneida; Fradj, Hosni Ben; Bakir, Dejla; Bouajina, Elyes; Kraiem, Chakib

    2013-01-01

    Le mal de Pott est la forme la plus commune de la tuberculose osseuse touchant essentiellement le rachis dorso-lombaire. La localisation sous-occipitale reste exceptionnelle. Le diagnostic de cette entité est le plus souvent tardif ce qui expose à des complications graves. Les radiographies standard ne sont parlantes qu’à un stade tardif de la maladie, d'où l'intérêt de l'imagerie moderne notamment la tomodensitométrie (TDM) et l'imagerie par résonance magnétique (IRM) qui permettent un diagnostic précoce. Nous rapportons un nouveau cas de tuberculose sous-occipitale. Le diagnostic était posé sur l'imagerie en coupe et confirmé histologiquement à la biopsie transorale. Sont rappelés les aspects en imagerie de cette localisation particulière du mal de Pott. PMID:23819005

  19. Two-dimensional Potts antiferromagnets with a phase transition at arbitrarily large q

    NASA Astrophysics Data System (ADS)

    Huang, Yuan; Chen, Kun; Deng, Youjin; Jacobsen, Jesper Lykke; Kotecký, Roman; Salas, Jesús; Sokal, Alan D.; Swart, Jan M.

    2013-01-01

    We exhibit infinite families of two-dimensional lattices (some of which are triangulations or quadrangulations of the plane) on which the q-state Potts antiferromagnet has a finite-temperature phase transition at arbitrarily large values of q. This unexpected result is proven rigorously by using a Peierls argument to measure the entropic advantage of sublattice long-range order. Additional numerical data are obtained using transfer matrices, Monte Carlo simulation, and a high-precision graph-theoretic method.

  20. q-state Potts-glass neural network based on pseudoinverse rule

    SciTech Connect

    Xiong Daxing; Zhao Hong

    2010-08-15

    We study the q-state Potts-glass neural network with the pseudoinverse (PI) rule. Its performance is investigated and compared with that of the counterpart network with the Hebbian rule instead. We find that there exists a critical point of q, i.e., q{sub cr}=14, below which the storage capacity and the retrieval quality can be greatly improved by introducing the PI rule. We show that the dynamics of the neural networks constructed with the two learning rules respectively are quite different; but however, regardless of the learning rules, in the q-state Potts-glass neural networks with q{>=}3 there is a common novel dynamical phase in which the spurious memories are completely suppressed. This property has never been noticed in the symmetric feedback neural networks. Free from the spurious memories implies that the multistate Potts-glass neural networks would not be trapped in the metastable states, which is a favorable property for their applications.

  1. Bilateral Psoas Abscess and Extensive Soft Tissue Involvement Due to Late Presentation of Pott's Disease of the Spine.

    PubMed

    Elnaim, Abdel Latif K

    2011-04-01

    Pott's disease of the spine with psoas abscess is currently rare form of Extra- pulmonary tuberculosis (TB) in the developed countries, however it is still seen in areas where TB is endemic. We describe a rare case if not the first (according to our knowledge) of bilateral ruptured psoas abscess with extensive tissue necrosis and pelvic organs exposure with limited neurological deficit presented late in young girl. In this case Pott's disease was associated with extensive tissue necrosis exposing pubic bones, urinary bladder and psoas muscle. PMID:22468071

  2. Pott's puffy tumour in a 5-year old boy: the role of ultrasound and contrast-enhanced CT imaging; surgical case report.

    PubMed

    Vanderveken, O M; De Smet, K; Dogan-Duyar, S; Desimpelaere, J; Duval, E L I M; De Praeter, M; Van Rompaey, D

    2012-01-01

    We report a case of Pott's puffy tumour, a subperiosteal abscess of the frontal bone associated with an underlying frontal osteomyelitis, in a 5-year-old boy. Ultrasonography played a crucial role in the diagnosis of our patient, suggesting the presence of a Pott's puffy tumour with epidural abscess by showing a subperiosteal abscess associated with erosion of the frontal bone. Subsequently, the diagnosis of Pott's puffy tumour with epidural abscess was confirmed by contrast-enhanced CT scanning. Prompt neurosurgical intervention with drainage of abscesses and debridement of bone sequestrate, together with prolonged antibiotic therapy, significantly contributes to a favorable outcome. PMID:22896932

  3. [Anterior instrumentation of spine in tuberculous spondylitis: Pott's disease: case report].

    PubMed

    Farage, Luciano; Martins, Johnny Wesley Gonçalves; Farage Filho, Miguel

    2002-03-01

    We report a case of a surgical treatment with anterior instrumentation in tuberculous spondylitis (Pott's disease), in a 71 years old woman, that was in treatment for pulmonary tuberculosis, with lumbar pain, progressive disability to walk, kyphotic deformity and vesical dysfunction. Magnetic resonance image presents a lesion in the bodies of T12 and L1, with paravertebral abscess. The patient was treated surgically by transthoracic-abdominal approach. The vertebral bodies were cut off and the spine were instrumented anteriorly with a mesh cage and a Z plate. This procedure permits a good arthrodesis and a immediately stabilization of the spine, without any complication of the infection. The patient was seen a year after the surgery and is free of infection, without motor deficit, pain or reminiscent kyphosis. PMID:11965425

  4. 38 CFR 13.3 - State legislation.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 1 2010-07-01 2010-07-01 false State legislation. 13.3... ADMINISTRATION, FIDUCIARY ACTIVITIES § 13.3 State legislation. Field facility Directors are authorized to... regarding any proposed legislation relating to fiduciary matters will be taken without the approval of...

  5. 46 CFR 309.3 - Stated valuation.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 46 Shipping 8 2013-10-01 2013-10-01 false Stated valuation. 309.3 Section 309.3 Shipping MARITIME ADMINISTRATION, DEPARTMENT OF TRANSPORTATION EMERGENCY OPERATIONS VALUES FOR WAR RISK INSURANCE § 309.3 Stated valuation. A stated valuation represents just compensation for the vessel to which it applies computed...

  6. 46 CFR 309.3 - Stated valuation.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 46 Shipping 8 2010-10-01 2010-10-01 false Stated valuation. 309.3 Section 309.3 Shipping MARITIME ADMINISTRATION, DEPARTMENT OF TRANSPORTATION EMERGENCY OPERATIONS VALUES FOR WAR RISK INSURANCE § 309.3 Stated valuation. A stated valuation represents just compensation for the vessel to which it applies computed...

  7. 46 CFR 309.3 - Stated valuation.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 46 Shipping 8 2011-10-01 2011-10-01 false Stated valuation. 309.3 Section 309.3 Shipping MARITIME ADMINISTRATION, DEPARTMENT OF TRANSPORTATION EMERGENCY OPERATIONS VALUES FOR WAR RISK INSURANCE § 309.3 Stated valuation. A stated valuation represents just compensation for the vessel to which it applies computed...

  8. 46 CFR 309.3 - Stated valuation.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 46 Shipping 8 2012-10-01 2012-10-01 false Stated valuation. 309.3 Section 309.3 Shipping MARITIME ADMINISTRATION, DEPARTMENT OF TRANSPORTATION EMERGENCY OPERATIONS VALUES FOR WAR RISK INSURANCE § 309.3 Stated valuation. A stated valuation represents just compensation for the vessel to which it applies computed...

  9. Iterative Potts and Blake–Zisserman minimization for the recovery of functions with discontinuities from indirect measurements

    PubMed Central

    Weinmann, Andreas; Storath, Martin

    2015-01-01

    Signals with discontinuities appear in many problems in the applied sciences ranging from mechanics, electrical engineering to biology and medicine. The concrete data acquired are typically discrete, indirect and noisy measurements of some quantities describing the signal under consideration. The task is to restore the signal and, in particular, the discontinuities. In this respect, classical methods perform rather poor, whereas non-convex non-smooth variational methods seem to be the correct choice. Examples are methods based on Mumford–Shah and piecewise constant Mumford–Shah functionals and discretized versions which are known as Blake–Zisserman and Potts functionals. Owing to their non-convexity, minimization of such functionals is challenging. In this paper, we propose a new iterative minimization strategy for Blake–Zisserman as well as Potts functionals and a related jump-sparsity problem dealing with indirect, noisy measurements. We provide a convergence analysis and underpin our findings with numerical experiments.

  10. [Anterior approach of cervical spine in Pott's disease. Apropos of 7 cases].

    PubMed

    Achouri, M; Hilmani, S; Lakhdar, H; Ait Ben Ali, S; Naja, A; Ouboukhlik, A; el Kamar, A; el Azhari, A; Boucetta, M

    1997-01-01

    This study reports 7 cases of cervical Pott's disease, gathered during 6 years in the department of neuro-surgery of Ibn Rochd U.H.C. 4 females and 3 males, aged between 9 and 52 years were included. All the patients complained of cervicobrachial pain and weakness of the limbs. Clinical features were: deterioration of general status, rachidian syndrome and neurological impairement with motor and sensitive deficit. Radiological analysis found a destructive and extensive lesion, cervical kyphosis from 10 degrees to 60 degrees, retropharyngeal abscess and intraspinal canal extension of infection. Diagnosis was confirmed by histological study in all cases. In addition to antituberculous therapy and preoperative cervical traction in 4 cases, all the patients had spinal fusion using an anterior approach. Post operative immobilization in a cervical collar varied from 9 to 12 months. All 7 patients had full neurological recovery, 6 patients had an excellent bony fusion and cervical kyphosis was corrected. For the remaining patient, the bone graft was mobilized without neurological disorders. This study confirms anterior arthrodesis efficiency. This procedure in conjunction with preoperative traction, allowed stabilization of the spine and healing of vertebral lesions with excellent kyphosis correction. PMID:9452797

  11. Medical-surgical treatment of progressive tuberculous (Pott's) paraplegia in Gabon.

    PubMed

    Loembe, P M

    1995-10-01

    The present study deals with the results of the medical-surgical treatment of 22 patients with Pott's tetraplegia or paraplegia. Seventeen had progressive tetraplegia-paraplegia which failed to respond solely to medical treatment. On admission, four patients exhibited an acute onset tetraplegia-paraplegia, and one had a 'spinal tumour syndrome'. In addition to antituberculous therapy, seven patients had anterior spinal surgery, consisting of four corporectomies, two anterior debridments and grafting, and one debridment alone. Moreover, one patient had a posterior interbody fusion, four had laminotomies, and 10 had laminectomies. The causes of the spinal cord or cauda equina compression, as was determined at operation, were extradural abscess in eight patients, bony compressions in 11, arachnoiditis in two, and posterior neural arch tuberculosis in one patient. Neurological recovery began between 10 and 21 days postoperatively. The mean length of follow-up was 42.36 months (range 8-144 months). Fourteen patients were found to be functionally and neurologically normal at follow-up examinations (63%). Eighty-two percent recovered sufficiently to walk unaided. Two patients were left paralysed and unable to walk. Two patients were able to get about on crutches. The onset of objective improvement soon after surgical decompression suggests a causal effect. It was concluded that early neural decompression and spinal stabilisation provided the maximum potential for neurological recovery. PMID:8848312

  12. From Potts Hill (Australia) to Pune (India): The journey of a radio astronomer

    NASA Astrophysics Data System (ADS)

    Swarup, Govind

    2006-06-01

    In this paper I recapitulate my initiation into the field of radio astronomy during 1953-1955 at CSIRO, Australia; the transfer of thirty-two parabolic dishes of six-feet (1.8-m) diameter from Potts Hill, Sydney, to India in 1958; and their erection at Kalyan, near Bombay (Mumbai), in 1963-1965. The Kalyan Radio Telescope was the first modern radio telescope built in India. This led to the establishment of a very active radio astronomy group at the Tata Institute of Fundamental Research, which subsequently built two world-class radio telescopes during the last forty years and also contributed to the development of an indigenous microwave antenna industry in India. The Ooty Radio Telescope, built during 1965-1970, has an ingenious design which takes advantage of India's location near the Earth's Equator. The long axis of this 530 m × 30 m parabolic cylinder was made parallel to the Equator, by placing it on a hill with the same slope as the geographic latitude (11 degrees), thus allowing it to track celestial sources continuously for 9.5 hours every day. By utilizing lunar occultations, the telescope was able to measure the angular sizes of a large number of faint radio galaxies and quasars with arc-second resolution for the first time. Subsequently, during the 1990s, the group set up the Giant Metrewave Radio Telescope (GMRT) near Pune in western India, in order to investigate certain astrophysical phenomena which are best studied at decimetre and metre wavelengths. The GMRT is an array of thirty fully-steerable parabolic dishes of 45 m diameter, which operates at several frequencies below 1.43 GHz. These efforts have also contributed to the recent international proposal to construct the Square Kilometre Array (SKA).

  13. Non-Hodgkin's lymphoma “masquerading” as Pott's disease in a 13-year old boy

    PubMed Central

    Adegboye, Olasunkanmi Abdulrasheed

    2011-01-01

    Lymphomas are malignant neoplasms of the lymphoid lineage. They are broadly classified as either Hodgkin disease or as non-Hodgkin lymphoma (NHL). Burkitt's lymphoma, a variety of NHL, is significantly most common in sub-Saharan Africa, where it accounts for approximately one half of childhood cancers. Lymphoblastic lymphoma is less common. A case of paravertebral high grade non-Hodgkin's lymphoma (lymphoblastic lymphoma) “masquerading” as Pott's disease in a 13-year-old child is reported. The present report was informed by the unusual presentation of this case and the intent of increasing the index of diagnostic suspicion. A brief appraisal is provided of the clinical parameters, management strategies and challenges. AT was a 13-year boy that presented on account of a slowly evolving and progressively increasing hunch on the back and inability to walk over 4 and 8 months duration, respectively. There was subsequent inability to control defecation and urination. There was no history of cough. He and his twin brother lived with their paternal grandfather who had chronic cough with associated weight loss. The grandfather died shortly before the child's admission. The child had no BCG immunization. The essential findings on examination were in keeping with lower motor neurons (LMN) paralysis of the lower limbs. The upper limbs appeared normal. There was loss of cutaneous sensation from the umbilicus (T10) downward. There was a firm, (rather tense), non-tender non-pulsatile, smooth swelling over the mid-third of the back (T6-L1) the mass had no differential warmth. It measures about 20×12 cm. Chest radiograph showed no active focal lung lesion, but the thoraco-lumbar spine showed a vertebral planner at L1 and a wedged collapse of T11-T12 vertebrae. There was sclerosis of the end plates of all the vertebral bodies with associated reduction in the bone density. He had an excision biopsy on the 90th day on admission, following which his clinical state rapidly

  14. Tuberculose ostéoarticulaire (mal de Pott exclu): à propos de 120 cas à Abidjan

    PubMed Central

    Gbané-Koné, Mariam; Koné, Samba; Ouali, Boubacar; Djaha, Kouassi Jean -Mermoz; Akoli, Ekoya Ondzala; Nseng, Ingrid Nseng; Eti, Edmond; Daboiko, Jean Claude; Touré, Stanislas André; Kouakou, N'zué Marcel

    2015-01-01

    Introduction La tuberculose ostéoarticulaire (TOA) représente 2 à 5% de l'ensemble des tuberculoses. Elle demeure d'actualité surtout dans les pays à forte endémicité tuberculeuse. L'objectif était de déterminer la prévalence, les aspects topographiques, radiologiques de la TOA en milieu hospitalier ivoirien. Méthodes Les auteurs rapportent une expérience de 11 ans, à travers une étude rétrospective de 120 dossiers de patients atteints de la tuberculose ostéoarticulaire (le mal de Pott est exclu de cette étude). N'ont pas été inclus dans l’étude les dossiers ne comportant pas d'imagerie. Résultats L'atteinte extra vertébrale représentait 09,2% de la tuberculose ostéoarticulaire. Il s'agissait de 54 hommes et 66 femmes, l’âge moyen était de 43,13 ans. On notait 123 cas d'ostéoarthrites, et 8 cas d'ostéites des os plats. L'atteinte des membres inférieurs prédominait dans 91,87% des cas. La hanche était la première localisation (45,04%), suivie du genou (25,19%). Les atteintes étaient multifocales dans 20% des cas. L'atteinte osseuse était associée à une tuberculose pulmonaire dans 05,83% des cas. Des localisations inhabituelles ont été rapportées: poignet (n = 2), branches ischiopubiennes (n = 4), atteinte sternoclaviculaire (n = 4), médiopieds (n = 2). Les lésions radiologiques étaient avancées (stades III et IV) dans 55,73% des cas. A la TDM, la prévalence des abcès était de 77%. Un geste chirurgical a été réalisé sur 16 articulations (2 épaules, 13 genoux, une cheville). Conclusion La TOA des membres est peu fréquente contrairement à l'atteinte vertébrale. La hanche est la principale localisation. Le retard au diagnostic explique l’étendue des lésions anatomoradiologiques. PMID:26587129

  15. Diffusion tensor imaging observation in Pott's spine with or without neurological deficit

    PubMed Central

    Abbas, Sohail; Jain, Anil Kumar; Saini, Namita Singh; Kumar, Sudhir; Mukunth, Rajagopalan; Kumar, Jaswant; Kumar, Pawan; Kaur, Prabhjot

    2015-01-01

    Background: Diffusion tensor imaging (DTI) is based upon the phenomenon of water diffusion known as “Brownian motion.” DTI can detect changes in compressed spinal cord earlier than magnetic resonance imaging and is more sensitive to subtle pathological changes of the spinal cord. DTI observation in compressed and noncompressed spinal cord in tuberculosis (TB) spine is not described. This study presents observations in Pott's spine patients with or without neural deficit. Materials and Methods: Thirty consecutive cases of TB spine with mean age of 32.1 years of either sexes with paradiscal lesion, with/without paraplegia divided into two groups: Group A: (n = 15) without paraplegia and group B: (n = 15) with paraplegia were evaluated by DTI. The average fractional anisotropy (FA) and mean diffusivity (MD) values were calculated at 3 different sites, above the lesion (SOL)/normal, at the lesion and below SOL for both groups and mean was compared. Visual impression of tractography was done to document changes in spinal tracts. Results: The mean canal encroachment in group A was 39.60% and group B 44.4% (insignificant). Group A mean FA values above SOL, at the lesion and below SOL were 0.608 ± 0.09, 0.554 ± 0.14, and 0.501 ± 0.16 respectively. For group B mean FA values above SOL, at the lesion and below SOL were 0.628 ± 0.09, 0.614 ± 0.12 and 0.487 ± 0.15 respectively. There was a significant difference in mean FA above the SOL as compared to the mean FA at and below SOL. P value above versus below the SOL was statistically significant for both groups (0.04), but P value for at versus below the SOL (0.01) was statistically significant only in group B. On tractography, disruption of fiber tract at SOL was found in 14/15 (93.3%) cases of group A and 14/15 cases (93.3%) of group B (6/6 grade 4, 3/3 grade 3 and 5/6 grade 2 paraplegic cases). Conclusion: The FA and MD above the lesion were same as reported for healthy volunteer hence can be taken as control. FA

  16. Benchmarking Inverse Statistical Approaches for Protein Structure and Design with Exactly Solvable Models

    PubMed Central

    Jacquin, Hugo; Shakhnovich, Eugene; Cocco, Simona; Monasson, Rémi

    2016-01-01

    Inverse statistical approaches to determine protein structure and function from Multiple Sequence Alignments (MSA) are emerging as powerful tools in computational biology. However the underlying assumptions of the relationship between the inferred effective Potts Hamiltonian and real protein structure and energetics remain untested so far. Here we use lattice protein model (LP) to benchmark those inverse statistical approaches. We build MSA of highly stable sequences in target LP structures, and infer the effective pairwise Potts Hamiltonians from those MSA. We find that inferred Potts Hamiltonians reproduce many important aspects of ‘true’ LP structures and energetics. Careful analysis reveals that effective pairwise couplings in inferred Potts Hamiltonians depend not only on the energetics of the native structure but also on competing folds; in particular, the coupling values reflect both positive design (stabilization of native conformation) and negative design (destabilization of competing folds). In addition to providing detailed structural information, the inferred Potts models used as protein Hamiltonian for design of new sequences are able to generate with high probability completely new sequences with the desired folds, which is not possible using independent-site models. Those are remarkable results as the effective LP Hamiltonians used to generate MSA are not simple pairwise models due to the competition between the folds. Our findings elucidate the reasons for the success of inverse approaches to the modelling of proteins from sequence data, and their limitations. PMID:27177270

  17. First-Order Transition in a Spin Model for Self-Organization

    NASA Astrophysics Data System (ADS)

    Bauvin, R.; Kamp, Y.

    The paper examines the emergence of self-organization in a population where tandem recruitment is combined with individual memory. The time evolution is modeled as a two-dimensional spin system with local interaction along the time axis and a mean-field interaction along the other axis. We generalize a previous result obtained with this model from the case of two sources to the multisource situation and show a twofold connection with the Potts model. First, when individual memory exceeds a critical value, a phase transition sets in, which is second order for two sources but first order beyond, similarly to the mean-field theory of the Potts model. In addition, the self-organization problem considered here relies on a special case of the one-dimensional nearest-neighbor Potts model with external field, which is shown to be explicitly solvable.

  18. A Rare Case of Pott's Disease (Spinal Tuberculosis) Mimicking Metastatic Disease in the Southern Region of Denmark.

    PubMed

    Osmanagic, Azra; Emamifar, Amir; Christian Bang, Jacob; Jensen Hansen, Inger Marie

    2016-01-01

    BACKGROUND Pott's disease (PD) or spinal tuberculosis is a rare condition which accounts for less than 1% of total tuberculosis (TB) cases. The incidence of PD has recently increased in Europe and the United States, mainly due to immigration; however, it is still a rare diagnosis in Scandinavian countries, and if overlooked it might lead to significant neurologic complications. CASE REPORT A 78-year-old woman, originally from Eastern Europe, presented to the emergency department with a complaint of nausea, vomiting, weight loss, and severe back pain. On admission she was febrile and had leukocytosis and increased C-reactive protein. Initial spinal x-ray was performed and revealed osteolytic changes in the vertebral body of T11 and T12. Magnetic resonance imaging (MRI) of the spine illustrated spondylitis of T10, T11, and T12, with multiple paravertebral and epidural abscesses, which was suggestive of PD. Polymerase chain reaction (PCR) of the patient's gastric fluid was positive for Mycobacterium tuberculosis (MT). Based on MRI and PCR findings, standard treatment for TB was initiated. Results of the spine biopsy and culture showed colonies of MT and confirmed the diagnosis afterwards. Due to the instability of the spine and severe and continuous pain, spine-stabilizing surgery was performed. Her TB was cured after nine months of treatment. CONCLUSIONS PD is an important differential diagnosis of malignancy that should be diagnosed instantly. History of exposure to TB and classic radiologic finding can help make the diagnosis. PMID:27272065

  19. Simulated Tempering and Swapping on Mean-Field Models

    NASA Astrophysics Data System (ADS)

    Bhatnagar, Nayantara; Randall, Dana

    2016-08-01

    Simulated and parallel tempering are families of Markov Chain Monte Carlo algorithms where a temperature parameter is varied during the simulation to overcome bottlenecks to convergence due to multimodality. In this work we introduce and analyze the convergence for a set of new tempering distributions which we call entropy dampening. For asymmetric exponential distributions and the mean field Ising model with an external field simulated tempering is known to converge slowly. We show that tempering with entropy dampening distributions mixes in polynomial time for these models. Examining slow mixing times of tempering more closely, we show that for the mean-field 3-state ferromagnetic Potts model, tempering converges slowly regardless of the temperature schedule chosen. On the other hand, tempering with entropy dampening distributions converges in polynomial time to stationarity. Finally we show that the slow mixing can be very expensive practically. In particular, the mixing time of simulated tempering is an exponential factor longer than the mixing time at the fixed temperature.

  20. Representation and Poly-time Approximation for Pressure of {Z}^2 Lattice Models in the Non-uniqueness Region

    NASA Astrophysics Data System (ADS)

    Adams, Stefan; Briceño, Raimundo; Marcus, Brian; Pavlov, Ronnie

    2016-02-01

    We develop a new pressure representation theorem for nearest-neighbour Gibbs interactions and apply this to obtain the existence of efficient algorithms for approximating the pressure in the 2-dimensional ferromagnetic Potts, multi-type Widom-Rowlinson and hard-core models. For Potts model, our results apply to every inverse temperature but the critical. For Widom-Rowlinson and hard-core models, they apply to certain subsets of both the subcritical and supercritical regions. The main novelty of our work is in the latter.

  1. 32 CFR 1903.3 - State law applicable.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 32 National Defense 6 2011-07-01 2011-07-01 false State law applicable. 1903.3 Section 1903.3 National Defense Other Regulations Relating to National Defense CENTRAL INTELLIGENCE AGENCY CONDUCT ON AGENCY INSTALLATIONS § 1903.3 State law applicable. (a) Unless specifically addressed by the...

  2. 32 CFR 1903.3 - State law applicable.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 32 National Defense 6 2010-07-01 2010-07-01 false State law applicable. 1903.3 Section 1903.3 National Defense Other Regulations Relating to National Defense CENTRAL INTELLIGENCE AGENCY CONDUCT ON AGENCY INSTALLATIONS § 1903.3 State law applicable. (a) Unless specifically addressed by the...

  3. 32 CFR 1903.3 - State law applicable.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 32 National Defense 6 2014-07-01 2014-07-01 false State law applicable. 1903.3 Section 1903.3 National Defense Other Regulations Relating to National Defense CENTRAL INTELLIGENCE AGENCY CONDUCT ON AGENCY INSTALLATIONS § 1903.3 State law applicable. (a) Unless specifically addressed by the...

  4. 32 CFR 1903.3 - State law applicable.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 32 National Defense 6 2013-07-01 2013-07-01 false State law applicable. 1903.3 Section 1903.3 National Defense Other Regulations Relating to National Defense CENTRAL INTELLIGENCE AGENCY CONDUCT ON AGENCY INSTALLATIONS § 1903.3 State law applicable. (a) Unless specifically addressed by the...

  5. 32 CFR 1903.3 - State law applicable.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 32 National Defense 6 2012-07-01 2012-07-01 false State law applicable. 1903.3 Section 1903.3 National Defense Other Regulations Relating to National Defense CENTRAL INTELLIGENCE AGENCY CONDUCT ON AGENCY INSTALLATIONS § 1903.3 State law applicable. (a) Unless specifically addressed by the...

  6. The results of anterior radical debridement and anterior instrumentation in Pott's disease and comparison with other surgical techniques.

    PubMed

    Benli, I T; Kiş, M; Akalin, S; Citak, M; Kanevetçi, S; Duman, E

    2000-04-01

    Classic procedure in the treatment of vertebral tuberculosis is drainage of the abscess, curettage of the devitalized vertebra and application of antituberculous chemotherapy regimen. Posterior instrumentation results are encouraging in the prevention or treatment of late kyphosis; however, a second stage operation is needed. Recently, posterolateral or transpedicular drainage without anterior drainage or posterior instrumentation following anterior drainage in the same session is preferred to avoid kyphotic deformity. Seventy-six patients with spinal tuberculosis were operated in the 1st Department of Orthopaedics and Traumatology, Ankara Social Security Hospital, between January 1987 and January 1997. There were four children in our series. Average follow-up period was 36.1 +/- 14.5 months and the average age at the time of operation was 40.8 +/- 15.2 years. This study reports the surgical results of 45 patients with Pott's disease who had anterior radical debridement with anterior fusion and anterior instrumentation [14 patients with Z-plate and 31 patients with Cotrel-Dubousset-Hopf (CDH system)]. The results are compared with those of 8 patients who had posterolateral drainage and posterior fusion, 12 patients who had only anterior drainage and anterior strut grafting and, 11 patients who had posterior instrumentation following anterior radical debridement in the same session in terms of fusion rates, correction of kyphotic deformity, recurrence rate and clinical results. All patients had one year consecutive triple drug therapy. Preoperative 23.2 degrees +/- 12.5 degrees local kyphosis angle was lowered to 6.1 degrees +/- 6.9 degrees with a correction rate of 77.4 +/- 22.3%. When the other three groups which had been instrumented were compared, the correction rates in the local kyphosis angle values were not statistically different and the variation in loss of correction at the last follow-up was also statistically insignificant. The sagittal contour of the

  7. Mutual information in classical spin models

    NASA Astrophysics Data System (ADS)

    Wilms, Johannes; Troyer, Matthias; Verstraete, Frank

    2011-10-01

    The total many-body correlations present in finite temperature classical spin systems are studied using the concept of mutual information. As opposed to zero-temperature quantum phase transitions, the total correlations are not maximal at the phase transition, but reach a maximum in the high-temperature paramagnetic phase. The Shannon mutual information and the Renyi mutual information in both Ising and Potts models in two dimensions are calculated numerically by combining matrix product state algorithms and Monte Carlo sampling techniques.

  8. On the nature of a supposed water model

    SciTech Connect

    Heckmann, Lotta Drossel, Barbara

    2014-08-15

    A cell model that has been proposed by Stanley and Franzese in 2002 for modeling water is based on Potts variables that represent the possible orientations of bonds between water molecules. We show that in the liquid phase, where all cells are occupied by a molecule, the Hamiltonian of the cell model can be rewritten as a Hamiltonian of a conventional Potts model, albeit with two types of coupling constants. We argue that such a model, while having a first-order phase transition, cannot display the critical end point that is postulated for the phase transition between a high- and low-density liquid. A closer look at the mean-field calculations that claim to find such an end point in the cell model reveals that the mean-field theory is constructed such that the symmetry constraints on the order parameter are violated. This is equivalent to introducing an external field. The introduction of such a field can be given a physical justification due to the fact that water does not have the type of long-range order occurring in the Potts model.

  9. Particle-based simulation of ellipse-shaped particle aggregation as a model for vascular network formation

    NASA Astrophysics Data System (ADS)

    Palachanis, Dimitrios; Szabó, András; Merks, Roeland M. H.

    2015-12-01

    Computational modeling is helpful for elucidating the cellular mechanisms driving biological morphogenesis. Previous simulation studies of blood vessel growth based on the cellular Potts model proposed that elongated, adhesive or mutually attractive endothelial cells suffice for the formation of blood vessel sprouts and vascular networks. Because each mathematical representation of a model introduces potential artifacts, it is important that model results are reproduced using alternative modeling paradigms. Here, we present a lattice-free, particle-based simulation of the cell elongation model of vasculogenesis. The new, particle-based simulations confirm the results obtained from the previous cellular Potts simulations. Furthermore, our current findings suggest that the emergence of order is possible with the application of a high enough attractive force or, alternatively, a longer attraction radius. The methodology will be applicable to a range of problems in morphogenesis and noisy particle aggregation in which cell shape is a key determining factor.

  10. A novel dynamics combination model reveals the hidden information of community structure

    NASA Astrophysics Data System (ADS)

    Li, Hui-Jia; Li, Huiying; Jia, Chuanliang

    2015-09-01

    The analysis of the dynamic details of community structure is an important question for scientists from many fields. In this paper, we propose a novel Markov-Potts framework to uncover the optimal community structures and their stabilities across multiple timescales. Specifically, we model the Potts dynamics to detect community structure by a Markov process, which has a clear mathematical explanation. Then the local uniform behavior of spin values revealed by our model is shown that can naturally reveal the stability of hierarchical community structure across multiple timescales. To prove the validity, phase transition of stochastic dynamic system is used to indicate that the stability of community structure we proposed is able to describe the significance of community structure based on eigengap theory. Finally, we test our framework on some example networks and find it does not have resolute limitation problem at all. Results have shown the model we proposed is able to uncover hierarchical structure in different scales effectively and efficiently.

  11. Dynamics of ordering in highly degenerate models with anisotropic grain-boundary potential: Effects of temperature and vortex formation

    NASA Astrophysics Data System (ADS)

    Jeppesen, Claus; Flyvbjerg, Henrik; Mouritsen, Ole G.

    1989-11-01

    Monte Carlo computer-simulation techniques are used to elucidate the equilibrium phase behavior as well as the late-stage ordering dynamics of some two-dimensional models with ground-state ordering of a high degeneracy Q. The models are Q-state Potts models with anisotropic grain-boundary potential on triangular lattices-essentially clock models, except that the potential is not a cosine, but a sine function of the angle between neighboring grain orientations. For not too small Q, these models display two thermally driven phase transitions, one which takes the system from a low-temperature Potts-ordered phase to an intermediate phase which lacks conventional long-range order, and another transition which takes the system to the high-temperature disordered phase. The linear nature of the sine potential used makes it a marginal case in the sense that it favors neither hard domain boundaries, like the standard Potts models do, nor a wetting of the boundaries, as the standard clock models do. Thermal fluctuations nevertheless cause wetting to occur for not too small temperatures. Specifically, we have studied models with Q=12 and 48. The models are quenched from infinity to zero as well as finite temperatures within the two low-temperature phases. The order parameter is a nonconserved quantity during these quenches. The nonequilibrium ordering process subsequent to the quench is studied as a function of time by calculating the interfacial energy, ΔE, associated with the entire grain-boundary network. The time evolution of this quantity is shown to obey the growth law, ΔE(t)~t-n, over an extended time range at late times. It is found that the zero-temperature dynamics is characterized by a special exponent value which for the Q=48 model is n~=0.25 in accordance with earlier work. However, for quenches to finite temperatures in the Potts-ordered phase there is a distinct crossover to the classical Lifshitz-Allen-Cahn exponent value, n=(1/2, for both values of Q. This

  12. Bubbly vertex dynamics: A dynamical and geometrical model for epithelial tissues with curved cell shapes

    NASA Astrophysics Data System (ADS)

    Ishimoto, Yukitaka; Morishita, Yoshihiro

    2014-11-01

    In order to describe two-dimensionally packed cells in epithelial tissues both mathematically and physically, there have been developed several sorts of geometrical models, such as the vertex model, the finite element model, the cell-centered model, and the cellular Potts model. So far, in any case, pressures have not neatly been dealt with and the curvatures of the cell boundaries have been even omitted through their approximations. We focus on these quantities and formulate them in the vertex model. Thus, a model with the curvatures is constructed, and its algorithm for simulation is provided. The possible extensions and applications of this model are also discussed.

  13. Structural changes in the S3 state of the oxygen evolving complex in photosystem II

    NASA Astrophysics Data System (ADS)

    Hatakeyama, Makoto; Ogata, Koji; Fujii, Katsushi; Yachandra, Vittal K.; Yano, Junko; Nakamura, Shinichiro

    2016-05-01

    The S3 state of the Mn4CaO5-cluster in photosystem II was investigated by DFT calculations and compared with EXAFS data. Considering previously proposed mechanism; a water molecule is inserted into an open coordination site of Mn upon S2 to S3 transition that becomes a substrate water, we examined if the water insertion is essential for the S3 formation, or if one cannot eliminate other possible routes that do not require a water insertion at the S3 stage. The novel S3 state structure consisting of only short 2.7-2.8 Å Mnsbnd Mn distances was discussed.

  14. 7 CFR 1900.3 - State, district, and county office employees.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 12 2010-01-01 2010-01-01 false State, district, and county office employees. 1900.3... AGRICULTURE PROGRAM REGULATIONS GENERAL Delegations of Authority § 1900.3 State, district, and county office... laws, for and on behalf of, and in the name of the United States of America or the Farmers...

  15. 7 CFR 1900.3 - State, district, and county office employees.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 12 2011-01-01 2011-01-01 false State, district, and county office employees. 1900.3... AGRICULTURE PROGRAM REGULATIONS GENERAL Delegations of Authority § 1900.3 State, district, and county office... laws, for and on behalf of, and in the name of the United States of America or the Farmers...

  16. 28 CFR 904.3 - State criminal history record screening standards.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... III System. (a) The State Criminal History Record Repository or an authorized agency in the receiving... 28 Judicial Administration 2 2012-07-01 2012-07-01 false State criminal history record screening... STATE CRIMINAL HISTORY RECORD SCREENING STANDARDS § 904.3 State criminal history record...

  17. 28 CFR 904.3 - State criminal history record screening standards.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 28 Judicial Administration 2 2013-07-01 2013-07-01 false State criminal history record screening... STATE CRIMINAL HISTORY RECORD SCREENING STANDARDS § 904.3 State criminal history record screening standards. The following record screening standards relate to criminal history record information...

  18. 28 CFR 904.3 - State criminal history record screening standards.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 28 Judicial Administration 2 2014-07-01 2014-07-01 false State criminal history record screening... STATE CRIMINAL HISTORY RECORD SCREENING STANDARDS § 904.3 State criminal history record screening standards. The following record screening standards relate to criminal history record information...

  19. 28 CFR 904.3 - State criminal history record screening standards.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 28 Judicial Administration 2 2010-07-01 2010-07-01 false State criminal history record screening... STATE CRIMINAL HISTORY RECORD SCREENING STANDARDS § 904.3 State criminal history record screening standards. The following record screening standards relate to criminal history record information...

  20. 28 CFR 904.3 - State criminal history record screening standards.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 28 Judicial Administration 2 2011-07-01 2011-07-01 false State criminal history record screening... STATE CRIMINAL HISTORY RECORD SCREENING STANDARDS § 904.3 State criminal history record screening standards. The following record screening standards relate to criminal history record information...

  1. Improved CUDA programs for GPU computing of Swendsen-Wang multi-cluster spin flip algorithm: 2D and 3D Ising, Potts, and XY models

    NASA Astrophysics Data System (ADS)

    Komura, Yukihiro; Okabe, Yutaka

    2016-03-01

    We present new versions of sample CUDA programs for the GPU computing of the Swendsen-Wang multi-cluster spin flip algorithm. In this update, we add the method of GPU-based cluster-labeling algorithm without the use of conventional iteration (Komura, 2015) to those programs. For high-precision calculations, we also add a random-number generator in the cuRAND library. Moreover, we fix several bugs and remove the extra usage of shared memory in the kernel functions.

  2. Local-states method for the calculation of free energies in Monte Carlo simulations of lattice models

    NASA Astrophysics Data System (ADS)

    Schlijper, A. G.; van Bergen, A. R. D.; Smit, B.

    1990-01-01

    We present and demonstrate an accurate, reliable, and computationally cheap method for the calculation of free energies in Monte Carlo simulations of lattice models. Even in the critical region it yields good results with comparatively short simulation runs. The method combines upper and lower bounds on the thermodynamic limit entropy density to yield not only an accurate estimate of the free energy but a bound on the possible error as well. The method is demonstrated on the two- and three-dimensional Ising models and the three-dimensional, three-states Potts model.

  3. Low T3 State Is Correlated with Cardiac Mitochondrial Impairments after Ischemia Reperfusion Injury: Evidence from a Proteomic Approach

    PubMed Central

    Forini, Francesca; Ucciferri, Nadia; Kusmic, Claudia; Nicolini, Giuseppina; Cecchettini, Antonella; Rocchiccioli, Silvia; Citti, Lorenzo; Iervasi, Giorgio

    2015-01-01

    Mitochondria are major determinants of cell fate in ischemia/reperfusion injury (IR) and common effectors of cardio-protective strategies in cardiac ischemic disease. Thyroid hormone homeostasis critically affects mitochondrial function and energy production. Since a low T3 state (LT3S) is frequently observed in the post infarction setting, the study was aimed to investigate the relationship between 72 h post IR T3 levels and both the cardiac function and the mitochondrial proteome in a rat model of IR. The low T3 group exhibits the most compromised cardiac performance along with the worst mitochondrial activity. Accordingly, our results show a different remodeling of the mitochondrial proteome in the presence or absence of a LT3S, with alterations in groups of proteins that play a key role in energy metabolism, quality control and regulation of cell death pathways. Overall, our findings highlight a relationship between LT3S in the early post IR and poor cardiac and mitochondrial outcomes, and suggest a potential implication of thyroid hormone in the cardio-protection and tissue remodeling in ischemic disease. PMID:26561807

  4. Gibbosité vertébrale congénitale évoquant un mal de Pott chez un nouveau-né de mère tuberculeuse: à propos d'un cas et revue de la literature

    PubMed Central

    Katamea, Tina; Mukuku, Olivier; Luboya, Oscar Numbi

    2014-01-01

    Les formes latentes de tuberculose chez la femme enceinte sont associées à un risque élevé de passage à une forme active qui augmente le risque de transmission de la mère infectée à l'enfant dans les 3 premières semaines de vie. Nous rapportons un cas de Gibbosité vertébrale congénitale évoquant un mal de Pott chez un nourrisson de mère tuberculeuse, observé à Lubumbashi, en République Démocratique du Congo. PMID:25478046

  5. Simulating tissue mechanics with agent-based models: concepts, perspectives and some novel results

    NASA Astrophysics Data System (ADS)

    Van Liedekerke, P.; Palm, M. M.; Jagiella, N.; Drasdo, D.

    2015-12-01

    In this paper we present an overview of agent-based models that are used to simulate mechanical and physiological phenomena in cells and tissues, and we discuss underlying concepts, limitations, and future perspectives of these models. As the interest in cell and tissue mechanics increase, agent-based models are becoming more common the modeling community. We overview the physical aspects, complexity, shortcomings, and capabilities of the major agent-based model categories: lattice-based models (cellular automata, lattice gas cellular automata, cellular Potts models), off-lattice models (center-based models, deformable cell models, vertex models), and hybrid discrete-continuum models. In this way, we hope to assist future researchers in choosing a model for the phenomenon they want to model and understand. The article also contains some novel results.

  6. The Fitness Landscape of HIV-1 Gag: Advanced Modeling Approaches and Validation of Model Predictions by In Vitro Testing

    PubMed Central

    Omarjee, Saleha; Walker, Bruce D.; Chakraborty, Arup; Ndung'u, Thumbi

    2014-01-01

    Viral immune evasion by sequence variation is a major hindrance to HIV-1 vaccine design. To address this challenge, our group has developed a computational model, rooted in physics, that aims to predict the fitness landscape of HIV-1 proteins in order to design vaccine immunogens that lead to impaired viral fitness, thus blocking viable escape routes. Here, we advance the computational models to address previous limitations, and directly test model predictions against in vitro fitness measurements of HIV-1 strains containing multiple Gag mutations. We incorporated regularization into the model fitting procedure to address finite sampling. Further, we developed a model that accounts for the specific identity of mutant amino acids (Potts model), generalizing our previous approach (Ising model) that is unable to distinguish between different mutant amino acids. Gag mutation combinations (17 pairs, 1 triple and 25 single mutations within these) predicted to be either harmful to HIV-1 viability or fitness-neutral were introduced into HIV-1 NL4-3 by site-directed mutagenesis and replication capacities of these mutants were assayed in vitro. The predicted and measured fitness of the corresponding mutants for the original Ising model (r = −0.74, p = 3.6×10−6) are strongly correlated, and this was further strengthened in the regularized Ising model (r = −0.83, p = 3.7×10−12). Performance of the Potts model (r = −0.73, p = 9.7×10−9) was similar to that of the Ising model, indicating that the binary approximation is sufficient for capturing fitness effects of common mutants at sites of low amino acid diversity. However, we show that the Potts model is expected to improve predictive power for more variable proteins. Overall, our results support the ability of the computational models to robustly predict the relative fitness of mutant viral strains, and indicate the potential value of this approach for understanding viral immune evasion

  7. On multiscale approaches to three-dimensional modelling of morphogenesis

    PubMed Central

    Chaturvedi, R; Huang, C; Kazmierczak, B; Schneider, T; Izaguirre, J.A; Glimm, T; Hentschel, H.G.E; Glazier, J.A; Newman, S.A; Alber, M.S

    2005-01-01

    In this paper we present the foundation of a unified, object-oriented, three-dimensional biomodelling environment, which allows us to integrate multiple submodels at scales from subcellular to those of tissues and organs. Our current implementation combines a modified discrete model from statistical mechanics, the Cellular Potts Model, with a continuum reaction–diffusion model and a state automaton with well-defined conditions for cell differentiation transitions to model genetic regulation. This environment allows us to rapidly and compactly create computational models of a class of complex-developmental phenomena. To illustrate model development, we simulate a simplified version of the formation of the skeletal pattern in a growing embryonic vertebrate limb. PMID:16849182

  8. Draft of M2 Report on Integration of the Hybrid Hydride Model into INL's MBM Framework for Review

    SciTech Connect

    Tikare, Veena; Weck, Philippe F.; Schultz, Peter A.; Clark, Blythe; Glazoff, Michael; Homer, Eric

    2014-07-01

    This report documents the development, demonstration and validation of a mesoscale, microstructural evolution model for simulation of zirconium hydride {delta}-ZrH{sub 1.5} precipitation in the cladding of used nuclear fuels that may occur during long-term dry storage. While the Zr-based claddings are manufactured free of any hydrogen, they absorb hydrogen during service, in the reactor by a process commonly termed ‘hydrogen pick-up’. The precipitation and growth of zirconium hydrides during dry storage is one of the most likely fuel rod integrity failure mechanisms either by embrittlement or delayed hydride cracking of the cladding. While the phenomenon is well documented and identified as a potential key failure mechanism during long-term dry storage (NUREG/CR-7116), the ability to actually predict the formation of hydrides is poor. The model being documented in this work is a computational capability for the prediction of hydride formation in different claddings of used nuclear fuels. This work supports the Used Fuel Disposition Research and Development Campaign in assessing the structural engineering performance of the cladding during and after long-term dry storage. This document demonstrates a basic hydride precipitation model that is built on a recently developed hybrid Potts-phase field model that combines elements of Potts-Monte Carlo and the phase-field models. The model capabilities are demonstrated along with the incorporation of the starting microstructure, thermodynamics of the Zr-H system and the hydride formation mechanism.

  9. Star-triangle relation for a three-dimensional model

    SciTech Connect

    Bazhanov, V.V. Institute for High Eenrgy Physics, Protvino, Moscow Region ); Baxter, R.J. Australian National Univ., Canberra )

    1993-06-01

    The solvable sl(n)-chiral Potts model can be interpreted as a three-dimensional lattice model with local interactions. To within a minor modification of the boundary conditions it is an Ising-type model on the body-centered cubic lattice with two- and three-spin interactions. The corresponding local Boltzmann weights obey a number of simple relations, including a restricted star-triangle relation, which is a modified version of the well-known star-triangle relation appearing in two-dimensional models. It is shown that these relations lead to remarkable symmetry properties of the Boltzmann weight function of an elementary cube of the lattice, related to the spatial symmetry group of the cubic lattice. These symmetry properties allow one to prove the commutativity of the row-to-row transfer matrices, bypassing the tetrahedron relation. The partition function per site for the infinite lattice is calculated exactly. 20 refs., 4 figs.

  10. Random matrix theory and classical statistical mechanics: Spin models

    NASA Astrophysics Data System (ADS)

    Meyer, H.; Angles D'Auriac, J.-C.

    1997-06-01

    We present a statistical analysis of spectra of transfer matrices of classical lattice spin models; this continues the work on the eight-vertex model of the preceding paper [H. Meyer, J.-C. Anglès d'Auriac, and J.-M. Maillard, Phys. Rev. E 55, 5261 (1997)]. We show that the statistical properties of these spectra can serve as a criterion of integrability. It also provides an operational numerical method to locate integrable varieties. In particular, we distinguish the notions of integrability and criticality, considering the two examples of the three-dimensional Ising critical point and the two-dimensional three-state Potts critical point. For complex spectra, which appear frequently in the context of transfer matrices, we show that the notion of independence of eigenvalues for integrable models still holds.

  11. app_hybridPotts-phasefield.cpp

    2012-09-12

    This application simulates microstructural and compositional evolution in two-phase, two-component systems. It is designed to run within the SPPARKS solver and combines the kMC with solution to the Cahn-Hilliard Eq. for phase field.

  12. Super-Resolution Using Hidden Markov Model and Bayesian Detection Estimation Framework

    NASA Astrophysics Data System (ADS)

    Humblot, Fabrice; Mohammad-Djafari, Ali

    2006-12-01

    This paper presents a new method for super-resolution (SR) reconstruction of a high-resolution (HR) image from several low-resolution (LR) images. The HR image is assumed to be composed of homogeneous regions. Thus, the a priori distribution of the pixels is modeled by a finite mixture model (FMM) and a Potts Markov model (PMM) for the labels. The whole a priori model is then a hierarchical Markov model. The LR images are assumed to be obtained from the HR image by lowpass filtering, arbitrarily translation, decimation, and finally corruption by a random noise. The problem is then put in a Bayesian detection and estimation framework, and appropriate algorithms are developed based on Markov chain Monte Carlo (MCMC) Gibbs sampling. At the end, we have not only an estimate of the HR image but also an estimate of the classification labels which leads to a segmentation result.

  13. Cell-based computational modeling of vascular morphogenesis using Tissue Simulation Toolkit.

    PubMed

    Daub, Josephine T; Merks, Roeland M H

    2015-01-01

    Computational modeling has become a widely used tool for unraveling the mechanisms of higher level cooperative cell behavior during vascular morphogenesis. However, experimenting with published simulation models or adding new assumptions to those models can be daunting for novice and even for experienced computational scientists. Here, we present a step-by-step, practical tutorial for building cell-based simulations of vascular morphogenesis using the Tissue Simulation Toolkit (TST). The TST is a freely available, open-source C++ library for developing simulations with the two-dimensional cellular Potts model, a stochastic, agent-based framework to simulate collective cell behavior. We will show the basic use of the TST to simulate and experiment with published simulations of vascular network formation. Then, we will present step-by-step instructions and explanations for building a recent simulation model of tumor angiogenesis. Demonstrated mechanisms include cell-cell adhesion, chemotaxis, cell elongation, haptotaxis, and haptokinesis. PMID:25468600

  14. Turnover control of photosystem II: Use of redox-active herbicides to form the S[sub 3] state

    SciTech Connect

    Bocarsly, J.R.; Brudvig, G.W. )

    1992-12-02

    The O[sub 2]-evolving center of photosystem II, which contains an active-site tetramanganese-oxo cluster, catalyzes the four-electron oxidation of two water molecules to dioxygen, with the concomitant production of four H[sup +] and four electrons. During catalytic turnover, the manganese-oxo cluster steps through five intermediate oxidation states, which are known as the S[sub i] states (i = 0-4). While methods have been found to manipulate the system into S[sub 1] and S[sub 2] in high yields, efficient production of the S[sub 3] state in good yield at high concentration has not yet been achieved. Previous methods have suffered from the requirement of low protein concentration so that actinic flashes are saturating; the use of temperature to control S-state advancement under continuous illumination, which can lead to S-state scrambling; or the use of herbicides that bind to the Q[sub B] site and restrict the system to one turnover. The authors describe here a method for the high-yield production of the S[sub 3] state in highly-concentrated samples of photosystem II, through the use of electron-accepting herbicides which bind to the Q[sub B] site. Redox-active herbicides can be used, in principle, to limit S-state cycling to any desired number of turnovers, given the appropriate herbicide. This work has fundamental methodological implications not only for the study of photosystem II but also for other multistate redox protein systems.

  15. Crawling and Gliding: A Computational Model for Shape-Driven Cell Migration

    PubMed Central

    Niculescu, Ioana; Textor, Johannes; de Boer, Rob J.

    2015-01-01

    Cell migration is a complex process involving many intracellular and extracellular factors, with different cell types adopting sometimes strikingly different morphologies. Modeling realistically behaving cells in tissues is computationally challenging because it implies dealing with multiple levels of complexity. We extend the Cellular Potts Model with an actin-inspired feedback mechanism that allows small stochastic cell rufflings to expand to cell protrusions. This simple phenomenological model produces realistically crawling and deforming amoeboid cells, and gliding half-moon shaped keratocyte-like cells. Both cell types can migrate randomly or follow directional cues. They can squeeze in between other cells in densely populated environments or migrate collectively. The model is computationally light, which allows the study of large, dense and heterogeneous tissues containing cells with realistic shapes and migratory properties. PMID:26488304

  16. Crawling and Gliding: A Computational Model for Shape-Driven Cell Migration.

    PubMed

    Niculescu, Ioana; Textor, Johannes; de Boer, Rob J

    2015-10-01

    Cell migration is a complex process involving many intracellular and extracellular factors, with different cell types adopting sometimes strikingly different morphologies. Modeling realistically behaving cells in tissues is computationally challenging because it implies dealing with multiple levels of complexity. We extend the Cellular Potts Model with an actin-inspired feedback mechanism that allows small stochastic cell rufflings to expand to cell protrusions. This simple phenomenological model produces realistically crawling and deforming amoeboid cells, and gliding half-moon shaped keratocyte-like cells. Both cell types can migrate randomly or follow directional cues. They can squeeze in between other cells in densely populated environments or migrate collectively. The model is computationally light, which allows the study of large, dense and heterogeneous tissues containing cells with realistic shapes and migratory properties. PMID:26488304

  17. On the critical parameters of the q ≤ 4 random-cluster model on isoradial graphs

    NASA Astrophysics Data System (ADS)

    Beffara, V.; Duminil-Copin, H.; Smirnov, S.

    2015-12-01

    The critical surface for the random-cluster model with cluster-weight q≥slant 4 on isoradial graphs is identified using parafermionic observables. Correlations are also shown to decay exponentially fast in the subcritical regime. While this result is restricted to random-cluster models with q≥slant 4, it extends the recent theorem of (Beffara and Duminil-Copin 2012 Probl. Theory Relat. Fields 153 511-42) to a large class of planar graphs. In particular, the anisotropic random-cluster model on the square lattice is shown to be critical if \\frac{{p}{{v}}{p}{{h}}}{(1-{p}{{v}})(1-{p}{{h}})}=q, where p v and p h denote the horizontal and vertical edge-weights respectively. We also mention consequences for Potts models.

  18. Hybrid models for the simulation of microstructural evolution influenced by coupled, multiple physical processes.

    SciTech Connect

    Tikare, Veena; Hernandez-Rivera, Efrain; Madison, Jonathan D.; Holm, Elizabeth Ann; Patterson, Burton R.; Homer, Eric R.

    2013-09-01

    Most materials microstructural evolution processes progress with multiple processes occurring simultaneously. In this work, we have concentrated on the processes that are active in nuclear materials, in particular, nuclear fuels. These processes are coarsening, nucleation, differential diffusion, phase transformation, radiation-induced defect formation and swelling, often with temperature gradients present. All these couple and contribute to evolution that is unique to nuclear fuels and materials. Hybrid model that combines elements from the Potts Monte Carlo, phase-field models and others have been developed to address these multiple physical processes. These models are described and applied to several processes in this report. An important feature of the models developed are that they are coded as applications within SPPARKS, a Sandiadeveloped framework for simulation at the mesoscale of microstructural evolution processes by kinetic Monte Carlo methods. This makes these codes readily accessible and adaptable for future applications.

  19. An approach to collective behavior in cell cultures: modeling and analysis of ECIS data

    NASA Astrophysics Data System (ADS)

    Rabson, David; Lafalce, Evan; Lovelady, Douglas; Lo, Chun-Min

    2011-03-01

    We review recent results in which statistical measures of noise in ECIS data distinguished healthy cell cultures from cancerous or poisoned ones: after subtracting the ``signal,'' the 1 /fα noise in the healthy cultures shows longer short-time and long-time correlations. We discuss application of an artificial neural network to detect the cancer signal, and we demonstrate a computational model of cell-cell communication that produces signals similar to those of the experimental data. The simulation is based on the q -state Potts model with inspiration from the Bak-Tang-Wiesenfeld sand-pile model. We view the level of organization larger than cells but smaller than organs or tissues as a kind of ``mesoscopic'' biological physics, in which few-body interactions dominate, and the experiments and computational model as ways of exploring this regime.

  20. An agent based multi-optional model for the diffusion of innovations

    NASA Astrophysics Data System (ADS)

    Laciana, Carlos E.; Oteiza-Aguirre, Nicolás

    2014-01-01

    We propose a model for the diffusion of several products competing in a common market based on the generalization of the Ising model of statistical mechanics (Potts model). Using an agent based implementation we analyze two problems: (i) a three options case, i.e. to adopt a product A, a product B, or non-adoption and (ii) a four option case, i.e. the adoption of product A, product B, both, or none. In the first case we analyze a launching strategy for one of the two products, which delays its launching with the objective of competing with improvements. Market shares reached by each product are then estimated at market saturation. Finally, simulations are carried out with varying degrees of social network topology, uncertainty, and population homogeneity.

  1. Bayesian approaches to spatial inference: Modelling and computational challenges and solutions

    NASA Astrophysics Data System (ADS)

    Moores, Matthew; Mengersen, Kerrie

    2014-12-01

    We discuss a range of Bayesian modelling approaches for spatial data and investigate some of the associated computational challenges. This paper commences with a brief review of Bayesian mixture models and Markov random fields, with enabling computational algorithms including Markov chain Monte Carlo (MCMC) and integrated nested Laplace approximation (INLA). Following this, we focus on the Potts model as a canonical approach, and discuss the challenge of estimating the inverse temperature parameter that controls the degree of spatial smoothing. We compare three approaches to addressing the doubly intractable nature of the likelihood, namely pseudo-likelihood, path sampling and the exchange algorithm. These techniques are applied to satellite data used to analyse water quality in the Great Barrier Reef.

  2. High-throughput detection of prostate cancer in histological sections using probabilistic pairwise Markov models.

    PubMed

    Monaco, James P; Tomaszewski, John E; Feldman, Michael D; Hagemann, Ian; Moradi, Mehdi; Mousavi, Parvin; Boag, Alexander; Davidson, Chris; Abolmaesumi, Purang; Madabhushi, Anant

    2010-08-01

    In this paper we present a high-throughput system for detecting regions of carcinoma of the prostate (CaP) in HSs from radical prostatectomies (RPs) using probabilistic pairwise Markov models (PPMMs), a novel type of Markov random field (MRF). At diagnostic resolution a digitized HS can contain 80Kx70K pixels - far too many for current automated Gleason grading algorithms to process. However, grading can be separated into two distinct steps: (1) detecting cancerous regions and (2) then grading these regions. The detection step does not require diagnostic resolution and can be performed much more quickly. Thus, we introduce a CaP detection system capable of analyzing an entire digitized whole-mount HS (2x1.75cm(2)) in under three minutes (on a desktop computer) while achieving a CaP detection sensitivity and specificity of 0.87 and 0.90, respectively. We obtain this high-throughput by tailoring the system to analyze the HSs at low resolution (8microm per pixel). This motivates the following algorithm: (Step 1) glands are segmented, (Step 2) the segmented glands are classified as malignant or benign, and (Step 3) the malignant glands are consolidated into continuous regions. The classification of individual glands leverages two features: gland size and the tendency for proximate glands to share the same class. The latter feature describes a spatial dependency which we model using a Markov prior. Typically, Markov priors are expressed as the product of potential functions. Unfortunately, potential functions are mathematical abstractions, and constructing priors through their selection becomes an ad hoc procedure, resulting in simplistic models such as the Potts. Addressing this problem, we introduce PPMMs which formulate priors in terms of probability density functions, allowing the creation of more sophisticated models. To demonstrate the efficacy of our CaP detection system and assess the advantages of using a PPMM prior instead of the Potts, we alternately

  3. High-Throughput Detection of Prostate Cancer in Histological Sections Using Probabilistic Pairwise Markov Models

    PubMed Central

    Monaco, James P.; Tomaszewski, John E.; Feldman, Michael D.; Hagemann, Ian; Moradi, Mehdi; Mousavi, Parvin; Boag, Alexander; Davidson, Chris; Abolmaesumi, Purang; Madabhushi, Anant

    2010-01-01

    In this paper we present a high-throughput system for detecting regions of carcinoma of the prostate (CaP) in HSs from radical prostatectomies (RPs) using probabilistic pairwise Markov models (PPMMs), a novel type of Markov random field (MRF). At diagnostic resolution a digitized HS can contain 80K×70K pixels — far too many for current automated Gleason grading algorithms to process. However, grading can be separated into two distinct steps: 1) detecting cancerous regions and 2) then grading these regions. The detection step does not require diagnostic resolution and can be performed much more quickly. Thus, we introduce a CaP detection system capable of analyzing an entire digitized whole-mount HS (2×1.75 cm2) in under three minutes (on a desktop computer) while achieving a CaP detection sensitivity and specificity of 0.87 and 0.90, respectively. We obtain this high-throughput by tailoring the system to analyze the HSs at low resolution (8 µm per pixel). This motivates the following algorithm: Step 1) glands are segmented, Step 2) the segmented glands are classified as malignant or benign, and Step 3) the malignant glands are consolidated into continuous regions. The classification of individual glands leverages two features: gland size and the tendency for proximate glands to share the same class. The latter feature describes a spatial dependency which we model using a Markov prior. Typically, Markov priors are expressed as the product of potential functions. Unfortunately, potential functions are mathematical abstractions, and constructing priors through their selection becomes an ad hoc procedure, resulting in simplistic models such as the Potts. Addressing this problem, we introduce PPMMs which formulate priors in terms of probability density functions, allowing the creation of more sophisticated models. To demonstrate the efficacy of our CaP detection system and assess the advantages of using a PPMM prior instead of the Potts, we alternately incorporate

  4. Multiscale dynamics of biological cells with chemotactic interactions: From a discrete stochastic model to a continuous description

    NASA Astrophysics Data System (ADS)

    Alber, Mark; Chen, Nan; Glimm, Tilmann; Lushnikov, Pavel M.

    2006-05-01

    The cellular Potts model (CPM) has been used for simulating various biological phenomena such as differential adhesion, fruiting body formation of the slime mold Dictyostelium discoideum, angiogenesis, cancer invasion, chondrogenesis in embryonic vertebrate limbs, and many others. We derive a continuous limit of a discrete one-dimensional CPM with the chemotactic interactions between cells in the form of a Fokker-Planck equation for the evolution of the cell probability density function. This equation is then reduced to the classical macroscopic Keller-Segel model. In particular, all coefficients of the Keller-Segel model are obtained from parameters of the CPM. Theoretical results are verified numerically by comparing Monte Carlo simulations for the CPM with numerics for the Keller-Segel model.

  5. Defect-phase-dynamics approach to statistical domain-growth problem of clock models

    NASA Technical Reports Server (NTRS)

    Kawasaki, K.

    1985-01-01

    The growth of statistical domains in quenched Ising-like p-state clock models with p = 3 or more is investigated theoretically, reformulating the analysis of Ohta et al. (1982) in terms of a phase variable and studying the dynamics of defects introduced into the phase field when the phase variable becomes multivalued. The resulting defect/phase domain-growth equation is applied to the interpretation of Monte Carlo simulations in two dimensions (Kaski and Gunton, 1983; Grest and Srolovitz, 1984), and problems encountered in the analysis of related Potts models are discussed. In the two-dimensional case, the problem is essentially that of a purely dissipative Coulomb gas, with a sq rt t growth law complicated by vertex-pinning effects at small t.

  6. Joint Segmentation and Deconvolution of Ultrasound Images Using a Hierarchical Bayesian Model Based on Generalized Gaussian Priors.

    PubMed

    Zhao, Ningning; Basarab, Adrian; Kouame, Denis; Tourneret, Jean-Yves

    2016-08-01

    This paper proposes a joint segmentation and deconvolution Bayesian method for medical ultrasound (US) images. Contrary to piecewise homogeneous images, US images exhibit heavy characteristic speckle patterns correlated with the tissue structures. The generalized Gaussian distribution (GGD) has been shown to be one of the most relevant distributions for characterizing the speckle in US images. Thus, we propose a GGD-Potts model defined by a label map coupling US image segmentation and deconvolution. The Bayesian estimators of the unknown model parameters, including the US image, the label map, and all the hyperparameters are difficult to be expressed in a closed form. Thus, we investigate a Gibbs sampler to generate samples distributed according to the posterior of interest. These generated samples are finally used to compute the Bayesian estimators of the unknown parameters. The performance of the proposed Bayesian model is compared with the existing approaches via several experiments conducted on realistic synthetic data and in vivo US images. PMID:27187959

  7. Proper encoding for snapshot-entropy scaling in two-dimensional classical spin models

    NASA Astrophysics Data System (ADS)

    Matsueda, Hiroaki; Ozaki, Dai

    2015-10-01

    We reexamine the snapshot entropy of the Ising and three-states Potts models on the L ×L square lattice. Focusing on how to encode the spin snapshot, we find that the entropy at Tc scales asymptotically as S ˜(1 /3 )lnL that strongly reminds us of the entanglement entropy in one-dimensional quantum critical systems. This finding seems to support that the snapshot entropy after the proper encoding is related to the holographic entanglement entropy. On the other hand, the anomalous scaling Sχ˜χηlnχ for the coarse-grained snapshot entropy holds even for the proper encoding. These features originate in the fact that the largest singular value of the snapshot matrix is regulated by the proper encoding.

  8. Metastates in Mean-Field Models with Random External Fields Generated by Markov Chains

    NASA Astrophysics Data System (ADS)

    Formentin, M.; Külske, C.; Reichenbachs, A.

    2012-01-01

    We extend the construction by Külske and Iacobelli of metastates in finite-state mean-field models in independent disorder to situations where the local disorder terms are a sample of an external ergodic Markov chain in equilibrium. We show that for non-degenerate Markov chains, the structure of the theorems is analogous to the case of i.i.d. variables when the limiting weights in the metastate are expressed with the aid of a CLT for the occupation time measure of the chain. As a new phenomenon we also show in a Potts example that for a degenerate non-reversible chain this CLT approximation is not enough, and that the metastate can have less symmetry than the symmetry of the interaction and a Gaussian approximation of disorder fluctuations would suggest.

  9. Bridges in the random-cluster model

    NASA Astrophysics Data System (ADS)

    Elçi, Eren Metin; Weigel, Martin; Fytas, Nikolaos G.

    2016-02-01

    The random-cluster model, a correlated bond percolation model, unifies a range of important models of statistical mechanics in one description, including independent bond percolation, the Potts model and uniform spanning trees. By introducing a classification of edges based on their relevance to the connectivity we study the stability of clusters in this model. We prove several exact relations for general graphs that allow us to derive unambiguously the finite-size scaling behavior of the density of bridges and non-bridges. For percolation, we are also able to characterize the point for which clusters become maximally fragile and show that it is connected to the concept of the bridge load. Combining our exact treatment with further results from conformal field theory, we uncover a surprising behavior of the (normalized) variance of the number of (non-)bridges, showing that it diverges in two dimensions below the value 4cos2 ⁡ (π /√{ 3}) = 0.2315891 ⋯ of the cluster coupling q. Finally, we show that a partial or complete pruning of bridges from clusters enables estimates of the backbone fractal dimension that are much less encumbered by finite-size corrections than more conventional approaches.

  10. Hierarchical max-flow segmentation framework for multi-atlas segmentation with Kohonen self-organizing map based Gaussian mixture modeling.

    PubMed

    Rajchl, Martin; Baxter, John S H; McLeod, A Jonathan; Yuan, Jing; Qiu, Wu; Peters, Terry M; Khan, Ali R

    2016-01-01

    The incorporation of intensity, spatial, and topological information into large-scale multi-region segmentation has been a topic of ongoing research in medical image analysis. Multi-region segmentation problems, such as segmentation of brain structures, pose unique challenges in image segmentation in which regions may not have a defined intensity, spatial, or topological distinction, but rely on a combination of the three. We propose a novel framework within the Advanced segmentation tools (ASETS)(2), which combines large-scale Gaussian mixture models trained via Kohonen self-organizing maps, with deformable registration, and a convex max-flow optimization algorithm incorporating region topology as a hierarchy or tree. Our framework is validated on two publicly available neuroimaging datasets, the OASIS and MRBrainS13 databases, against the more conventional Potts model, achieving more accurate segmentations. Each component is accelerated using general-purpose programming on graphics processing Units to ensure computational feasibility. PMID:26072170

  11. A MULTISCALE, CELL-BASED FRAMEWORK FOR MODELING CANCER DEVELOPMENT

    SciTech Connect

    JIANG, YI

    2007-01-16

    Cancer remains to be one of the leading causes of death due to diseases. We use a systems approach that combines mathematical modeling, numerical simulation, in vivo and in vitro experiments, to develop a predictive model that medical researchers can use to study and treat cancerous tumors. The multiscale, cell-based model includes intracellular regulations, cellular level dynamics and intercellular interactions, and extracellular level chemical dynamics. The intracellular level protein regulations and signaling pathways are described by Boolean networks. The cellular level growth and division dynamics, cellular adhesion and interaction with the extracellular matrix is described by a lattice Monte Carlo model (the Cellular Potts Model). The extracellular dynamics of the signaling molecules and metabolites are described by a system of reaction-diffusion equations. All three levels of the model are integrated through a hybrid parallel scheme into a high-performance simulation tool. The simulation results reproduce experimental data in both avasular tumors and tumor angiogenesis. By combining the model with experimental data to construct biologically accurate simulations of tumors and their vascular systems, this model will enable medical researchers to gain a deeper understanding of the cellular and molecular interactions associated with cancer progression and treatment.

  12. Study of the attractor structure of an agent-based sociological model

    NASA Astrophysics Data System (ADS)

    Timpanaro, André M.; Prado, Carmen P. C.

    2011-03-01

    The Sznajd model is a sociophysics model that is based in the Potts model, and used for describing opinion propagation in a society. It employs an agent-based approach and interaction rules favouring pairs of agreeing agents. It has been successfully employed in modeling some properties and scale features of both proportional and majority elections (see for instance the works of A. T. Bernardes and R. N. Costa Filho), but its stationary states are always consensus states. In order to explain more complicated behaviours, we have modified the bounded confidence idea (introduced before in other opinion models, like the Deffuant model), with the introduction of prejudices and biases (we called this modification confidence rules), and have adapted it to the discrete Sznajd model. This generalized Sznajd model is able to reproduce almost all of the previous versions of the Sznajd model, by using appropriate choices of parameters. We solved the attractor structure of the resulting model in a mean-field approach and made Monte Carlo simulations in a Barabási-Albert network. These simulations show great similarities with the mean-field, for the tested cases of 3 and 4 opinions. The dynamical systems approach that we devised allows for a deeper understanding of the potential of the Sznajd model as an opinion propagation model and can be easily extended to other models, like the voter model. Our modification of the bounded confidence rule can also be readily applied to other opinion propagation models.

  13. Monte Carlo simulation of classical spin models with chaotic billiards

    NASA Astrophysics Data System (ADS)

    Suzuki, Hideyuki

    2013-11-01

    It has recently been shown that the computing abilities of Boltzmann machines, or Ising spin-glass models, can be implemented by chaotic billiard dynamics without any use of random numbers. In this paper, we further numerically investigate the capabilities of the chaotic billiard dynamics as a deterministic alternative to random Monte Carlo methods by applying it to classical spin models in statistical physics. First, we verify that the billiard dynamics can yield samples that converge to the true distribution of the Ising model on a small lattice, and we show that it appears to have the same convergence rate as random Monte Carlo sampling. Second, we apply the billiard dynamics to finite-size scaling analysis of the critical behavior of the Ising model and show that the phase-transition point and the critical exponents are correctly obtained. Third, we extend the billiard dynamics to spins that take more than two states and show that it can be applied successfully to the Potts model. We also discuss the possibility of extensions to continuous-valued models such as the XY model.

  14. Observation of Rydberg blockade effects at very high n, n ~ 300 , using strontium n1F3 states

    NASA Astrophysics Data System (ADS)

    Zhang, Xinyue; Dunning, F. B.; Yoshida, Shuhei; Burgdörfer, Joachim

    2015-05-01

    Rydberg blockade at very high n, n ~ 300 , is examined using strontium n1F3 Rydberg atoms excited in a small volume defined by two tightly-focused crossed laser beams. Measurements of the number distribution of Rydberg atoms created show deviations from a Poisson distribution revealing sizeable blockade effects. The statistics of the number distribution are studied using a Monte Carlo method in which the interaction between strontium Rydberg atoms is evaluated by solving the Schrödinger equation within a two-active-electron model. The strength of blockade is analyzed in detail with respect to the alignment of two atoms relative to the laser polarizations. With careful control of the experimental parameters the probability for creating one, and only one, Rydberg atom, P(1) , in the excitation volume can be sufficiently large, P(1) > 0 . 6 , as to enable detailed studies of strongly-coupled Rydberg atom pairs. Research supported by the NSF, the Robert A. Welch Foundation, and the FWF (Austria).

  15. Simple model for multiple-choice collective decision making.

    PubMed

    Lee, Ching Hua; Lucas, Andrew

    2014-11-01

    We describe a simple model of heterogeneous, interacting agents making decisions between n≥2 discrete choices. For a special class of interactions, our model is the mean field description of random field Potts-like models and is effectively solved by finding the extrema of the average energy E per agent. In these cases, by studying the propagation of decision changes via avalanches, we argue that macroscopic dynamics is well captured by a gradient flow along E. We focus on the permutation symmetric case, where all n choices are (on average) the same, and spontaneous symmetry breaking (SSB) arises purely from cooperative social interactions. As examples, we show that bimodal heterogeneity naturally provides a mechanism for the spontaneous formation of hierarchies between decisions and that SSB is a preferred instability to discontinuous phase transitions between two symmetric points. Beyond the mean field limit, exponentially many stable equilibria emerge when we place this model on a graph of finite mean degree. We conclude with speculation on decision making with persistent collective oscillations. Throughout the paper, we emphasize analogies between methods of solution to our model and common intuition from diverse areas of physics, including statistical physics and electromagnetism. PMID:25493831

  16. Simple model for multiple-choice collective decision making

    NASA Astrophysics Data System (ADS)

    Lee, Ching Hua; Lucas, Andrew

    2014-11-01

    We describe a simple model of heterogeneous, interacting agents making decisions between n ≥2 discrete choices. For a special class of interactions, our model is the mean field description of random field Potts-like models and is effectively solved by finding the extrema of the average energy E per agent. In these cases, by studying the propagation of decision changes via avalanches, we argue that macroscopic dynamics is well captured by a gradient flow along E . We focus on the permutation symmetric case, where all n choices are (on average) the same, and spontaneous symmetry breaking (SSB) arises purely from cooperative social interactions. As examples, we show that bimodal heterogeneity naturally provides a mechanism for the spontaneous formation of hierarchies between decisions and that SSB is a preferred instability to discontinuous phase transitions between two symmetric points. Beyond the mean field limit, exponentially many stable equilibria emerge when we place this model on a graph of finite mean degree. We conclude with speculation on decision making with persistent collective oscillations. Throughout the paper, we emphasize analogies between methods of solution to our model and common intuition from diverse areas of physics, including statistical physics and electromagnetism.

  17. Building toy models of proteins using coevolutionary information

    NASA Astrophysics Data System (ADS)

    Cheng, Ryan; Raghunathan, Mohit; Onuchic, Jose

    2015-03-01

    Recent developments in global statistical methodologies have advanced the analysis of large collections of protein sequences for coevolutionary information. Coevolution between amino acids in a protein arises from compensatory mutations that are needed to maintain the stability or function of a protein over the course of evolution. This gives rise to quantifiable correlations between amino acid positions within the multiple sequence alignment of a protein family. Here, we use Direct Coupling Analysis (DCA) to infer a Potts model Hamiltonian governing the correlated mutations in a protein family to obtain the sequence-dependent interaction energies of a toy protein model. We demonstrate that this methodology predicts residue-residue interaction energies that are consistent with experimental mutational changes in protein stabilities as well as other computational methodologies. Furthermore, we demonstrate with several examples that DCA could be used to construct a structure-based model that quantitatively agrees with experimental data on folding mechanisms. This work serves as a potential framework for generating models of proteins that are enriched by evolutionary data that can potentially be used to engineer key functional motions and interactions in protein systems. This research has been supported by the NSF INSPIRE award MCB-1241332 and by the CTBP sponsored by the NSF (Grant PHY-1427654).

  18. Infrared and Microwave Spectra and Force Field of DBO: The Coriolis Interaction between the ν 1and ν 2+ ν 3States

    NASA Astrophysics Data System (ADS)

    Kawashima, Yoshiyuki; Colarusso, Pina; Zhang, K. Q.; Bernath, Peter; Hirota, Eizi

    1998-11-01

    The ν1and ν3bands of D11BO and the ν1band of D10BO were observed by using an infrared diode laser spectrometer. The DBO molecule was generated by an ac discharge in a mixture of BCl3, D2, O2, and He. As inferred previously, a strong Coriolis interaction was in fact found to take place between the ν1and ν2+ ν3states, and an analysis of the observed ν1spectra, which explicitly took into account this Coriolis interaction, predicted the pure rotational transition frequencies of DBO in the ν1state. Pure rotational lines were then detected by microwave spectroscopy, confirming the validity of the infrared assignment. In the microwave experiment DBO molecules were generated by a discharge in a mixture of B2D6and O2. The three fundamental bands and a hot band of D11BO, as well as the ν1and ν3bands of D10BO, were subsequently recorded in emission with a Fourier transform infrared spectrometer. DBO molecules were generated by the reaction of D2with HBO at temperatures above 800°C in a ceramic tube furnace. All of the observed spectra were simultaneously subjected to a least-squares analysis to obtain molecular parameters in the ground, ν1, ν2, ν3, and ν2+ ν3states. The results thus obtained improved the force field and molecular structure of the HBO/DBO molecules reported in a previous study (Y. Kawashima, Y. Endo, and E. Hirota, 1989,J. Mol. Spectrosc.133, 116-127).

  19. Entanglement Properties of a Quantum Lattice-Gas Model on Square and Triangular Ladders

    NASA Astrophysics Data System (ADS)

    Tanaka, Shu; Tamura, Ryo; Katsura, Hosho

    2014-03-01

    In this paper, we review the entanglement properties of a quantum lattice-gas model according to our previous paper [S. Tanaka, R. Tamura, and H. Katsura, Phys. Rev. A 86, 032326 (2012)]. The ground state of the model under consideration can be exactly obtained and expressed by the Rokhsar-Kivelson type quantum superposition. The reduced density matrices of the model on square and triangular ladders are related to the transfer matrices of the classical hard-square and hard-hexagon models, respectively. In our previous paper, we investigated the entanglement properties including the entanglement entropy, the entanglement spectrum, and the nested entanglement entropy. We found that the entanglement spectra are critical when parameters are chosen so that the corresponding classical model is critical. In order to further investigate the entanglement properties, we also considered the nested entanglement entropy. As a result, the entanglement properties of the model on square and triangular ladders are described by the critical phenomena of the Ising model and the three-state ferromagnetic Potts model in two dimension, respectively.

  20. Completely packed O(n) loop models and their relation with exactly solved coloring models.

    PubMed

    Wang, Yougang; Guo, Wenan; Blöte, Henk W J

    2015-03-01

    We investigate the completely packed O(n) loop model on the square lattice, and its generalization to an Eulerian graph model, which follows by including cubic vertices which connect the four incoming loop segments. This model includes crossing bonds as well. Our study was inspired by existing exact solutions of the so-called coloring model due to Schultz and Perk [Phys. Rev. Lett. 46, 629 (1981)], which is shown to be equivalent with our generalized loop model. We explore the physical properties and the phase diagram of this model by means of transfer-matrix calculations and finite-size scaling. The exact results, which include seven one-dimensional branches in the parameter space of our generalized loop model, are compared to our numerical results. The results for the phase behavior also extend to parts of the parameter space beyond the exactly solved subspaces. One of the exactly solved branches describes the case of nonintersecting loops and was already known to correspond with the ordering transition of the Potts model. Another exactly solved branch, describing a model with nonintersecting loops and cubic vertices, corresponds with a first-order, Ising-like phase transition for n>2. For 12 this branch is the locus of a first-order phase boundary between a phase with a hard-square, lattice-gas-like ordering and a phase dominated by cubic vertices. A mean-field argument explains the first-order nature of this transition. PMID:25871070

  1. Completely packed O (n ) loop models and their relation with exactly solved coloring models

    NASA Astrophysics Data System (ADS)

    Wang, Yougang; Guo, Wenan; Blöte, Henk W. J.

    2015-03-01

    We investigate the completely packed O (n ) loop model on the square lattice, and its generalization to an Eulerian graph model, which follows by including cubic vertices which connect the four incoming loop segments. This model includes crossing bonds as well. Our study was inspired by existing exact solutions of the so-called coloring model due to Schultz and Perk [Phys. Rev. Lett. 46, 629 (1981), 10.1103/PhysRevLett.46.629], which is shown to be equivalent with our generalized loop model. We explore the physical properties and the phase diagram of this model by means of transfer-matrix calculations and finite-size scaling. The exact results, which include seven one-dimensional branches in the parameter space of our generalized loop model, are compared to our numerical results. The results for the phase behavior also extend to parts of the parameter space beyond the exactly solved subspaces. One of the exactly solved branches describes the case of nonintersecting loops and was already known to correspond with the ordering transition of the Potts model. Another exactly solved branch, describing a model with nonintersecting loops and cubic vertices, corresponds with a first-order, Ising-like phase transition for n >2 . For 1 2 this branch is the locus of a first-order phase boundary between a phase with a hard-square, lattice-gas-like ordering and a phase dominated by cubic vertices. A mean-field argument explains the first-order nature of this transition.

  2. Duality methods in networks, computer science models, and disordered condensed matter systems

    NASA Astrophysics Data System (ADS)

    Mitchell, Joseph Dan

    In this thesis, I explore lattice independent duality and systems to which it can be applied. I first demonstrate classical duality on models in an external field, including the Ising, Potts, and x -- y models, showing in particular how this modifies duality to be lattice independent and applicable to networks. I then present a novel application of duality on the boolean satsifiability problem, one of the most important problems in computational complexity, through mapping to a low temperature Ising model. This establishes the equivalence between boolean satisfiability and a problem of enumerating the positive solutions to a Diophantine system of equations. I continue by combining duality with a prominent tool for models on networks, belief propagation, deriving a new message passing procedure, dual belief propagation. In the final part of my thesis, I shift to propose and examine a semiclassical model, the two-component Coulomb glass model, which can explain the giant magnetoresistance peak present in disordered films near a superconductor-insulator transition as the effect of competition between single particle and localized pair transport. I numerically analyze the density of states and transport properties of this model.

  3. Geometric entanglement and quantum phase transitions in two-dimensional quantum lattice models

    NASA Astrophysics Data System (ADS)

    Shi, Qian-Qian; Wang, Hong-Lei; Li, Sheng-Hao; Cho, Sam Young; Batchelor, Murray T.; Zhou, Huan-Qiang

    2016-06-01

    Geometric entanglement (GE), as a measure of multipartite entanglement, has been investigated as a universal tool to detect phase transitions in quantum many-body lattice models. In this paper we outline a systematic method to compute GE for two-dimensional (2D) quantum many-body lattice models based on the translational invariant structure of infinite projected entangled pair state (iPEPS) representations. By employing this method, the q -state quantum Potts model on the square lattice with q ∈{2 ,3 ,4 ,5 } is investigated as a prototypical example. Further, we have explored three 2D Heisenberg models: the antiferromagnetic spin-1/2 X X X and anisotropic X Y X models in an external magnetic field, and the antiferromagnetic spin-1 X X Z model. We find that continuous GE does not guarantee a continuous phase transition across a phase transition point. We observe and thus classify three different types of continuous GE across a phase transition point: (i) GE is continuous with maximum value at the transition point and the phase transition is continuous, (ii) GE is continuous with maximum value at the transition point but the phase transition is discontinuous, and (iii) GE is continuous with nonmaximum value at the transition point and the phase transition is continuous. For the models under consideration, we find that the second and the third types are related to a point of dual symmetry and a fully polarized phase, respectively.

  4. Ashkin-Teller model and diverse opinion phase transitions on multiplex networks

    NASA Astrophysics Data System (ADS)

    Jang, S.; Lee, J. S.; Hwang, S.; Kahng, B.

    2015-08-01

    Multiplex networks (MNs) have become a platform of recent research in network sciences because networks in many real-world systems interact and function together. One of the main scientific issues in MNs is how the interdependence changes the emerging patterns or phase transitions. Until now, studies of such an issue have concentrated on cluster-breakdown phenomena, aiming to understand the resilience of the system under random failures of edges. These studies have revealed that various phase transition (PT) types emerge in MNs. However, such studies are rather limited to percolation-related problems, i.e., the limit q →1 of the q -state Potts model. Thus, a systematic study of opinion formation in social networks with the effect of interdependence between different social communities, which may be seen as the study of the emerging pattern of the Ising model on MNs, is needed. Here we study a well-known spin model called the Ashkin-Teller (AT) model in scale-free networks. The AT model can be regarded as a model for interacting systems between two species of Ising spins placed on respective layers in double-layer networks. Our study shows that, depending on the interlayer coupling strength and a network topology, unconventional PT patterns can also emerge in interaction-based phenomena: continuous, discontinuous, successive, and mixed-order PTs and a continuous PT not satisfying the scaling relation. The origins of such rich PT patterns are elucidated in the framework of Landau-Ginzburg theory.

  5. Dynamical systems approach to the study of a sociophysics agent-based model

    SciTech Connect

    Timpanaro, Andre M.; Prado, Carmen P. C.

    2011-03-24

    The Sznajd model is a Potts-like model that has been studied in the context of sociophysics [1,2](where spins are interpreted as opinions). In a recent work [3], we generalized the Sznajd model to include assymetric interactions between the spins (interpreted as biases towards opinions) and used dynamical systems techniques to tackle its mean-field version, given by the flow: {eta}{sub {sigma}} = {Sigma}{sub {sigma}}'{sup M} = 1{eta}{sub {sigma}}{eta}{sigma}'({eta}{sub {sigma}}{rho}{sigma}'{yields}{sigma}-{sigma}'{rho}{sigma}{yields}{sigma}').Where hs is the proportion of agents with opinion (spin){sigma}', M is the number of opinions and {sigma}'{yields}{sigma}' is the probability weight for an agent with opinion {sigma} being convinced by another agent with opinion {sigma}'. We made Monte Carlo simulations of the model in a complex network (using Barabasi-Albert networks [4]) and they displayed the same attractors than the mean-field. Using linear stability analysis, we were able to determine the mean-field attractor structure analytically and to show that it has connections with well known graph theory problems (maximal independent sets and positive fluxes in directed graphs). Our dynamical systems approach is quite simple and can be used also in other models, like the voter model.

  6. Dynamical systems approach to the study of a sociophysics agent-based model

    NASA Astrophysics Data System (ADS)

    Timpanaro, André M.; Prado, Carmen P. C.

    2011-03-01

    The Sznajd model is a Potts-like model that has been studied in the context of sociophysics [1,2] (where spins are interpreted as opinions). In a recent work [3], we generalized the Sznajd model to include assymetric interactions between the spins (interpreted as biases towards opinions) and used dynamical systems techniques to tackle its mean-field version, given by the flow: ησ = ∑ σ' = 1Mησησ'(ησρσ'→σ-σ'ρσ→σ'). Where hs is the proportion of agents with opinion (spin) σ', M is the number of opinions and σ'→σ' is the probability weight for an agent with opinion σ being convinced by another agent with opinion σ'. We made Monte Carlo simulations of the model in a complex network (using Barabási-Albert networks [4]) and they displayed the same attractors than the mean-field. Using linear stability analysis, we were able to determine the mean-field attractor structure analytically and to show that it has connections with well known graph theory problems (maximal independent sets and positive fluxes in directed graphs). Our dynamical systems approach is quite simple and can be used also in other models, like the voter model.

  7. Ashkin-Teller model and diverse opinion phase transitions on multiplex networks.

    PubMed

    Jang, S; Lee, J S; Hwang, S; Kahng, B

    2015-08-01

    Multiplex networks (MNs) have become a platform of recent research in network sciences because networks in many real-world systems interact and function together. One of the main scientific issues in MNs is how the interdependence changes the emerging patterns or phase transitions. Until now, studies of such an issue have concentrated on cluster-breakdown phenomena, aiming to understand the resilience of the system under random failures of edges. These studies have revealed that various phase transition (PT) types emerge in MNs. However, such studies are rather limited to percolation-related problems, i.e., the limit q→1 of the q-state Potts model. Thus, a systematic study of opinion formation in social networks with the effect of interdependence between different social communities, which may be seen as the study of the emerging pattern of the Ising model on MNs, is needed. Here we study a well-known spin model called the Ashkin-Teller (AT) model in scale-free networks. The AT model can be regarded as a model for interacting systems between two species of Ising spins placed on respective layers in double-layer networks. Our study shows that, depending on the interlayer coupling strength and a network topology, unconventional PT patterns can also emerge in interaction-based phenomena: continuous, discontinuous, successive, and mixed-order PTs and a continuous PT not satisfying the scaling relation. The origins of such rich PT patterns are elucidated in the framework of Landau-Ginzburg theory. PMID:26382347

  8. Phase transition in a spatial Lotka-Volterra model

    SciTech Connect

    Szabo, Gyorgy; Czaran, Tamas

    2001-06-01

    Spatial evolution is investigated in a simulated system of nine competing and mutating bacterium strains, which mimics the biochemical war among bacteria capable of producing two different bacteriocins (toxins) at most. Random sequential dynamics on a square lattice is governed by very symmetrical transition rules for neighborhood invasions of sensitive strains by killers, killers by resistants, and resistants by sensitives. The community of the nine possible toxicity/resistance types undergoes a critical phase transition as the uniform transmutation rates between the types decreases below a critical value P{sub c} above that all the nine types of strains coexist with equal frequencies. Passing the critical mutation rate from above, the system collapses into one of three topologically identical (degenerated) states, each consisting of three strain types. Of the three possible final states each accrues with equal probability and all three maintain themselves in a self-organizing polydomain structure via cyclic invasions. Our Monte Carlo simulations support that this symmetry-breaking transition belongs to the universality class of the three-state Potts model.

  9. Phase transition in a spatial Lotka-Volterra model

    NASA Astrophysics Data System (ADS)

    Szabó, György; Czárán, Tamás

    2001-06-01

    Spatial evolution is investigated in a simulated system of nine competing and mutating bacterium strains, which mimics the biochemical war among bacteria capable of producing two different bacteriocins (toxins) at most. Random sequential dynamics on a square lattice is governed by very symmetrical transition rules for neighborhood invasions of sensitive strains by killers, killers by resistants, and resistants by sensitives. The community of the nine possible toxicity/resistance types undergoes a critical phase transition as the uniform transmutation rates between the types decreases below a critical value Pc above that all the nine types of strains coexist with equal frequencies. Passing the critical mutation rate from above, the system collapses into one of three topologically identical (degenerated) states, each consisting of three strain types. Of the three possible final states each accrues with equal probability and all three maintain themselves in a self-organizing polydomain structure via cyclic invasions. Our Monte Carlo simulations support that this symmetry-breaking transition belongs to the universality class of the three-state Potts model.

  10. Modeling Of Microstructure Evolution Of BCC Metals Subjected To Severe Plastic Deformation

    SciTech Connect

    Svyetlichnyy, Dmytro; Majta, Janusz; Muszka, Krzysztof; Lach, Lukasz

    2011-01-17

    Prediction of microstructure evolution and properties of ultrafine-grained materials is one of the most significant, current problems in materials science. Several advanced methods of analysis can be applied for this issue: vertex models, phase field models, Monte Carlo Potts, finite element method (FEM) discrete element method (DEM) and finally cellular automata (CA). The main asset of the CA is ability for a close correlation of the microstructure with the mechanical properties in micro- and meso-scale simulation. Joining CA with the DEM undoubtedly improves accuracy of modeling of coupled phenomena during the innovative forming processes in both micro- and macro-scale. Deformation in micro-scale shows anisotropy, which connected with that the polycrystalline material contains grains with different crystallographic orientation, and grain deformation is depended from configuration of directions of main stresses and axis of grain. Then, CA and DEM must be joint solutions of crystal plasticity theory. In the present model, deformation in macro-scale is transferred to meso-sale, where a block contains several, score or hundreds grains, and then is applied in micro-scale to each grain. Creation of low-angle boundaries and their development into high-angle boundaries are simulated by the cellular automata on the base of calculations using finite element method and crystal plasticity theory. The idea proposed in this study and particular solutions are discussed for the case of ultrafine-grained low-carbon steel.

  11. Genetic demixing and evolution in linear stepping stone models

    NASA Astrophysics Data System (ADS)

    Korolev, K. S.; Avlund, Mikkel; Hallatschek, Oskar; Nelson, David R.

    2010-04-01

    Results for mutation, selection, genetic drift, and migration in a one-dimensional continuous population are reviewed and extended. The population is described by a continuous limit of the stepping stone model, which leads to the stochastic Fisher-Kolmogorov-Petrovsky-Piscounov equation with additional terms describing mutations. Although the stepping stone model was first proposed for population genetics, it is closely related to “voter models” of interest in nonequilibrium statistical mechanics. The stepping stone model can also be regarded as an approximation to the dynamics of a thin layer of actively growing pioneers at the frontier of a colony of micro-organisms undergoing a range expansion on a Petri dish. The population tends to segregate into monoallelic domains. This segregation slows down genetic drift and selection because these two evolutionary forces can only act at the boundaries between the domains; the effects of mutation, however, are not significantly affected by the segregation. Although fixation in the neutral well-mixed (or “zero-dimensional”) model occurs exponentially in time, it occurs only algebraically fast in the one-dimensional model. An unusual sublinear increase is also found in the variance of the spatially averaged allele frequency with time. If selection is weak, selective sweeps occur exponentially fast in both well-mixed and one-dimensional populations, but the time constants are different. The relatively unexplored problem of evolutionary dynamics at the edge of an expanding circular colony is studied as well. Also reviewed are how the observed patterns of genetic diversity can be used for statistical inference and the differences are highlighted between the well-mixed and one-dimensional models. Although the focus is on two alleles or variants, q -allele Potts-like models of gene segregation are considered as well. Most of the analytical results are checked with simulations and could be tested against recent spatial

  12. Spatial Modeling of Drug Delivery Routes for Treatment of Disseminated Ovarian Cancer.

    PubMed

    Winner, Kimberly R Kanigel; Steinkamp, Mara P; Lee, Rebecca J; Swat, Maciej; Muller, Carolyn Y; Moses, Melanie E; Jiang, Yi; Wilson, Bridget S

    2016-03-15

    In ovarian cancer, metastasis is typically confined to the peritoneum. Surgical removal of the primary tumor and macroscopic secondary tumors is a common practice, but more effective strategies are needed to target microscopic spheroids persisting in the peritoneal fluid after debulking surgery. To treat this residual disease, therapeutic agents can be administered by either intravenous or intraperitoneal infusion. Here, we describe the use of a cellular Potts model to compare tumor penetration of two classes of drugs (cisplatin and pertuzumab) when delivered by these two alternative routes. The model considers the primary route when the drug is administered either intravenously or intraperitoneally, as well as the subsequent exchange into the other delivery volume as a secondary route. By accounting for these dynamics, the model revealed that intraperitoneal infusion is the markedly superior route for delivery of both small-molecule and antibody therapies into microscopic, avascular tumors typical of patients with ascites. Small tumors attached to peritoneal organs, with vascularity ranging from 2% to 10%, also show enhanced drug delivery via the intraperitoneal route, even though tumor vessels can act as sinks during the dissemination of small molecules. Furthermore, we assessed the ability of the antibody to enter the tumor by in silico and in vivo methods and suggest that optimization of antibody delivery is an important criterion underlying the efficacy of these and other biologics. The use of both delivery routes may provide the best total coverage of tumors, depending on their size and vascularity. PMID:26719526

  13. Domain-size heterogeneity in the Ising model: Geometrical and thermal transitions.

    PubMed

    de la Rocha, André R; de Oliveira, Paulo Murilo C; Arenzon, Jeferson J

    2015-04-01

    A measure of cluster size heterogeneity (H), introduced by Lee et al. [Phys. Rev. E 84, 020101 (2011)] in the context of explosive percolation, was recently applied to random percolation and to domains of parallel spins in the Ising and Potts models. It is defined as the average number of different domain sizes in a given configuration and a new exponent was introduced to explain its scaling with the size of the system. In thermal spin models, however, physical clusters take into account the temperature-dependent correlation between neighboring spins and encode the critical properties of the phase transition. We here extend the measure of H to these clusters and, moreover, present new results for the geometric domains for both d=2 and 3. We show that the heterogeneity associated with geometric domains has a previously unnoticed double peak, thus being able to detect both the thermal and percolative transitions. An alternative interpretation for the scaling of H that does not introduce a new exponent is also proposed. PMID:25974445

  14. Domain-size heterogeneity in the Ising model: Geometrical and thermal transitions

    NASA Astrophysics Data System (ADS)

    de la Rocha, André R.; de Oliveira, Paulo Murilo C.; Arenzon, Jeferson J.

    2015-04-01

    A measure of cluster size heterogeneity (H ), introduced by Lee et al. [Phys. Rev. E 84, 020101 (2011), 10.1103/PhysRevE.84.020101] in the context of explosive percolation, was recently applied to random percolation and to domains of parallel spins in the Ising and Potts models. It is defined as the average number of different domain sizes in a given configuration and a new exponent was introduced to explain its scaling with the size of the system. In thermal spin models, however, physical clusters take into account the temperature-dependent correlation between neighboring spins and encode the critical properties of the phase transition. We here extend the measure of H to these clusters and, moreover, present new results for the geometric domains for both d =2 and 3. We show that the heterogeneity associated with geometric domains has a previously unnoticed double peak, thus being able to detect both the thermal and percolative transitions. An alternative interpretation for the scaling of H that does not introduce a new exponent is also proposed.

  15. Investigation of SIBM driven recrystallization in alpha Zirconium based on EBSD data and Monte Carlo modeling

    NASA Astrophysics Data System (ADS)

    Jedrychowski, M.; Bacroix, B.; Salman, O. U.; Tarasiuk, J.; Wronski, S.

    2015-08-01

    The work focuses on the influence of moderate plastic deformation on subsequent partial recrystallization of hexagonal zirconium (Zr702). In the considered case, strain induced boundary migration (SIBM) is assumed to be the dominating recrystallization mechanism. This hypothesis is analyzed and tested in detail using experimental EBSD-OIM data and Monte Carlo computer simulations. An EBSD investigation is performed on zirconium samples, which were channel-die compressed in two perpendicular directions: normal direction (ND) and transverse direction (TD) of the initial material sheet. The maximal applied strain was below 17%. Then, samples were briefly annealed in order to achieve a partly recrystallized state. Obtained EBSD data were analyzed in terms of texture evolution associated with a microstructural characterization, including: kernel average misorientation (KAM), grain orientation spread (GOS), twinning, grain size distributions, description of grain boundary regions. In parallel, Monte Carlo Potts model combined with experimental microstructures was employed in order to verify two main recrystallization scenarios: SIBM driven growth from deformed sub-grains and classical growth of recrystallization nuclei. It is concluded that simulation results provided by the SIBM model are in a good agreement with experimental data in terms of texture as well as microstructural evolution.

  16. Synergy of cell–cell repulsion and vacuolation in a computational model of lumen formation

    PubMed Central

    Boas, Sonja E. M.; Merks, Roeland M. H.

    2014-01-01

    A key step in blood vessel development (angiogenesis) is lumen formation: the hollowing of vessels for blood perfusion. Two alternative lumen formation mechanisms are suggested to function in different types of blood vessels. The vacuolation mechanism is suggested for lumen formation in small vessels by coalescence of intracellular vacuoles, a view that was extended to extracellular lumen formation by exocytosis of vacuoles. The cell–cell repulsion mechanism is suggested to initiate extracellular lumen formation in large vessels by active repulsion of adjacent cells, and active cell shape changes extend the lumen. We used an agent-based computer model, based on the cellular Potts model, to compare and study both mechanisms separately and combined. An extensive sensitivity analysis shows that each of the mechanisms on its own can produce lumens in a narrow region of parameter space. However, combining both mechanisms makes lumen formation much more robust to the values of the parameters, suggesting that the mechanisms may work synergistically and operate in parallel, rather than in different vessel types. PMID:24430123

  17. Role of further-neighbor interactions in modulating the critical behavior of the Ising model with frustration.

    PubMed

    Liu, R M; Zhuo, W Z; Dong, S; Lu, X B; Gao, X S; Qin, M H; Liu, J-M

    2016-03-01

    In this work, we investigate the phase transitions and critical behaviors of the frustrated J(1)-J(2)-J(3) Ising model on the square lattice using Monte Carlo simulations, and particular attention goes to the effect of the second-next-nearest-neighbor interaction J(3) on the phase transition from a disordered state to the single stripe antiferromagnetic state. A continuous Ashkin-Teller-like transition behavior in a certain range of J(3) is identified, while the four-state Potts-critical end point [J(3)/J(1)](C) is estimated based on the analytic method reported in earlier work [Jin, Sen, and Sandvik, Phys. Rev. Lett. 108, 045702 (2012)]. It is suggested that the interaction J(3) can tune the transition temperature and in turn modulate the critical behaviors of the frustrated model. Furthermore, it is revealed that an antiferromagnetic J(3) can stabilize the staggered dimer state via a phase transition of strong first-order character. PMID:27078299

  18. Computer simulation of topological evolution in 2-d grain growth using a continuum diffuse-interface field model

    SciTech Connect

    Fan, D.; Geng, C.; Chen, L.Q.

    1997-03-01

    The local kinetics and topological phenomena during normal grain growth were studied in two dimensions by computer simulations employing a continuum diffuse-interface field model. The relationships between topological class and individual grain growth kinetics were examined, and compared with results obtained previously from analytical theories, experimental results and Monte Carlo simulations. It was shown that both the grain-size and grain-shape (side) distributions are time-invariant and the linear relationship between the mean radii of individual grains and topological class n was reproduced. The moments of the shape distribution were determined, and the differences among the data from soap froth. Potts model and the present simulation were discussed. In the limit when the grain size goes to zero, the average number of grain edges per grain is shown to be between 4 and 5, implying the direct vanishing of 4- and 5-sided grains, which seems to be consistent with recent experimental observations on thin films. Based on the simulation results, the conditions for the applicability of the familiar Mullins-Von Neumann law and the Hillert`s equation were discussed.

  19. Modeling

    SciTech Connect

    Loth, E.; Tryggvason, G.; Tsuji, Y.; Elghobashi, S. E.; Crowe, Clayton T.; Berlemont, A.; Reeks, M.; Simonin, O.; Frank, Th; Onishi, Yasuo; Van Wachem, B.

    2005-09-01

    Slurry flows occur in many circumstances, including chemical manufacturing processes, pipeline transfer of coal, sand, and minerals; mud flows; and disposal of dredged materials. In this section we discuss slurry flow applications related to radioactive waste management. The Hanford tank waste solids and interstitial liquids will be mixed to form a slurry so it can be pumped out for retrieval and treatment. The waste is very complex chemically and physically. The ARIEL code is used to model the chemical interactions and fluid dynamics of the waste.

  20. Statistical Models, Yang-Baxter Equation and Related Topics - Proceedings of the Satellite MEeting of STATPHYS-19; Symmetry, Statistical, Mechanical Models and Applications - Proceedings of the Seventh Nankai Workshop

    NASA Astrophysics Data System (ADS)

    Ge, M. L.; et al.

    1996-09-01

    The Table of Contents for the full book PDF is as follows: * Preface * Part I: Satellite Meeting of STATPHYS-19 * Boundary Yang-Baxter in the RSOS/SOS Representation * Quantum Domains in Ferromagnetic Anisotropic Heisenberg Chains * The Generalized Chiral Clock Model and its Phase Diagram * Algebraic Solution of the Coincidence Problem for Crystals and Quasicrystals * Reflection Equations and Surface Critical Phenomena * Fully Packed Loop Models * Quantum Field Theories in terms of Group-Valued Local Fields: An Overview * C-Statiscal Transition Transforms of the Heisenberg Spin Chain and Braided Symmetry * U(1)-Invariant Local and Integrable Lattice Formulation of the Massive Thirring Model * Corner Transfer Matrices and Novel Polynomials * Rigorous and Numerical Results on Two-Dimensional Oriented Self-Avoiding Walks * The Price for Quantum Group Symmetry: Chiral Versus 2D WZNW Model * Integrable Zn-Chiral Potts Model : The Missing Rapidity-Momentum Relation * Dilute Algebras and Solvable Lattice Models * Falicov-Kimball Model: Ground States and Flux Phase Problem * Mutual Exclusion Statistics in the Exactly Solvable Model of the Mott Metal-Insulator Transition * Quantum Group and the Hofstadter Problem * Domain Walls in the Spin-S Quantum Ising Chain * Quantization of Nonultralocal Models - Generalization of the Theorem for the Multiple Coproduct * Multipoint Functions(Form-factors) of Quantum sine-Gordon Field with Boundary * Three-Dimensional Vertex Model * Probability of Phase Separation and Two Point Temperature Correlation Functions for the Bose Gas with Delta Interaction * On the Fundamental Invariant of the Hecke Algebra Hn(q) * Ternary Z3-Graded Algebras and New Gauge Theories * Thermodynamics of Integrable Quantum Chains : Free Energy and Correlation Lengths * Quantum Integrable Systems and Classical Discrete Nonlinear Dynamics * Quantum Jacobi-Trudi Formula and Analytic Bethe Ansatz * On Boundary Condition of Single Particle and the Spectrum of Many

  1. Electron transfer pathways from the S2-states to the S3-states either after a Ca2+/Sr2+ or a Cl-/I- exchange in Photosystem II from Thermosynechococcus elongatus.

    PubMed

    Boussac, Alain; Rutherford, A William; Sugiura, Miwa

    2015-01-01

    The site for water oxidation in Photosystem II (PSII) goes through five sequential oxidation states (S0 to S4) before O2 is evolved. It consists of a Mn4CaO5-cluster close to a redox-active tyrosine residue (YZ). Cl- is also required for enzyme activity. By using EPR spectroscopy it has been shown that both Ca2+/Sr2+ exchange and Cl-/I- exchange perturb the proportions of centers showing high (S=5/2) and low spin (S=1/2) forms of the S2-state. The S3-state was also found to be heterogeneous with: i) a S=3 form that is detectable by EPR and not sensitive to near-infrared light; and ii) a form that is not EPR visible but in which Mn photochemistry occurs resulting in the formation of a (S2YZ)' split EPR signal upon near-infrared illumination. In Sr/Cl-PSII, the high spin (S=5/2) form of S2 shows a marked heterogeneity with a g=4.3 form generated at low temperature that converts to a relaxed form at g=4.9 at higher temperatures. The high spin g=4.9 form can then progress to the EPR detectable form of S3 at temperatures as low as 180K whereas the low spin (S=1/2) S2-state can only advance to the S3 state at temperatures≥235 K. Both of the two S2 configurations and the two S3 configurations are each shown to be in equilibrium at ≥235 K but not at 198 K. Since both S2 configurations are formed at 198 K, they likely arise from two specific populations of S1. The existence of heterogeneous populations in S1, S2 and S3 states may be related to the structural flexibility associated with the positioning of the oxygen O5 within the cluster highlighted in computational approaches and which has been linked to substrate exchange. These data are discussed in the context of recent in silico studies of the electron transfer pathways between the S2-state(s) and the S3-state(s). PMID:25843552

  2. Stepwise positional-orientational order and the multicritical-multistructural global phase diagram of the s =3 /2 Ising model from renormalization-group theory

    NASA Astrophysics Data System (ADS)

    Yunus, ćaǧın; Renklioǧlu, Başak; Keskin, Mustafa; Berker, A. Nihat

    2016-06-01

    The spin-3/2 Ising model, with nearest-neighbor interactions only, is the prototypical system with two different ordering species, with concentrations regulated by a chemical potential. Its global phase diagram, obtained in d =3 by renormalization-group theory in the Migdal-Kadanoff approximation or equivalently as an exact solution of a d =3 hierarchical lattice, with flows subtended by 40 different fixed points, presents a very rich structure containing eight different ordered and disordered phases, with more than 14 different types of phase diagrams in temperature and chemical potential. It exhibits phases with orientational and/or positional order. It also exhibits quintuple phase transition reentrances. Universality of critical exponents is conserved across different renormalization-group flow basins via redundant fixed points. One of the phase diagrams contains a plastic crystal sequence, with positional and orientational ordering encountered consecutively as temperature is lowered. The global phase diagram also contains double critical points, first-order and critical lines between two ordered phases, critical end points, usual and unusual (inverted) bicritical points, tricritical points, multiple tetracritical points, and zero-temperature criticality and bicriticality. The four-state Potts permutation-symmetric subspace is contained in this model.

  3. La structure de Jordan des matrices de transfert des modeles de boucles et la relation avec les hamiltoniens XXZ

    NASA Astrophysics Data System (ADS)

    Morin-Duchesne, Alexi

    Lattice models such as percolation, the Ising model and the Potts model are useful for the description of phase transitions in two dimensions. Finding analytical solutions is done by calculating the partition function, which in turn requires finding eigenvalues of transfer matrices. At the critical point, the two dimensional statistical models are invariant under conformal transformations and the construction of rational conformal field theories, as the continuum limit of these lattice models, allows one to compute the partition function at the critical point. Many researchers think however that the paradigm of rational conformal conformal field theories can be extended to include models with non diagonalizable transfer matrices. These models would then be described, in the scaling limit, by logarithmic conformal field theories and the representations of the Virasoro algebra coming into play would be indecomposable. We recall the construction of the double-row transfer matrix DN (λ, u) of the Fortuin-Kasteleyn model, seen as an element of the Temperley-Lieb algebra. This transfer matrix comes into play in physical theories through its representation in link modules (or standard modules). The vector space on which this representation acts decomposes into sectors labelled by a physical parameter d, the number of defects, which remains constant or decreases in the link representations. This thesis is devoted to the identification of the Jordan structure of DN(λ, u) in the link representations. The parameter β = 2 cos λ = -(q + q-1) fixes the theory : for instance β = 1 for percolation and 2 for the Ising model. On the geometry of the strip with open boundary conditions, we show that DN(λ, u) has the same Jordan blocks as its highest Fourier coefficient, FN. We study the non-diagonalizability of FN through the divergences of some of the eigenstates of ρ(F N) that appear at the critical values of λ. The Jordan cells we find in ρ(DN(λ, u)) have rank 2 and

  4. 18 CFR 740.3 - State applications.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 18 Conservation of Power and Water Resources 2 2012-04-01 2012-04-01 false State applications. 740.3 Section 740.3 Conservation of Power and Water Resources WATER RESOURCES COUNCIL STATE WATER... for completing the application; (2) The criteria to be used by the Council in assessing need for...

  5. 18 CFR 740.3 - State applications.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 18 Conservation of Power and Water Resources 2 2013-04-01 2012-04-01 true State applications. 740.3 Section 740.3 Conservation of Power and Water Resources WATER RESOURCES COUNCIL STATE WATER... for completing the application; (2) The criteria to be used by the Council in assessing need for...

  6. 18 CFR 740.3 - State applications.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 18 Conservation of Power and Water Resources 2 2014-04-01 2014-04-01 false State applications. 740.3 Section 740.3 Conservation of Power and Water Resources WATER RESOURCES COUNCIL STATE WATER... for completing the application; (2) The criteria to be used by the Council in assessing need for...

  7. 18 CFR 740.3 - State applications.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 18 Conservation of Power and Water Resources 2 2011-04-01 2011-04-01 false State applications. 740.3 Section 740.3 Conservation of Power and Water Resources WATER RESOURCES COUNCIL STATE WATER... for completing the application; (2) The criteria to be used by the Council in assessing need for...

  8. 18 CFR 740.3 - State applications.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 18 Conservation of Power and Water Resources 2 2010-04-01 2010-04-01 false State applications. 740.3 Section 740.3 Conservation of Power and Water Resources WATER RESOURCES COUNCIL STATE WATER... for completing the application; (2) The criteria to be used by the Council in assessing need for...

  9. Kinetic model of particle-inhibited grain growth

    NASA Astrophysics Data System (ADS)

    Thompson, Gary Scott

    made in 2-D and 3-D Monte Carlo-Potts Model simulations, it was concluded that the decrease in growth rate constant was most likely due to the removal of grain boundary curvature by particles.

  10. A Framework for Efficient Structured Max-Margin Learning of High-Order MRF Models.

    PubMed

    Komodakis, Nikos; Xiang, Bo; Paragios, Nikos

    2015-07-01

    We present a very general algorithm for structured prediction learning that is able to efficiently handle discrete MRFs/CRFs (including both pairwise and higher-order models) so long as they can admit a decomposition into tractable subproblems. At its core, it relies on a dual decomposition principle that has been recently employed in the task of MRF optimization. By properly combining such an approach with a max-margin learning method, the proposed framework manages to reduce the training of a complex high-order MRF to the parallel training of a series of simple slave MRFs that are much easier to handle. This leads to a very efficient and general learning scheme that relies on solid mathematical principles. We thoroughly analyze its theoretical properties, and also show that it can yield learning algorithms of increasing accuracy since it naturally allows a hierarchy of convex relaxations to be used for loss-augmented MAP-MRF inference within a max-margin learning approach. Furthermore, it can be easily adapted to take advantage of the special structure that may be present in a given class of MRFs. We demonstrate the generality and flexibility of our approach by testing it on a variety of scenarios, including training of pairwise and higher-order MRFs, training by using different types of regularizers and/or different types of dissimilarity loss functions, as well as by learning of appropriate models for a variety of vision tasks (including high-order models for compact pose-invariant shape priors, knowledge-based segmentation, image denoising, stereo matching as well as high-order Potts MRFs). PMID:26352450

  11. Lattice models and integrability: a special issue in honour of F Y Wu

    NASA Astrophysics Data System (ADS)

    Guttmann, A. J.; Jacobsen, J. L.

    2012-12-01

    published in the April issue of Physical Review Letters (PRL) of the same year [4], and in September 1967, Wu moved to Northeastern University to join Lieb's group. Wu taught at Northeastern for 39 years until his retirement in 2006 as the Matthews Distinguished University Professor of Physics. Over the years, Wu has published more than 230 papers and monographs, and he continues to publish after retirement. Most of his research since 1967 is in exact and rigorous analyses of lattice models and integrable systems, which is the theme of this special issue. In 1968, after Wu's arrival at Northeastern, Lieb and Wu obtained the exact solution of the ground state of the one-dimensional Hubbard model and published the result in PRL [5], a work which has since become highly important after the advent of high-temperature superconductivity. This Lieb-Wu paper and Wu's 1982 review of the Potts model in Reviews of Modern Physics [37] are among the most cited papers in condensed matter physics. Later in 1968 Lieb departed Northeastern for MIT. As a result, the full version of the solution was not published until 34 years later [38] when Lieb and Wu collaborated to work on the manuscript on the occasion of Wu's 70th birthday. Wu spent the summer of 1968 at Stony Brook as the guest of C N Yang. Working with Yang's student, C Fan, he extended the Pfaffian solution of the Ising model to general lattices and termed such models 'free-fermion', a term now in common use [6]. In 1972, Wu visited R J Baxter, whom he had met earlier in 1968 at MIT, in Canberra, Australia, with the support of a Fulbright grant. They solved the triangular-lattice Ising model with 3-spin interactions [7], a model now known as the Baxter-Wu model. It was an ideal collaboration. While Baxter derived the solution algebraically, Wu used graphical methods to reduce the problem to an Ashkin-Teller model, which greatly simplifies the presentation. While in Canberra, Wu also studied the 8-vertex model on the honeycomb

  12. Ovarian Tumor Attachment, Invasion, and Vascularization Reflect Unique Microenvironments in the Peritoneum: Insights from Xenograft and Mathematical Models

    PubMed Central

    Steinkamp, Mara P.; Winner, Kimberly Kanigel; Davies, Suzy; Muller, Carolyn; Zhang, Yong; Hoffman, Robert M.; Shirinifard, Abbas; Moses, Melanie; Jiang, Yi; Wilson, Bridget S.

    2013-01-01

    Ovarian cancer relapse is often characterized by metastatic spread throughout the peritoneal cavity with tumors attached to multiple organs. In this study, interaction of ovarian cancer cells with the peritoneal tumor microenvironment was evaluated in a xenograft model based on intraperitoneal injection of fluorescent SKOV3.ip1 ovarian cancer cells. Intra-vital microscopy of mixed GFP-red fluorescent protein (RFP) cell populations injected into the peritoneum demonstrated that cancer cells aggregate and attach as mixed spheroids, emphasizing the importance of homotypic adhesion in tumor formation. Electron microscopy provided high resolution structural information about local attachment sites. Experimental measurements from the mouse model were used to build a three-dimensional cellular Potts ovarian tumor model (OvTM) that examines ovarian cancer cell attachment, chemotaxis, growth, and vascularization. OvTM simulations provide insight into the relative influence of cancer cell–cell adhesion, oxygen availability, and local architecture on tumor growth and morphology. Notably, tumors on the mesentery, omentum, or spleen readily invade the “open” architecture, while tumors attached to the gut encounter barriers that restrict invasion and instead rapidly expand into the peritoneal space. Simulations suggest that rapid neovascularization of SKOV3.ip1 tumors is triggered by constitutive release of angiogenic factors in the absence of hypoxia. This research highlights the importance of cellular adhesion and tumor microenvironment in the seeding of secondary ovarian tumors on diverse organs within the peritoneal cavity. Results of the OvTM simulations indicate that invasion is strongly influenced by features underlying the mesothelial lining at different sites, but is also affected by local production of chemotactic factors. The integrated in vivo mouse model and computer simulations provide a unique platform for evaluating targeted therapies for ovarian cancer

  13. Modeling the viscoplastic micromechanical response of two-phase materials using fast Fourier transforms

    SciTech Connect

    Lebensohn, Ricardo A; Lee, Sukbin; Rollett, Anthony D

    2009-01-01

    A viscoplastic approach using the Fast Fourier Transform (FFT) method for obtaining local mechanical response is utilized to study microstructure-property relationships in composite materials. Specifically, three-dimensional, two-phase digital materials containing isotropically coarsened particles surrounded by a matrix phase, generated through a Kinetic Monte Carlo Potts model for Ostwald ripening, are used as instantiations in order to calculate the stress and strain rate fields under uniaxial tension. The effects of the morphology of the matrix phase, the volume fraction and the contiguity of particles, and the polycrystallinity of matrix phase, on the stress and strain rate fields under uniaxial tension are examined. It is found that the first moments of the stress and strain rate fields have a different dependence on the particle volume fraction and the particle contiguity from their second moments. The average stresses and average strain rates of both phases and of the overall composite have rather simple relationships with the particle volume fraction whereas their standard deviations vary strongly, especially when the particle volume fraction is high, and the contiguity of particles has a noticeable effect on the mechanical response. It is also found that the shape of stress distribution in the BCC hard particle phase evolves as the volume fraction of particles in the composite varies, such that it agrees with the stress field in the BCC polycrystal as the volume of particles approaches unity. Finally, it is observed that the stress and strain rate fields in the microstructures with a polycrystalline matrix are less sensitive to changes in volume fraction and contiguity of particles.

  14. The occurrence of the freshwater bryozoan Pottsiella erecta (Potts) 1884 (Gymnolaemata: Paludicellidae) in Lake Erie

    USGS Publications Warehouse

    Maciorowski, Anthony F.

    1974-01-01

    The collection of Pottsiella erecta in western Lake Erie in August 1972 represents the first reported occurrence of this species in the Great Lakes and a 110 km northward extension of its known range.

  15. Pott's Disease? AIDS-Associated Mycobacterium heckeshornense Spinal Osteomyelitis and Diskitis

    PubMed Central

    Graf, Paul C. F.

    2014-01-01

    Acid-fast bacillus (AFB) spinal osteomyelitis in a patient with AIDS is often presumed to be caused by reactivated Mycobacterium tuberculosis. However, other AFB pathogens can mimic M. tuberculosis and, to ensure appropriate and adequate therapy, should be considered by clinicians. We present a case of aggressive spinal osteomyelitis caused by Mycobacterium heckeshornense in an AIDS patient; a review of the literature is also included. PMID:25428153

  16. Surgical and transcatheter management alternatives in refractory pulmonary hypertension: Potts shunt.

    PubMed

    Kula, Serdar; Atasayan, Vildan

    2015-10-01

    Despite advances in the medical treatment of children with pulmonary arterial hypertension that have resulted in improved health quality and life expectancy, the progression of the disease is still the main problem for some patients. Because of this undesirable condition, the search for new treatment strategies continues for pediatric cardiologists. At this point, the Eisenmenger physiology is the main target because of the long-life expectancy and more stable hemodynamics of patients with Eisenmenger syndrome. Therefore, some invasive procedures may be used for conversion to Eisenmenger physiology with the aim of decompressing the right ventricle. PMID:26477721

  17. Spinal Tuberculosis (Pott's disease) Mimicking Paravertebral Malignant Tumor in a Child Presenting with Spinal Cord Compression

    PubMed Central

    Emir, Suna; Erdem, Arzu Y; Demir, Haci A; Kaçar, Ayper; Tunç, Bahattin

    2012-01-01

    Paravertebral tumors may interfere with the radiological and clinical features of spinal tuberculosis. We report a case of a 3-year-old boy with spinal tuberculosis who was initially misdiagnosed as having a paraspinal tumor. The diagnosis of tuberculosis was made on the basis of intraoperative findings and confirmed by histopathology. This case highlights the importance of awareness of the different radiographic features of spinal tuberculosis, which can mimic a spinal malignancy. In order to avoid delayed diagnosis, pediatricians and radiologists must be aware of spinal tuberculosis, which may interfere with other clinical conditions. PMID:23439455

  18. [Medico-surgical treatment of Pott's disease. Our attitude in Gabon].

    PubMed

    Loembe, P M

    1994-11-01

    Twenty-six of 95 adults treated for tuberculous spondylitis, between 1982 and 1993, underwent surgery. Twenty-one exhibited neurological deficits: radicular deficits: 4, and progressive spinal cord syndromes: 17 (incomplete, 13, complete, of acute onset: 4). Vertebral body compression fracture was the most prominent finding. Indications for surgery were neurologic: 11, mechanical: 1, etiologic: 1, and mixed: 13. Twelve patients had vertebrectomies, 3 laminotomies and 11 laminectomies. The average follow-up was 23 months. The neurological recovery was complete in 16 cases, partial in 4 cases and unchanged in one case. Bony consolidation occurred after 3-5 months. The medicosurgical treatment produced a very high cure rate, so rapidly, that it became the treatment of choice in our setting. Moreover, that allows to specify the diagnosis. Anterior decompression and fusion is recommended in the cervical and lumbar spine. In the thoracic segment, significant kyphosis is infrequent, so that surgical correction is rarely necessary. Laminotomy may occasionally be indicated for posterior decompression for abscess. Laminectomy is now preferred for uncommon cases of thoracolumbar posterior compression by tuberculous arachnoiditis or associated posterior vertebral tuberculosis. Indications for open biopsy are discussed. PMID:7874618

  19. [Is there a place for surgery in Pott's disease in adults? Our experience in Gabon].

    PubMed

    Loembe, P M; Chouteau, Y

    1994-01-01

    Tuberculous spondylitis treatment in developing nations remains controversial. We report our experience, working in a Center where appropriate medical and human structures are available. 22 of 78 adults treated at Jeanne-Ebori Hospital (Gabon), for tuberculous spondylitis, between August 1982 and June 1992, underwent surgery. The average age was 48 years (range, twenty-six to sixty-eight years). Eighteen patients had neurological complications: progressive spinal cord lesions: 15 cases (tetraplegia: 3, paraplegia: 11, tetraparesis: 1) and radicular syndromes (3 cases). The patients were seen in advanced stages of the disease with bone destruction, associated with collapse of vertebrae in ten cases. Indications for surgery were: neurologic in eleven cases, mechanical in one case, and mixed in ten cases (neurologic and mechanical: 5, etiologic and mechanical: 3, etiologic and neurologic: 2). Anterior approach were performed in 10 cases, posterior approach in 12 cases, generally, following an initial three weeks course of antituberculous therapy. The average length of time spent in hospital including rehabilitation had been 10.4 weeks. The average follow-up was 23.7 months (range: 8 months to 8 years). All patients obtained fusion, and stability was achieved after 3-5 months. The neurological recovery was complete in 9 cases, partial in 8 cases, unchanged in one case. All patients were considered medically cured. The analysis of material and socio economic difficulties obliges us to reduce the treatment length by favoring surgical intervention in relatively advanced lesions. Moreover, that allows to specify the diagnosis. PMID:7753296

  20. Psoas abscess secondary to Pott's disease--an unusual presentation in a young child.

    PubMed

    Afzal, Atif; Arshad, Muhammad; Ashraf, Omer

    2006-04-01

    Psoas abscess in neonates and infants are rare. Primary psoas abscesses are said to be more common in young children. Limping, fever and abdominal pain has been described to be the way psoas abscesses usually present. The authors describe the unusual presentation and successful treatment of a young child with a unilateral psoas abscess secondary to advanced spondylodiscitis. PMID:16711345

  1. A code for analysis of the fine structure in near-rigid weakly-bonded open-shell complexes that consist of a diatomic radical in a Σ3 state and a closed-shell molecule

    NASA Astrophysics Data System (ADS)

    Fawzy, Wafaa M.

    2010-10-01

    applied to analysis and fitting the observed high resolution infrared spectra of the O 2sbnd HF/O 2sbnd DF and O 2sbnd N 2O complexes. Test input file for simulation and fitting the high resolution infrared spectrum of the O 2sbnd DF complex is provided. Program summaryProgram title: TSIG_COMP Catalogue identifier: AEGM_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGM_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 10 030 No. of bytes in distributed program, including test data, etc.: 51 663 Distribution format: tar.gz Programming language: Fortran 90, free format Computer: SGI Origin 3400, workstations and PCs Operating system: Linux, UNIX and Windows (see Restrictions below) RAM: Case dependent Classification: 16.2 Nature of problem: TSIG_COMP calculates frequencies, relative intensities, and expectation values of the various quantum numbers and parities of bound states involved in allowed ro-vibrational transitions in semi-rigid planar weakly-bonded open-shell complexes. The complexes of interest contain a free radical in a Σ3 state and a closed-shell partner, where the electron-spin-electron-spin interaction, electron-spin rotation interaction, and centrifugal forces significantly modify the spectral patterns. To date, ab initio methods are incapable of taking these effects into account to provide accurate predictions for the ro-vibrational energy levels of the complexes of interest. In the TSIG_COMP program, the problem is solved by using the proper effective Hamiltonian and molecular basis set. Solution method: The program uses a Hamiltonian operator that takes into account vibration, end-over-end rotation, electron-spin-electron-spin and electron-spin rotation interactions as well as the various centrifugal distortion terms. The Hamiltonian operator

  2. How the Whole School, Whole Community, Whole Child Model Works: Creating Greater Alignment, Integration, and Collaboration between Health and Education

    ERIC Educational Resources Information Center

    Chiang, Rachelle Johnsson; Meagher, Whitney; Slade, Sean

    2015-01-01

    Background: The Whole School, Whole Community, Whole Child (WSCC) model calls for greater collaboration across the community, school, and health sectors to meet the needs and support the full potential of each child. This article reports on how 3 states and 2 local school districts have implemented aspects of the WSCC model through collaboration,…

  3. Measurements of Excitation Functions and Line Polarizations for Electron Impact Excitation of the n = 2, 3 States of Atomic Hydrogen in the Energy Range 11 - 2000 eV

    NASA Technical Reports Server (NTRS)

    James, G. K.; Ajello, J. M.; Kanik, I.; Slevin, J.; Franklin, B.; Shemansky, D.

    1993-01-01

    The electron-atomic hydrogen scattering system is an important testing ground for theoretical models and has received a great deal of attention from experimentalists and theoreticians alike over the years. A complete description of the excitation process requires a knowledge of many different parameters, and experimental measurements of these parameters have been performed in various laboratories around the world. As far as total cross section data are concerned it has been noted that the discrepancy between the data of Long et al. and Williams for n = 2 excitations needs to be resolved in the interests of any further refinement of theory. We report new measurements of total cross sections and atomic line polarizations for both n=2 and n=3 excitations at energies from threshold to 2000 eV...

  4. Classical Monte Carlo Study for Antiferro Quadrupole Orders in a Diamond Lattice

    NASA Astrophysics Data System (ADS)

    Hattori, Kazumasa; Tsunetsugu, Hirokazu

    2016-09-01

    We investigate antiferro quadrupole orders in a diamond lattice under magnetic fields by Monte Carlo simulations for two types of classical effective models. One is an XY model with Z3 anisotropy, and the other is a two-component ϕ4 model with a third-order anisotropy. We confirm that the universality class of the zero-field transition is that for the three-dimensional XY model. Magnetic field corresponds to a Z3 field in the effective model, and under this field, we find that collinear and canted antiferro-quadrupole orders compete. Each phase is characterized by symmetry breaking in the sector of (sublattice Z2) otimes (reflection Z2 for the order parameter). When Z3 anisotropy and magnetic field vary, it turns out that this system is a good playground for various multicritical points; bicritical and tetracritical points emerge in a finite field. Another important finding is about the scaling of parasitic ferro quadrupole order at the zero-field critical point. This is the secondary order parameter induced by the primary antiferro order, and its critical exponent β' = 0.815 clearly differs from the expected value that is twice the value for the primary order parameter. The corresponding correlation length exponent is also different, ν' = 0.597(12). We also discuss relation of the present effective quadrupole models with the 3-state Potts model as well as implication to understanding of orbital orders in Pr-based 1-2-20 compounds.

  5. 7 CFR 718.3 - State committee responsibilities.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... AGRICULTURE FARM MARKETING QUOTAS, ACREAGE ALLOTMENTS, AND PRODUCTION ADJUSTMENT PROVISIONS APPLICABLE TO... digital images. (b) The State committee shall submit to the Deputy Administrator requests to deviate...

  6. 7 CFR 718.3 - State committee responsibilities.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... AGRICULTURE FARM MARKETING QUOTAS, ACREAGE ALLOTMENTS, AND PRODUCTION ADJUSTMENT PROVISIONS APPLICABLE TO... digital images. (b) The State committee shall submit to the Deputy Administrator requests to deviate...

  7. 7 CFR 718.3 - State committee responsibilities.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... AGRICULTURE FARM MARKETING QUOTAS, ACREAGE ALLOTMENTS, AND PRODUCTION ADJUSTMENT PROVISIONS APPLICABLE TO... digital images. (b) The State committee shall submit to the Deputy Administrator requests to deviate...

  8. 7 CFR 718.3 - State committee responsibilities.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... AGRICULTURE FARM MARKETING QUOTAS, ACREAGE ALLOTMENTS, AND PRODUCTION ADJUSTMENT PROVISIONS APPLICABLE TO... digital images. (b) The State committee shall submit to the Deputy Administrator requests to deviate...

  9. 7 CFR 718.3 - State committee responsibilities.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... AGRICULTURE FARM MARKETING QUOTAS, ACREAGE ALLOTMENTS, AND PRODUCTION ADJUSTMENT PROVISIONS APPLICABLE TO... digital images. (b) The State committee shall submit to the Deputy Administrator requests to deviate...

  10. REX3DV1.0

    2002-03-28

    This code is a FORTRAN code for three-dimensional Monte Carol Potts Model (MCPM) Recrystallization and grain growth. A continuum grain structure is mapped onto a three-dimensional lattice. The mapping procedure is analogous to color bitmapping the grain structure; grains are clusters of pixels (sites) of the same color (spin). The total system energy is given by the Pott Hamiltonian and the kinetics of grain growth are determined through a Monte Carlo technique with a nonconservedmore » order parameter (Glauber dynamics). The code can be compiled and run on UNIX/Linux platforms.« less

  11. Leadership Models.

    ERIC Educational Resources Information Center

    Freeman, Thomas J.

    This paper discusses six different models of organizational structure and leadership, including the scalar chain or pyramid model, the continuum model, the grid model, the linking pin model, the contingency model, and the circle or democratic model. Each model is examined in a separate section that describes the model and its development, lists…

  12. Models and role models.

    PubMed

    ten Cate, Jacob M

    2015-01-01

    Developing experimental models to understand dental caries has been the theme in our research group. Our first, the pH-cycling model, was developed to investigate the chemical reactions in enamel or dentine, which lead to dental caries. It aimed to leverage our understanding of the fluoride mode of action and was also utilized for the formulation of oral care products. In addition, we made use of intra-oral (in situ) models to study other features of the oral environment that drive the de/remineralization balance in individual patients. This model addressed basic questions, such as how enamel and dentine are affected by challenges in the oral cavity, as well as practical issues related to fluoride toothpaste efficacy. The observation that perhaps fluoride is not sufficiently potent to reduce dental caries in the present-day society triggered us to expand our knowledge in the bacterial aetiology of dental caries. For this we developed the Amsterdam Active Attachment biofilm model. Different from studies on planktonic ('single') bacteria, this biofilm model captures bacteria in a habitat similar to dental plaque. With data from the combination of these models, it should be possible to study separate processes which together may lead to dental caries. Also products and novel agents could be evaluated that interfere with either of the processes. Having these separate models in place, a suggestion is made to design computer models to encompass the available information. Models but also role models are of the utmost importance in bringing and guiding research and researchers. PMID:25871413

  13. OpenACC programs of the Swendsen-Wang multi-cluster spin flip algorithm

    NASA Astrophysics Data System (ADS)

    Komura, Yukihiro

    2015-12-01

    We present sample OpenACC programs of the Swendsen-Wang multi-cluster spin flip algorithm. OpenACC is a directive-based programming model for accelerators without requiring modification to the underlying CPU code itself. In this paper, we deal with the classical spin models as with the sample CUDA programs (Komura and Okabe, 2014), that is, two-dimensional (2D) Ising model, three-dimensional (3D) Ising model, 2D Potts model, 3D Potts model, 2D XY model and 3D XY model. We explain the details of sample OpenACC programs and compare the performance of the present OpenACC implementations with that of the CUDA implementations for the 2D and 3D Ising models and the 2D and 3D XY models.

  14. Non linear identities between unitary minimal Virasoro characters

    NASA Astrophysics Data System (ADS)

    Taormina, Anne

    Non linear identities between unitary minimal Virasoro characters at low levels (m = 3, 4, 5) are presented as well as a sketch of some proofs. The first identity gives the Ising model characters (m = 3) as bilinears in tricritical Ising model characters (m = 4), while the second one gives the tricritical Ising model characters as bilinears in the Ising model characters and the six combinations of m = 5 Virasoro characters which do not appear in the spectrum of the three state Potts model.

  15. MODEL DEVELOPMENT - DOSE MODELS

    EPA Science Inventory

    Model Development

    Humans are exposed to mixtures of chemicals from multiple pathways and routes. These exposures may result from a single event or may accumulate over time if multiple exposure events occur. The traditional approach of assessing risk from a single chemica...

  16. Xtoys: Cellular automata on xwindows

    SciTech Connect

    Creutz, M.

    1995-08-15

    Xtoys is a collection of xwindow programs for demonstrating simulations of various statistical models. Included are xising, for the two dimensional Ising model, xpotts, for the q-state Potts model, xautomalab, for a fairly general class of totalistic cellular automata, xsand, for the Bak-Tang-Wiesenfield model of self organized criticality, and xfires, a simple forest fire simulation. The programs should compile on any machine supporting xwindows.

  17. Diffusion of two brands in competition: Cross-brand effect

    NASA Astrophysics Data System (ADS)

    Laciana, C. E.; Gual, G.; Kalmus, D.; Oteiza-Aguirre, N.; Rovere, S. L.

    2014-11-01

    We study the equilibrium points of a system of equations corresponding to a Bass based model that describes the diffusion of two brands in competition. To increase the understanding of the effects of the cross-brand parameters, we perform a sensitivity analysis. Finally, we show a comparison with an agent-based model inspired in the Potts model. Conclusions include that both models give the same diffusion curves only when the cross coefficients are not null.

  18. Three-body interactions in sociophysics and their role in coalition forming

    NASA Astrophysics Data System (ADS)

    Naumis, Gerardo G.; Samaniego-Steta, F.; del Castillo-Mussot, M.; Vázquez, G. J.

    2007-06-01

    An study of the effects of three-body interactions in the process of coalition formation is presented. In particular, we modify a spin glass model of bimodal propensities and also a Potts model in order to include a particular three-body Hamiltonian that reproduces the main features of the required interactions. The model can be used to study conflicts, political struggles, political parties, social networks, wars and organizational structures. As an application, we analyze a simplified model of the Iraq war.

  19. Promoting Models

    NASA Astrophysics Data System (ADS)

    Li, Qin; Zhao, Yongxin; Wu, Xiaofeng; Liu, Si

    There can be multitudinous models specifying aspects of the same system. Each model has a bias towards one aspect. These models often override in specific aspects though they have different expressions. A specification written in one model can be refined by introducing additional information from other models. The paper proposes a concept of promoting models which is a methodology to obtain refinements with support from cooperating models. It refines a primary model by integrating the information from a secondary model. The promotion principle is not merely an academic point, but also a reliable and robust engineering technique which can be used to develop software and hardware systems. It can also check the consistency between two specifications from different models. A case of modeling a simple online shopping system with the cooperation of the guarded design model and CSP model illustrates the practicability of the promotion principle.

  20. Parameters for pyrethroid insecticide QSAR and PBPK/PD models for human risk assessment.

    PubMed

    Knaak, James B; Dary, Curtis C; Zhang, Xiaofei; Gerlach, Robert W; Tornero-Velez, R; Chang, Daniel T; Goldsmith, Rocky; Blancato, Jerry N

    2012-01-01

    ), and Colmenarejo (2003). QikProp(Schrodinger, LLC) was used to obtain Fu values for calculating partition coefficients and for calculating permeation constants (Caco-2, MDCK, and logBBB). ADMET Predictor (Simulations Plus Inc.) provided Vm~,x and Km values for the hydroxylation of drugs/pyrethroids by human liver recombinant cytochrome P450 enzymes making the values available for possible use in PBPK/PD models.The Caco-2 permeability constants and CYP3A4 Vmax and Km values are needed in PBPK/PD models with GI ACAT sub models. Modeling work by Chang et al.(2009) produced rate constants (kcat) for the hydrolysis of pyrethroids by rat serumcarboxylesterases. The skin permeation model of Potts and Guy (1992) was used topredict K, values for the dermal absorption of the 15 pyrethroids.The electrophysiological studies by Narahashi (1971) and others (Breckenridgeet al. 2009; Shafer et al. 2005; Soderlund et al. 2002; Wolansky and Harrill 2008)demonstrated that the mode of action of pyrethroids on nerves is to interfere with the changes in sodium and potassium ion currents. The pyrethroids, being highly lipid soluble, are bound or distributed in lipid bilayers of the nerve cell membrane and exert their action on sodium channel proteins. The rising phase of the action potential is caused by sodium influx (sodium activation), while the falling phase is caused by sodium activation being turned off, and an increase in potassium efflux(potassium activation). The action of allethrin and other pyrethroids is caused by an inhibition or block of the normal currents. An equation by Tatebayashi and Narahashi (1994) that describes the action of pyrethroids on sodium channels was found in the literature. This equation, or some variation of it, may be suitable for use in the PD portion of pyrethroid PBPK models. PMID:22610175

  1. The scaling state in two-dimensional grain growth

    SciTech Connect

    Mulheran, P.A. . Dept. of Physics)

    1994-11-01

    A new model of normal grain growth in two-dimensional systems is derived from considerations of Potts model simulations. This Randomly Connected Bubble model is based on Hillert's theory and combines the essential topological features of the grain boundary network with the action of capillarity. It successfully predicts what the scaling state of the network should be and explains why the system evolves into this state. The implications for grain growth in real materials are also discussed.

  2. Models, Part IV: Inquiry Models.

    ERIC Educational Resources Information Center

    Callison, Daniel

    2002-01-01

    Discusses models for information skills that include inquiry-oriented activities. Highlights include WebQuest, which uses Internet resources supplemented with videoconferencing; Minnesota's Inquiry Process based on the Big Six model for information problem-solving; Indiana's Student Inquiry Model; constructivist learning models for inquiry; and…

  3. Supermatrix models

    SciTech Connect

    Yost, S.A.

    1991-05-01

    Radom matrix models based on an integral over supermatrices are proposed as a natural extension of bosonic matrix models. The subtle nature of superspace integration allows these models to have very different properties from the analogous bosonic models. Two choices of integration slice are investigated. One leads to a perturbative structure which is reminiscent of, and perhaps identical to, the usual Hermitian matrix models. Another leads to an eigenvalue reduction which can be described by a two component plasma in one dimension. A stationary point of the model is described.

  4. Supermatrix models

    SciTech Connect

    Yost, S.A. . Dept. of Physics and Astronomy)

    1992-09-30

    In this paper, random matrix models based on an integral over supermatrices are proposed as a natural extension of bosonic matrix models. The subtle nature of superspace integration allows these models to have very different properties from the analogous bosonic models. Two choices of integration slice are investigated. One leads to a perturbative structure which is reminiscent of, and perhaps identical to, the usual Hermitian matrix models. Another leads to an eigenvalue reduction which can be described by a two-component plasma in one dimension. A stationary point of the model is described.

  5. Capturing the state transitions of seizure-like events using Hidden Markov models.

    PubMed

    Guirgis, Mirna; Serletis, Demitre; Carlen, Peter L; Bardakjian, Berj L

    2011-01-01

    The purpose of this study was to investigate the number of states present in the progression of a seizure-like event (SLE). Of particular interest is to determine if there are more than two clearly defined states, as this would suggest that there is a distinct state preceding an SLE. Whole-intact hippocampus from C57/BL mice was used to model epileptiform activity induced by the perfusion of a low Mg(2+)/high K(+) solution while extracellular field potentials were recorded from CA3 pyramidal neurons. Hidden Markov models (HMM) were used to model the state transitions of the recorded SLEs by incorporating various features of the Hilbert transform into the training algorithm; specifically, 2- and 3-state HMMs were explored. Although the 2-state model was able to distinguish between SLE and nonSLE behavior, it provided no improvements compared to visual inspection alone. However, the 3-state model was able to capture two distinct nonSLE states that visual inspection failed to discriminate. Moreover, by developing an HMM based system a priori knowledge of the state transitions was not required making this an ideal platform for seizure prediction algorithms. PMID:22254742

  6. MODELS - 3

    EPA Science Inventory

    Models-3 is a third generation air quality modeling system that contains a variety of tools to perform research and analysis of critical environmental questions and problems. These tools provide regulatory analysts and scientists with quicker results, greater scientific accuracy ...

  7. ENTRAINMENT MODELS

    EPA Science Inventory

    This presentation presented information on entrainment models. Entrainment models use entrainment hypotheses to express the continuity equation. The advantage is that plume boundaries are known. A major disadvantage is that the problems that can be solved are rather simple. The ...

  8. Turbulence modeling

    NASA Technical Reports Server (NTRS)

    Rubesin, Morris W.

    1987-01-01

    Recent developments at several levels of statistical turbulence modeling applicable to aerodynamics are briefly surveyed. Emphasis is on examples of model improvements for transonic, two-dimensional flows. Experience with the development of these improved models is cited to suggest methods of accelerating the modeling process necessary to keep abreast of the rapid movement of computational fluid dynamics into the computation of complex three-dimensional flows.

  9. Bayesian segmentation of hyperspectral images

    NASA Astrophysics Data System (ADS)

    Mohammadpour, Adel; Féron, Olivier; Mohammad-Djafari, Ali

    2004-11-01

    In this paper we consider the problem of joint segmentation of hyperspectral images in the Bayesian framework. The proposed approach is based on a Hidden Markov Modeling (HMM) of the images with common segmentation, or equivalently with common hidden classification label variables which is modeled by a Potts Markov Random Field. We introduce an appropriate Markov Chain Monte Carlo (MCMC) algorithm to implement the method and show some simulation results.

  10. Exploring new frontiers in statistical physics with a new, parallel Wang-Landau framework

    SciTech Connect

    Vogel, Thomas; Li, Ying Wai; Wuest, Thomas; Landau, David P

    2014-01-01

    Combining traditional Wang Landau sampling for multiple replica systems with an exchange of densities of states between replicas we describe a general framework for simulations on massively parallel Petaflop supercomputers. The advantages and general applicability of the method for simulations of complex systems are demonstrated for the classical 2D Potts spin model featuring a strong first-order transition and the self-assembly of lipid bilayers in amphiphilic solutions in a continuous model.

  11. Waveguide model

    NASA Technical Reports Server (NTRS)

    1981-01-01

    A model is presented which quantifies the electromagnetic modes (field configurations) in the immediate vicinity of the rectenna element. Specifically, the waveguide model characterizes the electromagnetic modes generated by planar waves normal to the array. The model applies only to incidence normal to the array.

  12. Phoenix model

    EPA Science Inventory

    Phoenix (formerly referred to as the Second Generation Model or SGM) is a global general equilibrium model designed to analyze energy-economy-climate related questions and policy implications in the medium- to long-term. This model disaggregates the global economy into 26 industr...

  13. Radiation Models

    ERIC Educational Resources Information Center

    James, W. G. G.

    1970-01-01

    Discusses the historical development of both the wave and the corpuscular photon model of light. Suggests that students should be informed that the two models are complementary and that each model successfully describes a wide range of radiation phenomena. Cites 19 references which might be of interest to physics teachers and students. (LC)

  14. Simulating convergent extension by way of anisotropic differential adhesion.

    PubMed

    Zajac, Mark; Jones, Gerald L; Glazier, James A

    2003-05-21

    Simulations using the Extended Potts Model suggest that anisotropic differential adhesion can account for convergent extension, as observed during embryonic development of the frog Xenopus laevis for example. During gastrulation in these frogs, convergent extension produces longitudinal tissue growth from latitudinal elongation and migration of aligned constituent cells. The Extended Potts Model employs clustered points on a grid to represent subdivided cells with probabilistic displacement of cell boundaries such that small changes in energy drive gradual tissue development. For modeling convergent extension, simulations include anisotropic differential adhesion: the degree of attachment between adjacent elongated cells depends on their relative orientation. Without considering additional mechanisms, simulations based on anisotropic differential adhesion reproduce the hallmark stages of convergent extension in the correct sequence, with random fluctuations as sufficient impetus for cell reorganization. PMID:12727459

  15. Hydrological models are mediating models

    NASA Astrophysics Data System (ADS)

    Babel, L. V.; Karssenberg, D.

    2013-08-01

    Despite the increasing role of models in hydrological research and decision-making processes, only few accounts of the nature and function of models exist in hydrology. Earlier considerations have traditionally been conducted while making a clear distinction between physically-based and conceptual models. A new philosophical account, primarily based on the fields of physics and economics, transcends classes of models and scientific disciplines by considering models as "mediators" between theory and observations. The core of this approach lies in identifying models as (1) being only partially dependent on theory and observations, (2) integrating non-deductive elements in their construction, and (3) carrying the role of instruments of scientific enquiry about both theory and the world. The applicability of this approach to hydrology is evaluated in the present article. Three widely used hydrological models, each showing a different degree of apparent physicality, are confronted to the main characteristics of the "mediating models" concept. We argue that irrespective of their kind, hydrological models depend on both theory and observations, rather than merely on one of these two domains. Their construction is additionally involving a large number of miscellaneous, external ingredients, such as past experiences, model objectives, knowledge and preferences of the modeller, as well as hardware and software resources. We show that hydrological models convey the role of instruments in scientific practice by mediating between theory and the world. It results from these considerations that the traditional distinction between physically-based and conceptual models is necessarily too simplistic and refers at best to the stage at which theory and observations are steering model construction. The large variety of ingredients involved in model construction would deserve closer attention, for being rarely explicitly presented in peer-reviewed literature. We believe that devoting

  16. Model Experiments and Model Descriptions

    NASA Technical Reports Server (NTRS)

    Jackman, Charles H.; Ko, Malcolm K. W.; Weisenstein, Debra; Scott, Courtney J.; Shia, Run-Lie; Rodriguez, Jose; Sze, N. D.; Vohralik, Peter; Randeniya, Lakshman; Plumb, Ian

    1999-01-01

    The Second Workshop on Stratospheric Models and Measurements Workshop (M&M II) is the continuation of the effort previously started in the first Workshop (M&M I, Prather and Remsberg [1993]) held in 1992. As originally stated, the aim of M&M is to provide a foundation for establishing the credibility of stratospheric models used in environmental assessments of the ozone response to chlorofluorocarbons, aircraft emissions, and other climate-chemistry interactions. To accomplish this, a set of measurements of the present day atmosphere was selected. The intent was that successful simulations of the set of measurements should become the prerequisite for the acceptance of these models as having a reliable prediction for future ozone behavior. This section is divided into two: model experiment and model descriptions. In the model experiment, participant were given the charge to design a number of experiments that would use observations to test whether models are using the correct mechanisms to simulate the distributions of ozone and other trace gases in the atmosphere. The purpose is closely tied to the needs to reduce the uncertainties in the model predicted responses of stratospheric ozone to perturbations. The specifications for the experiments were sent out to the modeling community in June 1997. Twenty eight modeling groups responded to the requests for input. The first part of this section discusses the different modeling group, along with the experiments performed. Part two of this section, gives brief descriptions of each model as provided by the individual modeling groups.

  17. Model Reduction in Groundwater Modeling

    NASA Astrophysics Data System (ADS)

    Yeh, W. W. G.

    2014-12-01

    Model reduction has been shown to be a very effective method for reducing the computational burden of large-scale simulations. Model reduction techniques preserve much of the physical knowledge of the system and primarily seek to remove components from the model that do not provide significant information of interest. Proper Orthogonal Decomposition (POD) is a model reduction technique by which a system of ordinary equations is projected onto a much smaller subspace in such a way that the span of the subspace is equal to the span of the original full model space. Basically, the POD technique selects a small number of orthonormal basis functions (principal components) that span the spatial variability of the solutions. In this way the state variable (head) is approximated by a linear combination of these basis functions and, using a Galerkin projection, the dimension of the problem is significantly reduced. It has been shown that for a highly discritized model, the reduced model can be two to three orders of magnitude smaller than the original model and runs 1,000 faster. More importantly, the reduced model captures the dominating characteristics of the full model and produces sufficiently accurate solutions. One of the major tasks in the development of the reduced model is the selection of snapshots which are used to determine the dominant eigenvectors. This paper discusses ways to optimize the snapshot selection. Additionally, the paper also discusses applications of the reduced model to parameter estimation, Monte Carlo simulation and experimental design in groundwater modeling.

  18. Modeling Pharmacokinetics.

    PubMed

    Bois, Frederic Y; Brochot, Céline

    2016-01-01

    Pharmacokinetics is the study of the fate of xenobiotics in a living organism. Physiologically based pharmacokinetic (PBPK) models provide realistic descriptions of xenobiotics' absorption, distribution, metabolism, and excretion processes. They model the body as a set of homogeneous compartments representing organs, and their parameters refer to anatomical, physiological, biochemical, and physicochemical entities. They offer a quantitative mechanistic framework to understand and simulate the time-course of the concentration of a substance in various organs and body fluids. These models are well suited for performing extrapolations inherent to toxicology and pharmacology (e.g., between species or doses) and for integrating data obtained from various sources (e.g., in vitro or in vivo experiments, structure-activity models). In this chapter, we describe the practical development and basic use of a PBPK model from model building to model simulations, through implementation with an easily accessible free software. PMID:27311461

  19. Critical nonequilibrium relaxation in the Swendsen-Wang algorithm in the Berezinsky-Kosterlitz-Thouless and weak first-order phase transitions

    NASA Astrophysics Data System (ADS)

    Nonomura, Yoshihiko; Tomita, Yusuke

    2015-12-01

    Recently we showed that the critical nonequilibrium relaxation in the Swendsen-Wang algorithm is widely described by the stretched-exponential relaxation of physical quantities in the Ising or Heisenberg models. Here we make a similar analysis in the Berezinsky-Kosterlitz-Thouless phase transition in the two-dimensional (2D) X Y model and in the first-order phase transition in the 2D q =5 Potts model and find that these phase transitions are described by the simple exponential relaxation and power-law relaxation of physical quantities, respectively. We compare the relaxation behaviors of these phase transitions with those of the second-order phase transition in the three- and four-dimensional X Y models and in the 2D q -state Potts models for 2 ≤q ≤4 and show that the species of phase transitions can be clearly characterized by the present analysis. We also compare the size dependence of relaxation behaviors of the first-order phase transition in the 2D q =5 and 6 Potts models and propose a quantitative criterion on "weakness" of the first-order phase transition.

  20. Ventilation Model

    SciTech Connect

    H. Yang

    1999-11-04

    The purpose of this analysis and model report (AMR) for the Ventilation Model is to analyze the effects of pre-closure continuous ventilation in the Engineered Barrier System (EBS) emplacement drifts and provide heat removal data to support EBS design. It will also provide input data (initial conditions, and time varying boundary conditions) for the EBS post-closure performance assessment and the EBS Water Distribution and Removal Process Model. The objective of the analysis is to develop, describe, and apply calculation methods and models that can be used to predict thermal conditions within emplacement drifts under forced ventilation during the pre-closure period. The scope of this analysis includes: (1) Provide a general description of effects and heat transfer process of emplacement drift ventilation. (2) Develop a modeling approach to simulate the impacts of pre-closure ventilation on the thermal conditions in emplacement drifts. (3) Identify and document inputs to be used for modeling emplacement ventilation. (4) Perform calculations of temperatures and heat removal in the emplacement drift. (5) Address general considerations of the effect of water/moisture removal by ventilation on the repository thermal conditions. The numerical modeling in this document will be limited to heat-only modeling and calculations. Only a preliminary assessment of the heat/moisture ventilation effects and modeling method will be performed in this revision. Modeling of moisture effects on heat removal and emplacement drift temperature may be performed in the future.

  1. Climate Models

    NASA Technical Reports Server (NTRS)

    Druyan, Leonard M.

    2012-01-01

    Climate models is a very broad topic, so a single volume can only offer a small sampling of relevant research activities. This volume of 14 chapters includes descriptions of a variety of modeling studies for a variety of geographic regions by an international roster of authors. The climate research community generally uses the rubric climate models to refer to organized sets of computer instructions that produce simulations of climate evolution. The code is based on physical relationships that describe the shared variability of meteorological parameters such as temperature, humidity, precipitation rate, circulation, radiation fluxes, etc. Three-dimensional climate models are integrated over time in order to compute the temporal and spatial variations of these parameters. Model domains can be global or regional and the horizontal and vertical resolutions of the computational grid vary from model to model. Considering the entire climate system requires accounting for interactions between solar insolation, atmospheric, oceanic and continental processes, the latter including land hydrology and vegetation. Model simulations may concentrate on one or more of these components, but the most sophisticated models will estimate the mutual interactions of all of these environments. Advances in computer technology have prompted investments in more complex model configurations that consider more phenomena interactions than were possible with yesterday s computers. However, not every attempt to add to the computational layers is rewarded by better model performance. Extensive research is required to test and document any advantages gained by greater sophistication in model formulation. One purpose for publishing climate model research results is to present purported advances for evaluation by the scientific community.

  2. Phenomenological models

    SciTech Connect

    Braby, L.A.

    1990-09-01

    The biological effects of ionizing radiation exposure are the result of a complex sequence of physical, chemical, biochemical, and physiological interactions. One way to begin a search for an understanding of health effects of radiation is through the development of phenomenological models of the response. Many models have been presented and tested in the slowly evolving process of characterizing cellular response. A range of models covering different endpoints and phenomena has developed in parallel. Many of these models employ similar assumptions about some underlying processes while differing about the nature of others. An attempt is made to organize many of the models into groups with similar features and to compare the consequences of those features with the actual experimental observations. It is assumed that by showing that some assumptions are inconsistent with experimental observations, the job of devising and testing mechanistic models can be simplified. 43 refs., 13 figs.

  3. Building models

    SciTech Connect

    Burr, M.T.

    1995-04-01

    As developers make progress on independent power projects around the world, models for success are beginning to emerge. Different models are evolving to create ownership structures that accomoate a complex system of regulatory requirements. Other frameworks make use of previously untapped fuel resources, or establish new sources of financing; however, not all models may be applied to a given project. This article explores how developers are finding new alternatives for overcoming development challenges that are common to projects in many countries.

  4. Spin systems and Political Districting Problem

    NASA Astrophysics Data System (ADS)

    Chou, Chung-I.; Li, Sai-Ping

    2007-03-01

    The aim of the Political Districting Problem is to partition a territory into electoral districts subject to some constraints such as contiguity, population equality, etc. In this paper, we apply statistical physics methods to Political Districting Problem. We will show how to transform the political problem to a spin system, and how to write down a q-state Potts model-like energy function in which the political constraints can be written as interactions between sites or external fields acting on the system. Districting into q voter districts is equivalent to finding the ground state of this q-state Potts model. Searching for the ground state becomes an optimization problem, where optimization algorithms such as the simulated annealing method and Genetic Algorithm can be employed here.

  5. Improving Wang-Landau sampling with adaptive windows

    NASA Astrophysics Data System (ADS)

    Cunha-Netto, A. G.; Caparica, A. A.; Tsai, Shan-Ho; Dickman, Ronald; Landau, D. P.

    2008-11-01

    Wang-Landau sampling (WLS) of large systems requires dividing the energy range into “windows” and joining the results of simulations in each window. The resulting density of states (and associated thermodynamic functions) is shown to suffer from boundary effects in simulations of lattice polymers and the five-state Potts model. Here, we implement WLS using adaptive windows. Instead of defining fixed energy windows (or windows in the energy-magnetization plane for the Potts model), the boundary positions depend on the set of energy values on which the histogram is flat at a given stage of the simulation. Shifting the windows each time the modification factor f is reduced, we eliminate border effects that arise in simulations using fixed windows. Adaptive windows extend significantly the range of system sizes that may be studied reliably using WLS.

  6. Ventilation Model

    SciTech Connect

    V. Chipman

    2002-10-05

    The purpose of the Ventilation Model is to simulate the heat transfer processes in and around waste emplacement drifts during periods of forced ventilation. The model evaluates the effects of emplacement drift ventilation on the thermal conditions in the emplacement drifts and surrounding rock mass, and calculates the heat removal by ventilation as a measure of the viability of ventilation to delay the onset of peak repository temperature and reduce its magnitude. The heat removal by ventilation is temporally and spatially dependent, and is expressed as the fraction of heat carried away by the ventilation air compared to the fraction of heat produced by radionuclide decay. One minus the heat removal is called the wall heat fraction, or the remaining amount of heat that is transferred via conduction to the surrounding rock mass. Downstream models, such as the ''Multiscale Thermohydrologic Model'' (BSC 2001), use the wall heat fractions as outputted from the Ventilation Model to initialize their post-closure analyses. The Ventilation Model report was initially developed to analyze the effects of preclosure continuous ventilation in the Engineered Barrier System (EBS) emplacement drifts, and to provide heat removal data to support EBS design. Revision 00 of the Ventilation Model included documentation of the modeling results from the ANSYS-based heat transfer model. The purposes of Revision 01 of the Ventilation Model are: (1) To validate the conceptual model for preclosure ventilation of emplacement drifts and verify its numerical application in accordance with new procedural requirements as outlined in AP-SIII-10Q, Models (Section 7.0). (2) To satisfy technical issues posed in KTI agreement RDTME 3.14 (Reamer and Williams 2001a). Specifically to demonstrate, with respect to the ANSYS ventilation model, the adequacy of the discretization (Section 6.2.3.1), and the downstream applicability of the model results (i.e. wall heat fractions) to initialize post

  7. Model Selection for Geostatistical Models

    SciTech Connect

    Hoeting, Jennifer A.; Davis, Richard A.; Merton, Andrew A.; Thompson, Sandra E.

    2006-02-01

    We consider the problem of model selection for geospatial data. Spatial correlation is typically ignored in the selection of explanatory variables and this can influence model selection results. For example, the inclusion or exclusion of particular explanatory variables may not be apparent when spatial correlation is ignored. To address this problem, we consider the Akaike Information Criterion (AIC) as applied to a geostatistical model. We offer a heuristic derivation of the AIC in this context and provide simulation results that show that using AIC for a geostatistical model is superior to the often used approach of ignoring spatial correlation in the selection of explanatory variables. These ideas are further demonstrated via a model for lizard abundance. We also employ the principle of minimum description length (MDL) to variable selection for the geostatistical model. The effect of sampling design on the selection of explanatory covariates is also explored.

  8. Turbulence modeling

    NASA Technical Reports Server (NTRS)

    Bardina, Jorge E.

    1995-01-01

    The objective of this work is to develop, verify, and incorporate the baseline two-equation turbulence models which account for the effects of compressibility into the three-dimensional Reynolds averaged Navier-Stokes (RANS) code and to provide documented descriptions of the models and their numerical procedures so that they can be implemented into 3-D CFD codes for engineering applications.

  9. Budget Model.

    ERIC Educational Resources Information Center

    Washington State Board for Community Coll. Education, Olympia.

    Computerized formula-driven budget models are used by the Washington community college system to define resource needs for legislative budget requests and to distribute legislative appropriations among 22 community college districts. This manual outlines the sources of information needed to operate the model and illustrates the principles on which…

  10. Dispersion Modeling.

    ERIC Educational Resources Information Center

    Budiansky, Stephen

    1980-01-01

    This article discusses the need for more accurate and complete input data and field verification of the various models of air pollutant dispension. Consideration should be given to changing the form of air quality standards based on enhanced dispersion modeling techniques. (Author/RE)

  11. Modeling Sunspots

    ERIC Educational Resources Information Center

    Oh, Phil Seok; Oh, Sung Jin

    2013-01-01

    Modeling in science has been studied by education researchers for decades and is now being applied broadly in school. It is among the scientific practices featured in the "Next Generation Science Standards" ("NGSS") (Achieve Inc. 2013). This article describes modeling activities in an extracurricular science club in a high…

  12. Phonological Models.

    ERIC Educational Resources Information Center

    Ballard, W.L.

    1968-01-01

    The article discusses models of synchronic and diachronic phonology and suggests changes in them. The basic generative model of phonology is outlined with the author's reinterpretations. The systematic phonemic level is questioned in terms of its unreality with respect to linguistic performance and its lack of validity with respect to historical…

  13. Zitterbewegung modeling

    SciTech Connect

    Hestenes, D. )

    1993-03-01

    Guidelines for constructing point particle models of the electron with [ital zitterbewegung] and other features of the Dirac theory are discussed. Such models may at least be useful approximations to the Dirac theory, but the more exciting possibility is that this approach may lead to a more fundamental reality. 6 refs.

  14. Statistical mechanics of human resource allocation

    NASA Astrophysics Data System (ADS)

    Inoue, Jun-Ichi; Chen, He

    2014-03-01

    We provide a mathematical platform to investigate the network topology of agents, say, university graduates who are looking for their positions in labor markets. The basic model is described by the so-called Potts spin glass which is well-known in the research field of statistical physics. In the model, each Potts spin (a tiny magnet in atomic scale length) represents the action of each student, and it takes a discrete variable corresponding to the company he/she applies for. We construct the energy to include three distinct effects on the students' behavior, namely, collective effect, market history and international ranking of companies. In this model system, the correlations (the adjacent matrix) between students are taken into account through the pairwise spin-spin interactions. We carry out computer simulations to examine the efficiency of the model. We also show that some chiral representation of the Potts spin enables us to obtain some analytical insights into our labor markets. This work was financially supported by Grant-in-Aid for Scientific Research (C) of Japan Society for the Promotion of Science No. 25330278.

  15. Efficient parallel tempering for first-order phase transitions.

    PubMed

    Neuhaus, T; Magiera, M P; Hansmann, U H E

    2007-10-01

    We present a Monte Carlo algorithm that facilitates efficient parallel tempering simulations of the density of states g(E) . We show that the algorithm eliminates the supercritical slowing down in the case of the Q=20 and Q=256 Potts models in two dimensions, typical examples for systems with extreme first-order phase transitions. As recently predicted, and shown here, the microcanonical heat capacity along the calorimetric curve has negative values for finite systems. PMID:17995052

  16. Spin-spin correlation functions of spin systems coupled to 2-d quantum gravity for 0 < c < 1.

    NASA Astrophysics Data System (ADS)

    Ambjørn, J.; Anagnostopoulos, K. N.; Magnea, U.; Thorleifsson, G.

    1997-02-01

    We perform Monte Carlo simulations of 2-d dynamically triangulated surfaces coupled to Ising and three-states Potts model matter. By measuring spin-spin correlation functions as a function of the geodesic distance we provide substantial evidence for a diverging correlation length at βc. The corresponding scaling exponents are directly related to the KPZ exponents of the matter fields as conjectured in [4].

  17. OSPREY Model

    SciTech Connect

    Veronica J. Rutledge

    2013-01-01

    The absence of industrial scale nuclear fuel reprocessing in the U.S. has precluded the necessary driver for developing the advanced simulation capability now prevalent in so many other countries. Thus, it is essential to model complex series of unit operations to simulate, understand, and predict inherent transient behavior and feedback loops. A capability of accurately simulating the dynamic behavior of advanced fuel cycle separation processes will provide substantial cost savings and many technical benefits. The specific fuel cycle separation process discussed in this report is the off-gas treatment system. The off-gas separation consists of a series of scrubbers and adsorption beds to capture constituents of interest. Dynamic models are being developed to simulate each unit operation involved so each unit operation can be used as a stand-alone model and in series with multiple others. Currently, an adsorption model has been developed within Multi-physics Object Oriented Simulation Environment (MOOSE) developed at the Idaho National Laboratory (INL). Off-gas Separation and REcoverY (OSPREY) models the adsorption of off-gas constituents for dispersed plug flow in a packed bed under non-isothermal and non-isobaric conditions. Inputs to the model include gas, sorbent, and column properties, equilibrium and kinetic data, and inlet conditions. The simulation outputs component concentrations along the column length as a function of time from which breakthrough data is obtained. The breakthrough data can be used to determine bed capacity, which in turn can be used to size columns. It also outputs temperature along the column length as a function of time and pressure drop along the column length. Experimental data and parameters were input into the adsorption model to develop models specific for krypton adsorption. The same can be done for iodine, xenon, and tritium. The model will be validated with experimental breakthrough curves. Customers will be given access to

  18. A hidden markov model derived structural alphabet for proteins.

    PubMed

    Camproux, A C; Gautier, R; Tufféry, P

    2004-06-01

    Understanding and predicting protein structures depends on the complexity and the accuracy of the models used to represent them. We have set up a hidden Markov model that discretizes protein backbone conformation as series of overlapping fragments (states) of four residues length. This approach learns simultaneously the geometry of the states and their connections. We obtain, using a statistical criterion, an optimal systematic decomposition of the conformational variability of the protein peptidic chain in 27 states with strong connection logic. This result is stable over different protein sets. Our model fits well the previous knowledge related to protein architecture organisation and seems able to grab some subtle details of protein organisation, such as helix sub-level organisation schemes. Taking into account the dependence between the states results in a description of local protein structure of low complexity. On an average, the model makes use of only 8.3 states among 27 to describe each position of a protein structure. Although we use short fragments, the learning process on entire protein conformations captures the logic of the assembly on a larger scale. Using such a model, the structure of proteins can be reconstructed with an average accuracy close to 1.1A root-mean-square deviation and for a complexity of only 3. Finally, we also observe that sequence specificity increases with the number of states of the structural alphabet. Such models can constitute a very relevant approach to the analysis of protein architecture in particular for protein structure prediction. PMID:15147844

  19. Phenomenological models.

    PubMed

    Braby, L A

    1991-01-01

    The biological effects of ionizing radiation exposure are the result of a complex sequence of physical, chemical, biochemical, and physiological interactions which are modified by characteristics of the radiation, the timing of its administration, the chemical and physical environment, and the nature of the biological system. However, it is generally agreed that the health effects in animals originate from changes in individual cells, or possibly small groups of cells, and that these cellular changes are initiated by ionizations and excitations produced by the passage of charged particles through the cells. One way to begin a search for an understanding of health effects of radiation is through the development of phenomenological models of the response. Many models have been presented and tested in the slowly evolving process of characterizing cellular response. Different phenomena (LET dependence, dose rate effect, oxygen effect etc.) and different end points (cell survival, aberration formation, transformation, etc.) have been observed, and no single model has been developed to cover all of them. Instead, a range of models covering different end points and phenomena have developed in parallel. Many of these models employ similar assumptions about some underlying processes while differing about the nature of others. An attempt is made to organize many of the models into groups with similar features and to compare the consequences of those features with the actual experimental observations. It is assumed that by showing that some assumptions are inconsistent with experimental observations, the job of devising and testing mechanistic models can be simplified. PMID:1811477

  20. Stereometric Modelling

    NASA Astrophysics Data System (ADS)

    Grimaldi, P.

    2012-07-01

    These mandatory guidelines are provided for preparation of papers accepted for publication in the series of Volumes of The The stereometric modelling means modelling achieved with : - the use of a pair of virtual cameras, with parallel axes and positioned at a mutual distance average of 1/10 of the distance camera-object (in practice the realization and use of a stereometric camera in the modeling program); - the shot visualization in two distinct windows - the stereoscopic viewing of the shot while modelling. Since the definition of "3D vision" is inaccurately referred to as the simple perspective of an object, it is required to add the word stereo so that "3D stereo vision " shall stand for "three-dimensional view" and ,therefore, measure the width, height and depth of the surveyed image. Thanks to the development of a stereo metric model , either real or virtual, through the "materialization", either real or virtual, of the optical-stereo metric model made visible with a stereoscope. It is feasible a continuous on line updating of the cultural heritage with the help of photogrammetry and stereometric modelling. The catalogue of the Architectonic Photogrammetry Laboratory of Politecnico di Bari is available on line at: http://rappresentazione.stereofot.it:591/StereoFot/FMPro?-db=StereoFot.fp5&-lay=Scheda&-format=cerca.htm&-view

  1. Model hydrographs

    USGS Publications Warehouse

    Mitchell, W.D.

    1972-01-01

    Model hydrographs are composed of pairs of dimensionless ratios, arrayed in tabular form, which, when modified by the appropriate values of rainfall exceed and by the time and areal characteristics of the drainage basin, satisfactorily represent the flood hydrograph for the basin. Model bydrographs are developed from a dimensionless translation hydrograph, having a time base of T hours and appropriately modified for storm duration by routing through reservoir storage, S=kOx. Models fall into two distinct classes: (1) those for which the value of x is unity and which have all the characteristics of true unit hydrographs and (2) those for which the value of x is other than unity and to which the unit-hydrograph principles of proportionality and superposition do not apply. Twenty-six families of linear models and eight families of nonlinear models in tabular form from the principal subject of this report. Supplemental discussions describe the development of the models and illustrate their application. Other sections of the report, supplemental to the tables, describe methods of determining the hydrograph characteristics, T, k, and x, both from observed hydrograph and from the physical characteristics of the drainage basin. Five illustrative examples of use show that the models, when properly converted to incorporate actual rainfall excess and the time and areal characteristics of the drainage basins, do indeed satisfactorily represent the observed flood hydrographs for the basins.

  2. Replica inference approach to unsupervised multiscale image segmentation

    NASA Astrophysics Data System (ADS)

    Hu, Dandan; Ronhovde, Peter; Nussinov, Zohar

    2012-01-01

    We apply a replica-inference-based Potts model method to unsupervised image segmentation on multiple scales. This approach was inspired by the statistical mechanics problem of “community detection” and its phase diagram. Specifically, the problem is cast as identifying tightly bound clusters (“communities” or “solutes”) against a background or “solvent.” Within our multiresolution approach, we compute information-theory-based correlations among multiple solutions (“replicas”) of the same graph over a range of resolutions. Significant multiresolution structures are identified by replica correlations manifest by information theory overlaps. We further employ such information theory measures (such as normalized mutual information and variation of information), thermodynamic quantities such as the system entropy and energy, and dynamic measures monitoring the convergence time to viable solutions as metrics for transitions between various solvable and unsolvable phases. Within the solvable phase, transitions between contending solutions (such as those corresponding to segmentations on different scales) may also appear. With the aid of these correlations as well as thermodynamic measures, the phase diagram of the corresponding Potts model is analyzed at both zero and finite temperatures. Optimal parameters corresponding to a sensible unsupervised segmentations appear within the “easy phase” of the Potts model. Our algorithm is fast and shown to be at least as accurate as the best algorithms to date and to be especially suited to the detection of camouflaged images.

  3. Statistics and dynamics of attractor networks with inter-correlated patterns

    NASA Astrophysics Data System (ADS)

    Kropff, E.

    2007-02-01

    In an embodied feature representation view, the semantic memory represents concepts in the brain by the associated activation of the features that describe it, each one of them processed in a differentiated region of the cortex. This system has been modeled with a Potts attractor network. Several studies of feature representation show that the correlation between patterns plays a crucial role in semantic memory. The present work focuses on two aspects of the effect of correlations in attractor networks. In first place, it assesses how a Potts network can store a set of patterns with non-trivial correlations between them. This is done through a simple and biologically plausible modification to the classical learning rule. In second place, it studies the complexity of latching transitions between attractor states, and how this complexity can be controlled.

  4. Bayesian inversion for optical diffraction tomography

    NASA Astrophysics Data System (ADS)

    Ayasso, H.; Duchêne, B.; Mohammad-Djafari, A.

    2010-05-01

    In this paper, optical diffraction tomography is considered as a non-linear inverse scattering problem and tackled within the Bayesian estimation framework. The object under test is a man-made object known to be composed of compact regions made of a finite number of different homogeneous materials. This a priori knowledge is appropriately translated by a Gauss-Markov-Potts prior. Hence, a Gauss-Markov random field is used to model the contrast distribution whereas a hidden Potts-Markov field accounts for the compactness of the regions. First, we express the a posteriori distributions of all the unknowns and then a Gibbs sampling algorithm is used to generate samples and estimate the posterior mean of the unknowns. Some preliminary results, obtained by applying the inversion algorithm to laboratory controlled data, are presented.

  5. Programming models

    SciTech Connect

    Daniel, David J; Mc Pherson, Allen; Thorp, John R; Barrett, Richard; Clay, Robert; De Supinski, Bronis; Dube, Evi; Heroux, Mike; Janssen, Curtis; Langer, Steve; Laros, Jim

    2011-01-14

    A programming model is a set of software technologies that support the expression of algorithms and provide applications with an abstract representation of the capabilities of the underlying hardware architecture. The primary goals are productivity, portability and performance.

  6. Energy Models

    EPA Science Inventory

    Energy models characterize the energy system, its evolution, and its interactions with the broader economy. The energy system consists of primary resources, including both fossil fuels and renewables; power plants, refineries, and other technologies to process and convert these r...

  7. Mechanistic models

    SciTech Connect

    Curtis, S.B.

    1990-09-01

    Several models and theories are reviewed that incorporate the idea of radiation-induced lesions (repairable and/or irreparable) that can be related to molecular lesions in the DNA molecule. Usually the DNA double-strand or chromatin break is suggested as the critical lesion. In the models, the shoulder on the low-LET survival curve is hypothesized as being due to one (or more) of the following three mechanisms: (1) ``interaction`` of lesions produced by statistically independent particle tracks; (2) nonlinear (i.e., linear-quadratic) increase in the yield of initial lesions, and (3) saturation of repair processes at high dose. Comparisons are made between the various approaches. Several significant advances in model development are discussed; in particular, a description of the matrix formulation of the Markov versions of the RMR and LPL models is given. The more advanced theories have incorporated statistical fluctuations in various aspects of the energy-loss and lesion-formation process. An important direction is the inclusion of physical and chemical processes into the formulations by incorporating relevant track structure theory (Monte Carlo track simulations) and chemical reactions of radiation-induced radicals. At the biological end, identification of repair genes and how they operate as well as a better understanding of how DNA misjoinings lead to lethal chromosome aberrations are needed for appropriate inclusion into the theories. More effort is necessary to model the complex end point of radiation-induced carcinogenesis.

  8. Mechanistic models

    SciTech Connect

    Curtis, S.B.

    1990-09-01

    Several models and theories are reviewed that incorporate the idea of radiation-induced lesions (repairable and/or irreparable) that can be related to molecular lesions in the DNA molecule. Usually the DNA double-strand or chromatin break is suggested as the critical lesion. In the models, the shoulder on the low-LET survival curve is hypothesized as being due to one (or more) of the following three mechanisms: (1) interaction'' of lesions produced by statistically independent particle tracks; (2) nonlinear (i.e., linear-quadratic) increase in the yield of initial lesions, and (3) saturation of repair processes at high dose. Comparisons are made between the various approaches. Several significant advances in model development are discussed; in particular, a description of the matrix formulation of the Markov versions of the RMR and LPL models is given. The more advanced theories have incorporated statistical fluctuations in various aspects of the energy-loss and lesion-formation process. An important direction is the inclusion of physical and chemical processes into the formulations by incorporating relevant track structure theory (Monte Carlo track simulations) and chemical reactions of radiation-induced radicals. At the biological end, identification of repair genes and how they operate as well as a better understanding of how DNA misjoinings lead to lethal chromosome aberrations are needed for appropriate inclusion into the theories. More effort is necessary to model the complex end point of radiation-induced carcinogenesis.

  9. Modeling reality

    NASA Technical Reports Server (NTRS)

    Denning, Peter J.

    1990-01-01

    Although powerful computers have allowed complex physical and manmade hardware systems to be modeled successfully, we have encountered persistent problems with the reliability of computer models for systems involving human learning, human action, and human organizations. This is not a misfortune; unlike physical and manmade systems, human systems do not operate under a fixed set of laws. The rules governing the actions allowable in the system can be changed without warning at any moment, and can evolve over time. That the governing laws are inherently unpredictable raises serious questions about the reliability of models when applied to human situations. In these domains, computers are better used, not for prediction and planning, but for aiding humans. Examples are systems that help humans speculate about possible futures, offer advice about possible actions in a domain, systems that gather information from the networks, and systems that track and support work flows in organizations.

  10. Molecular Modeling

    NASA Astrophysics Data System (ADS)

    Holmes, Jon L.

    1999-06-01

    Molecular modeling has trickled down from the realm of pharmaceutical and research laboratories into the realm of undergraduate chemistry instruction. It has opened avenues for the visualization of chemical concepts that previously were difficult or impossible to convey. I am sure that many of you have developed exercises using the various molecular modeling tools. It is the desire of this Journal to become an avenue for you to share these exercises among your colleagues. It is to this end that Ron Starkey has agreed to edit such a column and to publish not only the description of such exercises, but also the software documents they use. The WWW is the obvious medium to distribute this combination and so accepted submissions will appear online as a feature of JCE Internet. Typical molecular modeling exercise: finding conformation energies. Molecular Modeling Exercises and Experiments is the latest feature column of JCE Internet, joining Conceptual Questions and Challenge Problems, Hal's Picks, and Mathcad in the Chemistry Curriculum. JCE Internet continues to seek submissions in these areas of interest and submissions of general interest. If you have developed materials and would like to submit them, please see our Guide to Submissions for more information. The Chemical Education Resource Shelf, Equipment Buyers Guide, and WWW Site Review would also like to hear about chemistry textbooks and software, equipment, and WWW sites, respectively. Please consult JCE Internet Features to learn more about these resources at JCE Online. Email Announcements Would you like to be informed by email when the latest issue of the Journal is available online? when a new JCE Software title is shipping? when a new JCE Internet article has been published or is available for Open Review? when your subscription is about to expire? A new feature of JCE Online makes this possible. Visit our Guestbook to learn how. When

  11. Supernova models

    SciTech Connect

    Woosley, S.E.; Weaver, T.A.

    1980-01-01

    Recent progress in understanding the observed properties of Type I supernovae as a consequence of the thermonuclear detonation of white dwarf stars and the ensuing decay of the /sup 56/Ni produced therein is reviewed. Within the context of this model for Type I explosions and the 1978 model for Type II explosions, the expected nucleosynthesis and gamma-line spectra from both kinds of supernovae are presented. Finally, a qualitatively new approach to the problem of massive star death and Type II supernovae based upon a combination of rotation and thermonuclear burning is discussed.

  12. Atmospheric Modeling

    EPA Science Inventory

    Although air quality models have been applied historically to address issues specific to ambient air quality standards (i.e., one criteria pollutant at a time) or welfare (e.g.. acid deposition or visibility impairment). they are inherently multipollutant based. Therefore. in pri...

  13. Ensemble Models

    EPA Science Inventory

    Ensemble forecasting has been used for operational numerical weather prediction in the United States and Europe since the early 1990s. An ensemble of weather or climate forecasts is used to characterize the two main sources of uncertainty in computer models of physical systems: ...

  14. Modeling Convection

    ERIC Educational Resources Information Center

    Ebert, James R.; Elliott, Nancy A.; Hurteau, Laura; Schulz, Amanda

    2004-01-01

    Students must understand the fundamental process of convection before they can grasp a wide variety of Earth processes, many of which may seem abstract because of the scales on which they operate. Presentation of a very visual, concrete model prior to instruction on these topics may facilitate students' understanding of processes that are largely…

  15. Painting models

    NASA Astrophysics Data System (ADS)

    Baart, F.; Donchyts, G.; van Dam, A.; Plieger, M.

    2015-12-01

    The emergence of interactive art has blurred the line between electronic, computer graphics and art. Here we apply this art form to numerical models. Here we show how the transformation of a numerical model into an interactive painting can both provide insights and solve real world problems. The cases that are used as an example include forensic reconstructions, dredging optimization, barrier design. The system can be fed using any source of time varying vector fields, such as hydrodynamic models. The cases used here, the Indian Ocean (HYCOM), the Wadden Sea (Delft3D Curvilinear), San Francisco Bay (3Di subgrid and Delft3D Flexible Mesh), show that the method used is suitable for different time and spatial scales. High resolution numerical models become interactive paintings by exchanging their velocity fields with a high resolution (>=1M cells) image based flow visualization that runs in a html5 compatible web browser. The image based flow visualization combines three images into a new image: the current image, a drawing, and a uv + mask field. The advection scheme that computes the resultant image is executed in the graphics card using WebGL, allowing for 1M grid cells at 60Hz performance on mediocre graphic cards. The software is provided as open source software. By using different sources for a drawing one can gain insight into several aspects of the velocity fields. These aspects include not only the commonly represented magnitude and direction, but also divergence, topology and turbulence .

  16. Entrepreneurship Models.

    ERIC Educational Resources Information Center

    Finger Lakes Regional Education Center for Economic Development, Mount Morris, NY.

    This guide describes seven model programs that were developed by the Finger Lakes Regional Center for Economic Development (New York) to meet the training needs of female and minority entrepreneurs to help their businesses survive and grow and to assist disabled and dislocated workers and youth in beginning small businesses. The first three models…

  17. Modeling Lessons

    ERIC Educational Resources Information Center

    Casey, Katherine

    2011-01-01

    As teachers learn new pedagogical strategies, they crave explicit demonstrations that show them how the new strategies will work with their students in their classrooms. Successful instructional coaches, therefore, understand the importance of modeling lessons to help teachers develop a vision of effective instruction. The author, an experienced…

  18. Modeling Muscles

    ERIC Educational Resources Information Center

    Goodwyn, Lauren; Salm, Sarah

    2007-01-01

    Teaching the anatomy of the muscle system to high school students can be challenging. Students often learn about muscle anatomy by memorizing information from textbooks or by observing plastic, inflexible models. Although these mediums help students learn about muscle placement, the mediums do not facilitate understanding regarding integration of…

  19. Criticality Model

    SciTech Connect

    A. Alsaed

    2004-09-14

    The ''Disposal Criticality Analysis Methodology Topical Report'' (YMP 2003) presents the methodology for evaluating potential criticality situations in the monitored geologic repository. As stated in the referenced Topical Report, the detailed methodology for performing the disposal criticality analyses will be documented in model reports. Many of the models developed in support of the Topical Report differ from the definition of models as given in the Office of Civilian Radioactive Waste Management procedure AP-SIII.10Q, ''Models'', in that they are procedural, rather than mathematical. These model reports document the detailed methodology necessary to implement the approach presented in the Disposal Criticality Analysis Methodology Topical Report and provide calculations utilizing the methodology. Thus, the governing procedure for this type of report is AP-3.12Q, ''Design Calculations and Analyses''. The ''Criticality Model'' is of this latter type, providing a process evaluating the criticality potential of in-package and external configurations. The purpose of this analysis is to layout the process for calculating the criticality potential for various in-package and external configurations and to calculate lower-bound tolerance limit (LBTL) values and determine range of applicability (ROA) parameters. The LBTL calculations and the ROA determinations are performed using selected benchmark experiments that are applicable to various waste forms and various in-package and external configurations. The waste forms considered in this calculation are pressurized water reactor (PWR), boiling water reactor (BWR), Fast Flux Test Facility (FFTF), Training Research Isotope General Atomic (TRIGA), Enrico Fermi, Shippingport pressurized water reactor, Shippingport light water breeder reactor (LWBR), N-Reactor, Melt and Dilute, and Fort Saint Vrain Reactor spent nuclear fuel (SNF). The scope of this analysis is to document the criticality computational method. The criticality

  20. Modeling Molecules

    NASA Technical Reports Server (NTRS)

    2000-01-01

    The molecule modeling method known as Multibody Order (N) Dynamics, or MBO(N)D, was developed by Moldyn, Inc. at Goddard Space Flight Center through funding provided by the SBIR program. The software can model the dynamics of molecules through technology which stimulates low-frequency molecular motions and properties, such as movements among a molecule's constituent parts. With MBO(N)D, a molecule is substructured into a set of interconnected rigid and flexible bodies. These bodies replace the computation burden of mapping individual atoms. Moldyn's technology cuts computation time while increasing accuracy. The MBO(N)D technology is available as Insight II 97.0 from Molecular Simulations, Inc. Currently the technology is used to account for forces on spacecraft parts and to perform molecular analyses for pharmaceutical purposes. It permits the solution of molecular dynamics problems on a moderate workstation, as opposed to on a supercomputer.

  1. Dendrite Model

    NASA Technical Reports Server (NTRS)

    1999-01-01

    Dr. Donald Gilles, the Discipline Scientist for Materials Science in NASA's Microgravity Materials Science and Applications Department, demonstrates to Carl Dohrman a model of dendrites, the branch-like structures found in many metals and alloys. Dohrman was recently selected by the American Society for Metals International as their 1999 ASM International Foundation National Merit Scholar. The University of Illinois at Urbana-Champaign freshman recently toured NASA's materials science facilities at the Marshall Space Flight Center.

  2. Model checking

    NASA Technical Reports Server (NTRS)

    Dill, David L.

    1995-01-01

    Automatic formal verification methods for finite-state systems, also known as model-checking, successfully reduce labor costs since they are mostly automatic. Model checkers explicitly or implicitly enumerate the reachable state space of a system, whose behavior is described implicitly, perhaps by a program or a collection of finite automata. Simple properties, such as mutual exclusion or absence of deadlock, can be checked by inspecting individual states. More complex properties, such as lack of starvation, require search for cycles in the state graph with particular properties. Specifications to be checked may consist of built-in properties, such as deadlock or 'unspecified receptions' of messages, another program or implicit description, to be compared with a simulation, bisimulation, or language inclusion relation, or an assertion in one of several temporal logics. Finite-state verification tools are beginning to have a significant impact in commercial designs. There are many success stories of verification tools finding bugs in protocols or hardware controllers. In some cases, these tools have been incorporated into design methodology. Research in finite-state verification has been advancing rapidly, and is showing no signs of slowing down. Recent results include probabilistic algorithms for verification, exploitation of symmetry and independent events, and the use symbolic representations for Boolean functions and systems of linear inequalities. One of the most exciting areas for further research is the combination of model-checking with theorem-proving methods.

  3. Modeling biomembranes.

    SciTech Connect

    Plimpton, Steven James; Heffernan, Julieanne; Sasaki, Darryl Yoshio; Frischknecht, Amalie Lucile; Stevens, Mark Jackson; Frink, Laura J. Douglas

    2005-11-01

    Understanding the properties and behavior of biomembranes is fundamental to many biological processes and technologies. Microdomains in biomembranes or ''lipid rafts'' are now known to be an integral part of cell signaling, vesicle formation, fusion processes, protein trafficking, and viral and toxin infection processes. Understanding how microdomains form, how they depend on membrane constituents, and how they act not only has biological implications, but also will impact Sandia's effort in development of membranes that structurally adapt to their environment in a controlled manner. To provide such understanding, we created physically-based models of biomembranes. Molecular dynamics (MD) simulations and classical density functional theory (DFT) calculations using these models were applied to phenomena such as microdomain formation, membrane fusion, pattern formation, and protein insertion. Because lipid dynamics and self-organization in membranes occur on length and time scales beyond atomistic MD, we used coarse-grained models of double tail lipid molecules that spontaneously self-assemble into bilayers. DFT provided equilibrium information on membrane structure. Experimental work was performed to further help elucidate the fundamental membrane organization principles.

  4. Impact of smoke-free residence hall policies: the views of administrators at 3 state universities.

    PubMed

    Gerson, Megan; Allard, Jennifer L; Towvim, Laura Gomberg

    2005-01-01

    Nationwide efforts to protect the public against the health effects of secondhand smoke have prompted college and university administrators to adopt more restrictive smoking policies. Some campus officials are concerned that new policies will lead to student backlash, increased staff workloads, and an increased economic burden. To understand the impact of smoke-free residence hall policies, we conducted key informant interviews and gathered archival data at 3 large state universities. The implementation of smoke-free residence hall policies imposed little economic burden. We noted positive impacts in several key areas, including decreased damage to residence hall buildings, increased student retention, and improved enforcement of marijuana policies. Increased costs, such as the purchase of outdoor cigarette receptacles, were outweighed by the benefits. Findings from this study should encourage college and university administrators to enact smoke-free residence hall policies. PMID:16335315

  5. Defining the Nature of Thermal Intermediate in 3 State Folding Proteins: Apoflavodoxin, a Study Case

    PubMed Central

    García-Fandiño, Rebeca; Bernadó, Pau; Ayuso-Tejedor, Sara; Sancho, Javier; Orozco, Modesto

    2012-01-01

    The early stages of the thermal unfolding of apoflavodoxin have been determined by using atomistic multi microsecond-scale molecular dynamics (MD) simulations complemented with a variety of experimental techniques. Results strongly suggest that the intermediate is reached very early in the thermal unfolding process and that it has the properties of an “activated” form of the native state, where thermal fluctuations in the loops break loop-loop contacts. The unrestrained loops gain then kinetic energy corrupting short secondary structure elements without corrupting the core of the protein. The MD-derived ensembles agree with experimental observables and draw a picture of the intermediate state inconsistent with a well-defined structure and characteristic of a typical partially disordered protein. Our results allow us to speculate that proteins with a well packed core connected by long loops might behave as partially disordered proteins under native conditions, or alternatively behave as three state folders. Small details in the sequence, easily tunable by evolution, can yield to one or the other type of proteins. PMID:22927805

  6. Trends in Energy Management Technology - Part 3: State of Practiceof Energy Management, Control, and Information Systems

    SciTech Connect

    Yee, Gaymond; Webster, Tom

    2004-02-01

    In this report, the third in a series, we provide an evaluation of several products that exemplify the current state of practice of Energy Management, Control, and Information Systems (EMCIS). The available features for these products are summarized and analyzed with regard to emerging trends in EMCIS and potential benefits to the federal sector. The first report [1] covered enabling technologies for emerging energy management systems. The second report [2] serves as a basic reference for building control system (BCS) networking fundamentals and includes an assessment of current approaches to open communications. Part 4 of this series will discuss applications software from a user's perspective. It is important for energy managers in the Federal sector to have a high level of knowledge and understanding of these complex energy management systems. This series of reports provides energy practitioners with some basic informational and educational tools to help make decisions relative to energy management systems design, specification, procurement, and energy savings potential.

  7. 7 CFR 1900.3 - State, district, and county office employees.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... disposition: Chief, Farmer Programs/Specialist; Chief, Rural Housing/Specialist; Chief, Community Programs..., and in the absence or disability of any such official or employee, the person acting in the position....

  8. 50 CFR 70.3 - State cooperation in national fish hatchery area management.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 50 Wildlife and Fisheries 6 2010-10-01 2010-10-01 false State cooperation in national fish hatchery area management. 70.3 Section 70.3 Wildlife and Fisheries UNITED STATES FISH AND WILDLIFE SERVICE, DEPARTMENT OF THE INTERIOR (CONTINUED) MANAGEMENT OF FISHERIES CONSERVATION AREAS NATIONAL FISH...

  9. 50 CFR 70.3 - State cooperation in national fish hatchery area management.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 50 Wildlife and Fisheries 8 2011-10-01 2011-10-01 false State cooperation in national fish hatchery area management. 70.3 Section 70.3 Wildlife and Fisheries UNITED STATES FISH AND WILDLIFE SERVICE, DEPARTMENT OF THE INTERIOR (CONTINUED) MANAGEMENT OF FISHERIES CONSERVATION AREAS NATIONAL FISH...

  10. Higher Education Spending and the State Fiscal Stabilization Fund, Part 3: State Case Studies

    ERIC Educational Resources Information Center

    Cohen, Jennifer

    2011-01-01

    By late 2008, the United States was in the midst of its most severe economic recession since the 1930s, brought on by a collapse in real estate prices and exacerbated by the failure of many large banks and financial institutions. Heeding calls from economists, Congress and the Obama administration passed an historic law in early 2009 to stimulate…

  11. Impact of Smoke-Free Residence Hall Policies: The Views of Administrators at 3 State Universities

    ERIC Educational Resources Information Center

    Gerson, Megan

    2005-01-01

    Nationwide efforts to protect the public against the health effects of secondhand smoke have prompted college and university administrators to adopt more restrictive smoking policies. Some campus officials are concerned that new policies will lead to student backlash, increased staff workloads, and an increased economic burden. To understand the…

  12. 50 CFR 70.3 - State cooperation in national fish hatchery area management.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 50 Wildlife and Fisheries 9 2014-10-01 2014-10-01 false State cooperation in national fish hatchery area management. 70.3 Section 70.3 Wildlife and Fisheries UNITED STATES FISH AND WILDLIFE SERVICE, DEPARTMENT OF THE INTERIOR (CONTINUED) MANAGEMENT OF FISHERIES CONSERVATION AREAS NATIONAL FISH...

  13. 50 CFR 70.3 - State cooperation in national fish hatchery area management.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 50 Wildlife and Fisheries 9 2012-10-01 2012-10-01 false State cooperation in national fish hatchery area management. 70.3 Section 70.3 Wildlife and Fisheries UNITED STATES FISH AND WILDLIFE SERVICE, DEPARTMENT OF THE INTERIOR (CONTINUED) MANAGEMENT OF FISHERIES CONSERVATION AREAS NATIONAL FISH...

  14. 50 CFR 70.3 - State cooperation in national fish hatchery area management.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 50 Wildlife and Fisheries 9 2013-10-01 2013-10-01 false State cooperation in national fish hatchery area management. 70.3 Section 70.3 Wildlife and Fisheries UNITED STATES FISH AND WILDLIFE SERVICE, DEPARTMENT OF THE INTERIOR (CONTINUED) MANAGEMENT OF FISHERIES CONSERVATION AREAS NATIONAL FISH...

  15. 10. MOVABLE BED SEDIMENTATION MODELS. DOGTOOTH BEND MODEL (MODEL SCALE: ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    10. MOVABLE BED SEDIMENTATION MODELS. DOGTOOTH BEND MODEL (MODEL SCALE: 1' = 400' HORIZONTAL, 1' = 100' VERTICAL), AND GREENVILLE BRIDGE MODEL (MODEL SCALE: 1' = 360' HORIZONTAL, 1' = 100' VERTICAL). - Waterways Experiment Station, Hydraulics Laboratory, Halls Ferry Road, 2 miles south of I-20, Vicksburg, Warren County, MS

  16. Students' Models of Curve Fitting: A Models and Modeling Perspective

    ERIC Educational Resources Information Center

    Gupta, Shweta

    2010-01-01

    The Models and Modeling Perspectives (MMP) has evolved out of research that began 26 years ago. MMP researchers use Model Eliciting Activities (MEAs) to elicit students' mental models. In this study MMP was used as the conceptual framework to investigate the nature of students' models of curve fitting in a problem-solving environment consisting of…

  17. Biomimetic modelling.

    PubMed Central

    Vincent, Julian F V

    2003-01-01

    Biomimetics is seen as a path from biology to engineering. The only path from engineering to biology in current use is the application of engineering concepts and models to biological systems. However, there is another pathway: the verification of biological mechanisms by manufacture, leading to an iterative process between biology and engineering in which the new understanding that the engineering implementation of a biological system can bring is fed back into biology, allowing a more complete and certain understanding and the possibility of further revelations for application in engineering. This is a pathway as yet unformalized, and one that offers the possibility that engineers can also be scientists. PMID:14561351

  18. Noise-induced absorbing phase transition in a model of opinion formation

    NASA Astrophysics Data System (ADS)

    Vieira, Allan R.; Crokidakis, Nuno

    2016-08-01

    In this work we study a 3-state (+1, -1, 0) opinion model in the presence of noise and disorder. We consider pairwise competitive interactions, with a fraction p of those interactions being negative (disorder). Moreover, there is a noise q that represents the probability of an individual spontaneously change his opinion to the neutral state. Our aim is to study how the increase/decrease of the fraction of neutral agents affects the critical behavior of the system and the evolution of opinions. We derive analytical expressions for the order parameter of the model, as well as for the stationary fraction of each opinion, and we show that there are distinct phase transitions. One is the usual ferro-paramagnetic transition, that is in the Ising universality class. In addition, there are para-absorbing and ferro-absorbing transitions, presenting the directed percolation universality class. Our results are complemented by numerical simulations.

  19. Modeling fatigue.

    PubMed Central

    Sumner, Walton; Xu, Jin Zhong

    2002-01-01

    The American Board of Family Practice is developing a patient simulation program to evaluate diagnostic and management skills. The simulator must give temporally and physiologically reasonable answers to symptom questions such as "Have you been tired?" A three-step process generates symptom histories. In the first step, the simulator determines points in time where it should calculate instantaneous symptom status. In the second step, a Bayesian network implementing a roughly physiologic model of the symptom generates a value on a severity scale at each sampling time. Positive, zero, and negative values represent increased, normal, and decreased status, as applicable. The simulator plots these values over time. In the third step, another Bayesian network inspects this plot and reports how the symptom changed over time. This mechanism handles major trends, multiple and concurrent symptom causes, and gradually effective treatments. Other temporal insights, such as observations about short-term symptom relief, require complimentary mechanisms. PMID:12463924

  20. Modeling uncertainty: quicksand for water temperature modeling

    USGS Publications Warehouse

    Bartholow, John M.

    2003-01-01

    Uncertainty has been a hot topic relative to science generally, and modeling specifically. Modeling uncertainty comes in various forms: measured data, limited model domain, model parameter estimation, model structure, sensitivity to inputs, modelers themselves, and users of the results. This paper will address important components of uncertainty in modeling water temperatures, and discuss several areas that need attention as the modeling community grapples with how to incorporate uncertainty into modeling without getting stuck in the quicksand that prevents constructive contributions to policy making. The material, and in particular the reference, are meant to supplement the presentation given at this conference.

  1. Pre-Modeling Ensures Accurate Solid Models

    ERIC Educational Resources Information Center

    Gow, George

    2010-01-01

    Successful solid modeling requires a well-organized design tree. The design tree is a list of all the object's features and the sequential order in which they are modeled. The solid-modeling process is faster and less prone to modeling errors when the design tree is a simple and geometrically logical definition of the modeled object. Few high…

  2. Skylab Model

    NASA Technical Reports Server (NTRS)

    1967-01-01

    This photograph is of a model of the Skylab with the Command/Service Module being docked. In an early effort to extend the use of Apollo for further applications, NASA established the Apollo Applications Program (AAP) in August of 1965. The AAP was to include long duration Earth orbital missions during which astronauts would carry out scientific, technological, and engineering experiments in space by utilizing modified Saturn launch vehicles and the Apollo spacecraft. Established in 1970, the Skylab Program was the forerurner of the AAP. The goals of the Skylab were to enrich our scientific knowledge of the Earth, the Sun, the stars, and cosmic space; to study the effects of weightlessness on living organisms, including man; to study the effects of the processing and manufacturing of materials utilizing the absence of gravity; and to conduct Earth resource observations. The Skylab also conducted 19 selected experiments submitted by high school students. Skylab's 3 different 3-man crews spent up to 84 days in Earth orbit. The Marshall Space Flight Center (MSFC) had responsibility for developing and integrating most of the major components of the Skylab: the Orbital Workshop (OWS), Airlock Module (AM), Multiple Docking Adapter (MDA), Apollo Telescope Mount (ATM), Payload Shroud (PS), and most of the experiments. MSFC was also responsible for providing the Saturn IB launch vehicles for three Apollo spacecraft and crews and a Saturn V launch vehicle for the Skylab.

  3. Comparison of experimentally determined and mathematically predicted percutaneous penetration rates of chemicals.

    PubMed

    Korinth, Gintautas; Schaller, Karl Heinz; Bader, Michael; Bartsch, Rüdiger; Göen, Thomas; Rossbach, Bernd; Drexler, Hans

    2012-03-01

    The aim of the study was to evaluate the predictive potential of three different mathematical models for the percutaneous penetration of industrial solvents with respect to our experimental data. Percutaneous penetration rates (fluxes) from diffusion cell experiments of 11 chemicals were compared with fluxes predicted by mathematical models. The chemicals considered were three glycol ethers (2-butoxyethanol, diethylene glycol monobutyl ether and 1-ethoxy-2-propanol), three alcohols (ethanol, isopropanol and methanol), two glycols (ethylene glycol and 1,2-propanediol), one aromatic hydrocarbon (toluene) and two aromatic amines (aniline and o-toluidine). For the mathematical prediction of fluxes, models described by Fiserova-Bergerova et al. (Am J Ind Med 17:617-635 1990), Guy and Potts (Am J Ind Med 23:711-719 1993) and Wilschut et al. (Chemosphere 30:1275-1296 1995) were used. The molecular weights, octanol-water partition coefficients (LogP) and water solubilities of the compounds were obtained from a database for modelling. The fit between the mathematically predicted and experimentally determined fluxes was poor (R(2) = 0.04-0.29; linear regression). The flux differences ranged up to a factor of 412. For 4 compounds, the Guy and Potts model showed a closer fit with the experimental flux than the other models. The Wilschut et al. model showed a lower flux difference for 4 compounds as compared to experimental data than the models of Fiserova-Bergerova et al. and Guy and Potts. The Fiserova-Bergerova et al. model showed for 3 compounds a lower flux difference to experimental data than the other models. This study demonstrates large differences between mathematically predicted and experimentally determined fluxes. The percutaneous penetration as determined in diffusion cell experiments may be considerably overestimated as well as underestimated by mathematical models. Although the number of compounds in our comparison study is small, the results point out that none

  4. CISNET lung models: Comparison of model assumptions and model structures

    PubMed Central

    McMahon, Pamela M.; Hazelton, William; Kimmel, Marek; Clarke, Lauren

    2012-01-01

    Sophisticated modeling techniques can be powerful tools to help us understand the effects of cancer control interventions on population trends in cancer incidence and mortality. Readers of journal articles are however rarely supplied with modeling details. Six modeling groups collaborated as part of the National Cancer Institute’s Cancer Intervention and Surveillance Modeling Network (CISNET) to investigate the contribution of US tobacco control efforts towards reducing lung cancer deaths over the period 1975 to 2000. The models included in this monograph were developed independently and use distinct, complementary approaches towards modeling the natural history of lung cancer. The models used the same data for inputs and agreed on the design of the analysis and the outcome measures. This article highlights aspects of the models that are most relevant to similarities of or differences between the results. Structured comparisons can increase the transparency of these complex models. PMID:22882887

  5. Direct handling of sharp interfacial energy for microstructural evolution

    DOE PAGESBeta

    Hernández–Rivera, Efraín; Tikare, Veena; Noirot, Laurence; Wang, Lumin

    2014-08-24

    In this study, we introduce a simplification to the previously demonstrated hybrid Potts–phase field (hPPF), which relates interfacial energies to microstructural sharp interfaces. The model defines interfacial energy by a Potts-like discrete interface approach of counting unlike neighbors, which we use to compute local curvature. The model is compared to the hPPF by studying interfacial characteristics and grain growth behavior. The models give virtually identical results, while the new model allows the simulator more direct control of interfacial energy.

  6. Epithelial to mesenchymal transition-the roles of cell morphology, labile adhesion and junctional coupling.

    PubMed

    Abdulla, Tariq; Luna-Zurita, Luis; de la Pompa, José Luis; Schleich, Jean-Marc; Summers, Ron

    2013-08-01

    Epithelial to mesenchymal transition (EMT) is a fundamental process during development and disease, including development of the heart valves and tumour metastases. An extended cellular Potts model was implemented to represent the behaviour emerging from autonomous cell morphology, labile adhesion, junctional coupling and cell motility. Computer simulations normally focus on these functional changes independently whereas this model facilitates exploration of the interplay between cell shape changes, adhesion and migration. The simulation model is fitted to an in vitro model of endocardial EMT, and agrees with the finding that Notch signalling increases cell-matrix adhesion in addition to modulating cell-cell adhesion. PMID:23787029

  7. Building Mental Models by Dissecting Physical Models

    ERIC Educational Resources Information Center

    Srivastava, Anveshna

    2016-01-01

    When students build physical models from prefabricated components to learn about model systems, there is an implicit trade-off between the physical degrees of freedom in building the model and the intensity of instructor supervision needed. Models that are too flexible, permitting multiple possible constructions require greater supervision to…

  8. I&C Modeling in SPAR Models

    SciTech Connect

    John A. Schroeder

    2012-06-01

    The Standardized Plant Analysis Risk (SPAR) models for the U.S. commercial nuclear power plants currently have very limited instrumentation and control (I&C) modeling [1]. Most of the I&C components in the operating plant SPAR models are related to the reactor protection system. This was identified as a finding during the industry peer review of SPAR models. While the Emergency Safeguard Features (ESF) actuation and control system was incorporated into the Peach Bottom Unit 2 SPAR model in a recent effort [2], various approaches to expend resources for detailed I&C modeling in other SPAR models are investigated.

  9. Comparative Protein Structure Modeling Using Modeller

    PubMed Central

    Eswar, Narayanan; Marti-Renom, Marc A.; Madhusudhan, M.S.; Eramian, David; Shen, Min-yi; Pieper, Ursula

    2014-01-01

    Functional characterization of a protein sequence is one of the most frequent problems in biology. This task is usually facilitated by accurate three-dimensional (3-D) structure of the studied protein. In the absence of an experimentally determined structure, comparative or homology modeling can sometimes provide a useful 3-D model for a protein that is related to at least one known protein structure. Comparative modeling predicts the 3-D structure of a given protein sequence (target) based primarily on its alignment to one or more proteins of known structure (templates). The prediction process consists of fold assignment, target-template alignment, model building, and model evaluation. This unit describes how to calculate comparative models using the program MODELLER and discusses all four steps of comparative modeling, frequently observed errors, and some applications. Modeling lactate dehydrogenase from Trichomonas vaginalis (TvLDH) is described as an example. The download and installation of the MODELLER software is also described. PMID:18428767

  10. Forward model nonlinearity versus inverse model nonlinearity

    USGS Publications Warehouse

    Mehl, S.

    2007-01-01

    The issue of concern is the impact of forward model nonlinearity on the nonlinearity of the inverse model. The question posed is, "Does increased nonlinearity in the head solution (forward model) always result in increased nonlinearity in the inverse solution (estimation of hydraulic conductivity)?" It is shown that the two nonlinearities are separate, and it is not universally true that increased forward model nonlinearity increases inverse model nonlinearity. ?? 2007 National Ground Water Association.

  11. Modeling cholera outbreaks

    PubMed Central

    Longini, Ira M.; Morris, J. Glenn

    2014-01-01

    Mathematical modeling can be a valuable tool for studying infectious disease outbreak dynamics and simulating the effects of possible interventions. Here, we describe approaches to modeling cholera outbreaks and how models have been applied to explore intervention strategies, particularly in Haiti. Mathematical models can play an important role in formulating and evaluating complex cholera outbreak response options. Major challenges to cholera modeling are insufficient data for calibrating models and the need to tailor models for different outbreak scenarios. PMID:23412687

  12. Uncertainty Modeling Via Frequency Domain Model Validation

    NASA Technical Reports Server (NTRS)

    Waszak, Martin R.; Andrisani, Dominick, II

    1999-01-01

    Abstract The majority of literature on robust control assumes that a design model is available and that the uncertainty model bounds the actual variations about the nominal model. However, methods for generating accurate design models have not received as much attention in the literature. The influence of the level of accuracy of the uncertainty model on closed loop performance has received even less attention. The research reported herein is an initial step in applying and extending the concept of model validation to the problem of obtaining practical uncertainty models for robust control analysis and design applications. An extension of model validation called 'sequential validation' is presented and applied to a simple spring-mass-damper system to establish the feasibility of the approach and demonstrate the benefits of the new developments.

  13. Model selection for logistic regression models

    NASA Astrophysics Data System (ADS)

    Duller, Christine

    2012-09-01

    Model selection for logistic regression models decides which of some given potential regressors have an effect and hence should be included in the final model. The second interesting question is whether a certain factor is heterogeneous among some subsets, i.e. whether the model should include a random intercept or not. In this paper these questions will be answered with classical as well as with Bayesian methods. The application show some results of recent research projects in medicine and business administration.

  14. Modeling transient rootzone salinity (SWS Model)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The combined, water quality criteria for irrigation, water and ion processes in soils, and plant and soil response is sufficiently complex that adequate analysis requires computer models. Models for management are also needed but these models must consider that the input requirements must be reasona...

  15. China model: Energy modeling the modern dynasty

    SciTech Connect

    Shaw, Jason

    1996-05-01

    In this paper a node-based microeconomic analysis is used to model the Chinese energy system. This model is run across multiple periods employing Lagrangian Relaxation techniques to achieve general equilibrium. Later, carbon dioxide emissions are added and the model is run to answer the question, {open_quotes}How can greenhouse gas emissions be reduced{close_quotes}?

  16. "Bohr's Atomic Model."

    ERIC Educational Resources Information Center

    Willden, Jeff

    2001-01-01

    "Bohr's Atomic Model" is a small interactive multimedia program that introduces the viewer to a simplified model of the atom. This interactive simulation lets students build an atom using an atomic construction set. The underlying design methodology for "Bohr's Atomic Model" is model-centered instruction, which means the central model of the…

  17. Multilevel Model Prediction

    ERIC Educational Resources Information Center

    Frees, Edward W.; Kim, Jee-Seon

    2006-01-01

    Multilevel models are proven tools in social research for modeling complex, hierarchical systems. In multilevel modeling, statistical inference is based largely on quantification of random variables. This paper distinguishes among three types of random variables in multilevel modeling--model disturbances, random coefficients, and future response…

  18. Building mental models by dissecting physical models.

    PubMed

    Srivastava, Anveshna

    2016-01-01

    When students build physical models from prefabricated components to learn about model systems, there is an implicit trade-off between the physical degrees of freedom in building the model and the intensity of instructor supervision needed. Models that are too flexible, permitting multiple possible constructions require greater supervision to ensure focused learning; models that are too constrained require less supervision, but can be constructed mechanically, with little to no conceptual engagement. We propose "model-dissection" as an alternative to "model-building," whereby instructors could make efficient use of supervisory resources, while simultaneously promoting focused learning. We report empirical results from a study conducted with biology undergraduate students, where we demonstrate that asking them to "dissect" out specific conceptual structures from an already built 3D physical model leads to a significant improvement in performance than asking them to build the 3D model from simpler components. Using questionnaires to measure understanding both before and after model-based interventions for two cohorts of students, we find that both the "builders" and the "dissectors" improve in the post-test, but it is the latter group who show statistically significant improvement. These results, in addition to the intrinsic time-efficiency of "model dissection," suggest that it could be a valuable pedagogical tool. PMID:26712513

  19. Towards a Model of Stewardship and Accountability in Support of Innovation and "Good" Failure.

    PubMed

    Denny, Keith; Veillard, Jeremy

    2015-01-01

    From an evolutionary perspective, failures of imagination and missed opportunities to learn from experimentation are as potentially harmful for the health system as failures of practice. The conundrum is encapsulated in the fact that while commentators are steadfast about the need on the part of the stewards of the health system to avoid any waste of public dollars, they are also insistent about the need for innovation. There is tension between these two imperatives that is often unrecognized: the pursuit of efficiency, narrowly defined, can crowd out the goal of innovation by insisting on the elimination of "good waste" (the costs of experimentation) as well as "bad waste" (the costs of inefficiency) (Potts 2009). This tension is mirrored in the two broad drivers of performance reporting in health systems: public accountability and quality improvement. Health organizations, predominantly funded by public funds, are necessarily accountable for the ways in which those funds are used and outcomes achieved. This paper reviews how accountability relationships should be re-examined to create room for "good failure" and to ensure that system accountability does not become a barrier to performance improvement. PMID:26853610

  20. Geologic Framework Model Analysis Model Report

    SciTech Connect

    R. Clayton

    2000-12-19

    The purpose of this report is to document the Geologic Framework Model (GFM), Version 3.1 (GFM3.1) with regard to data input, modeling methods, assumptions, uncertainties, limitations, and validation of the model results, qualification status of the model, and the differences between Version 3.1 and previous versions. The GFM represents a three-dimensional interpretation of the stratigraphy and structural features of the location of the potential Yucca Mountain radioactive waste repository. The GFM encompasses an area of 65 square miles (170 square kilometers) and a volume of 185 cubic miles (771 cubic kilometers). The boundaries of the GFM were chosen to encompass the most widely distributed set of exploratory boreholes (the Water Table or WT series) and to provide a geologic framework over the area of interest for hydrologic flow and radionuclide transport modeling through the unsaturated zone (UZ). The depth of the model is constrained by the inferred depth of the Tertiary-Paleozoic unconformity. The GFM was constructed from geologic map and borehole data. Additional information from measured stratigraphy sections, gravity profiles, and seismic profiles was also considered. This interim change notice (ICN) was prepared in accordance with the Technical Work Plan for the Integrated Site Model Process Model Report Revision 01 (CRWMS M&O 2000). The constraints, caveats, and limitations associated with this model are discussed in the appropriate text sections that follow. The GFM is one component of the Integrated Site Model (ISM) (Figure l), which has been developed to provide a consistent volumetric portrayal of the rock layers, rock properties, and mineralogy of the Yucca Mountain site. The ISM consists of three components: (1) Geologic Framework Model (GFM); (2) Rock Properties Model (RPM); and (3) Mineralogic Model (MM). The ISM merges the detailed project stratigraphy into model stratigraphic units that are most useful for the primary downstream models and the

  1. Models of Magnetism.

    ERIC Educational Resources Information Center

    Borges, A. Tarciso; Gilbert, John K.

    1998-01-01

    Investigates the mental models that people construct about magnetic phenomena. Involves students, physics teachers, engineers, and practitioners. Proposes five models following a progression from simple description to a field model. Contains 28 references. (DDR)

  2. Educating with Aircraft Models

    ERIC Educational Resources Information Center

    Steele, Hobie

    1976-01-01

    Described is utilization of aircraft models, model aircraft clubs, and model aircraft magazines to promote student interest in aerospace education. The addresses for clubs and magazines are included. (SL)

  3. Mesoscale Benchmark Demonstration Problem 1: Mesoscale Simulations of Intra-granular Fission Gas Bubbles in UO2 under Post-irradiation Thermal Annealing

    SciTech Connect

    Li, Yulan; Hu, Shenyang Y.; Montgomery, Robert; Gao, Fei; Sun, Xin; Tonks, Michael; Biner, Bullent; Millet, Paul; Tikare, Veena; Radhakrishnan, Balasubramaniam; Andersson , David

    2012-04-11

    A study was conducted to evaluate the capabilities of different numerical methods used to represent microstructure behavior at the mesoscale for irradiated material using an idealized benchmark problem. The purpose of the mesoscale benchmark problem was to provide a common basis to assess several mesoscale methods with the objective of identifying the strengths and areas of improvement in the predictive modeling of microstructure evolution. In this work, mesoscale models (phase-field, Potts, and kinetic Monte Carlo) developed by PNNL, INL, SNL, and ORNL were used to calculate the evolution kinetics of intra-granular fission gas bubbles in UO2 fuel under post-irradiation thermal annealing conditions. The benchmark problem was constructed to include important microstructural evolution mechanisms on the kinetics of intra-granular fission gas bubble behavior such as the atomic diffusion of Xe atoms, U vacancies, and O vacancies, the effect of vacancy capture and emission from defects, and the elastic interaction of non-equilibrium gas bubbles. An idealized set of assumptions was imposed on the benchmark problem to simplify the mechanisms considered. The capability and numerical efficiency of different models are compared against selected experimental and simulation results. These comparisons find that the phase-field methods, by the nature of the free energy formulation, are able to represent a larger subset of the mechanisms influencing the intra-granular bubble growth and coarsening mechanisms in the idealized benchmark problem as compared to the Potts and kinetic Monte Carlo methods. It is recognized that the mesoscale benchmark problem as formulated does not specifically highlight the strengths of the discrete particle modeling used in the Potts and kinetic Monte Carlo methods. Future efforts are recommended to construct increasingly more complex mesoscale benchmark problems to further verify and validate the predictive capabilities of the mesoscale modeling

  4. Statistical Mechanics in Np-Complete Optimization Problems and Simulations of Spin Glass on Graphs with Finite Coordination Number.

    NASA Astrophysics Data System (ADS)

    Lai, Pik-Yin

    Methods of statistical mechanics are applied to two important NP-complete combinatorial optimization problems. The first is the chromatic number problem which seeks the minimal number of colors necessary to color a graph such that no two sites connected by an edge have the same color. The second is partitioning of a graph into q equal subgraphs so as to minimize inter-subgraph connections. Both models are mapped into a frustrated Potts model which is related to the q-state Potts spin glass. For the first problem, we obtain very good agreement with numerical simulations and theoretical bounds using the annealed approximation. The quenched model is also discussed. For the second problem we obtain analytic and numerical results by evaluating the ground state energy of the q = 3 and 4 Potts spin glass using Parisi's replica symmetry breaking. We also performed some numerical simulations to test the theoretical result and obtained very good agreement. In the second part of the thesis, we simulate the Ising spin-glass model on a random lattice with a finite (average) coordination number and also on the Bethe lattice with various different boundary conditions. In particular, we calculate the overlap function P(q) for two independent samples. For the random lattice, the results are consistent with a spin-glass transition above which P(q) converges to a Dirac delta -function for large N (number of sites) and below which P(q) has in addition a long tail similar to previous results obtained for the infinite ranged model. For the Bethe lattice, we obtain results in the interior by discarding the two outer shells of the Cayley tree when calculating the thermal averages. For fixed (uncorrelated) boundary conditions, P(q) seems to converge to a delta -function even below the spin-glass transition whereas for a "closed" lattice (correlated boundary conditions) P(q) has a long tail similar to its behavior in the random lattice case.

  5. Forest succession models

    SciTech Connect

    Shugart, H.H. Jr.; West, D.C.

    1980-05-01

    Studies in succession attempt to determine the changes in species composition and other ecosystem attributes expected to occur over periods of time. Mathematical models developed in forestry and ecology to study ecological succession are reviewed. Tree models, gap models and forest models are discussed. Model validation or testing procedures are described. Model applications can involve evaluating large-scale and long-term changes in the ambient levels of pollutants and assessing the effects of climate change on the environment. (RJC)

  6. Orbital Debris Modeling

    NASA Technical Reports Server (NTRS)

    Liou, J. C.

    2012-01-01

    Presentation outlne: (1) The NASA Orbital Debris (OD) Engineering Model -- A mathematical model capable of predicting OD impact risks for the ISS and other critical space assets (2) The NASA OD Evolutionary Model -- A physical model capable of predicting future debris environment based on user-specified scenarios (3) The NASA Standard Satellite Breakup Model -- A model describing the outcome of a satellite breakup (explosion or collision)

  7. FAST TRACK COMMUNICATION: Exact and simple results for the XYZ and strongly interacting fermion chains

    NASA Astrophysics Data System (ADS)

    Fendley, Paul; Hagendorf, Christian

    2010-10-01

    We conjecture exact and simple formulas for some physical quantities in two quantum chains. A classic result of this type is Onsager, Kaufman and Yang's formula for the spontaneous magnetization in the Ising model, subsequently generalized to the chiral Potts models. We conjecture that analogous results occur in the XYZ chain when the couplings obey JxJy + JyJz + JxJz = 0, and in a related fermion chain with strong interactions and supersymmetry. We find exact formulas for the magnetization and gap in the former, and the staggered density in the latter, by exploiting the fact that certain quantities are independent of finite-size effects.

  8. Chiral phase from three-spin interactions in an optical lattice

    SciTech Connect

    D'Cruz, Christian; Pachos, Jiannis K.

    2005-10-15

    A spin-1/2 chain model that includes three-spin interactions can effectively describe the dynamics of two species of bosons trapped in an optical lattice with a triangular-ladder configuration. A perturbative theoretical approach and numerical study of its ground state is performed that reveals a rich variety of phases and criticalities. We identify phases with periodicity one, two, or three, as well as critical points that belong in the same universality class as the Ising or the three-state Potts model. We establish a range of parameters, corresponding to a large degeneracy present between phases with period 2 and 3, that nests a gapless incommensurate chiral phase.

  9. The free energy in a class of quantum spin systems and interchange processes

    NASA Astrophysics Data System (ADS)

    Björnberg, J. E.

    2016-07-01

    We study a class of quantum spin systems in the mean-field setting of the complete graph. For spin S = 1/2, the model is the Heisenberg ferromagnet, and for general spin S ∈ 1/2 N, it has a probabilistic representation as a cycle-weighted interchange process. We determine the free energy and the critical temperature (recovering results by Tóth and by Penrose when S = 1/2). The critical temperature is shown to coincide (as a function of S) with that of the q = 2S + 1 state classical Potts model, and the phase transition is discontinuous when S ≥ 1.

  10. Continuous system modeling

    NASA Technical Reports Server (NTRS)

    Cellier, Francois E.

    1991-01-01

    A comprehensive and systematic introduction is presented for the concepts associated with 'modeling', involving the transition from a physical system down to an abstract description of that system in the form of a set of differential and/or difference equations, and basing its treatment of modeling on the mathematics of dynamical systems. Attention is given to the principles of passive electrical circuit modeling, planar mechanical systems modeling, hierarchical modular modeling of continuous systems, and bond-graph modeling. Also discussed are modeling in equilibrium thermodynamics, population dynamics, and system dynamics, inductive reasoning, artificial neural networks, and automated model synthesis.

  11. Regularized Structural Equation Modeling

    PubMed Central

    Jacobucci, Ross; Grimm, Kevin J.; McArdle, John J.

    2016-01-01

    A new method is proposed that extends the use of regularization in both lasso and ridge regression to structural equation models. The method is termed regularized structural equation modeling (RegSEM). RegSEM penalizes specific parameters in structural equation models, with the goal of creating easier to understand and simpler models. Although regularization has gained wide adoption in regression, very little has transferred to models with latent variables. By adding penalties to specific parameters in a structural equation model, researchers have a high level of flexibility in reducing model complexity, overcoming poor fitting models, and the creation of models that are more likely to generalize to new samples. The proposed method was evaluated through a simulation study, two illustrative examples involving a measurement model, and one empirical example involving the structural part of the model to demonstrate RegSEM’s utility. PMID:27398019

  12. ROCK PROPERTIES MODEL ANALYSIS MODEL REPORT

    SciTech Connect

    Clinton Lum

    2002-02-04

    The purpose of this Analysis and Model Report (AMR) is to document Rock Properties Model (RPM) 3.1 with regard to input data, model methods, assumptions, uncertainties and limitations of model results, and qualification status of the model. The report also documents the differences between the current and previous versions and validation of the model. The rock properties models are intended principally for use as input to numerical physical-process modeling, such as of ground-water flow and/or radionuclide transport. The constraints, caveats, and limitations associated with this model are discussed in the appropriate text sections that follow. This work was conducted in accordance with the following planning documents: WA-0344, ''3-D Rock Properties Modeling for FY 1998'' (SNL 1997, WA-0358), ''3-D Rock Properties Modeling for FY 1999'' (SNL 1999), and the technical development plan, Rock Properties Model Version 3.1, (CRWMS M&O 1999c). The Interim Change Notice (ICNs), ICN 02 and ICN 03, of this AMR were prepared as part of activities being conducted under the Technical Work Plan, TWP-NBS-GS-000003, ''Technical Work Plan for the Integrated Site Model, Process Model Report, Revision 01'' (CRWMS M&O 2000b). The purpose of ICN 03 is to record changes in data input status due to data qualification and verification activities. These work plans describe the scope, objectives, tasks, methodology, and implementing procedures for model construction. The constraints, caveats, and limitations associated with this model are discussed in the appropriate text sections that follow. The work scope for this activity consists of the following: (1) Conversion of the input data (laboratory measured porosity data, x-ray diffraction mineralogy, petrophysical calculations of bound water, and petrophysical calculations of porosity) for each borehole into stratigraphic coordinates; (2) Re-sampling and merging of data sets; (3) Development of geostatistical simulations of porosity; (4

  13. Better models are more effectively connected models

    NASA Astrophysics Data System (ADS)

    Nunes, João Pedro; Bielders, Charles; Darboux, Frederic; Fiener, Peter; Finger, David; Turnbull-Lloyd, Laura; Wainwright, John

    2016-04-01

    The concept of hydrologic and geomorphologic connectivity describes the processes and pathways which link sources (e.g. rainfall, snow and ice melt, springs, eroded areas and barren lands) to accumulation areas (e.g. foot slopes, streams, aquifers, reservoirs), and the spatial variations thereof. There are many examples of hydrological and sediment connectivity on a watershed scale; in consequence, a process-based understanding of connectivity is crucial to help managers understand their systems and adopt adequate measures for flood prevention, pollution mitigation and soil protection, among others. Modelling is often used as a tool to understand and predict fluxes within a catchment by complementing observations with model results. Catchment models should therefore be able to reproduce the linkages, and thus the connectivity of water and sediment fluxes within the systems under simulation. In modelling, a high level of spatial and temporal detail is desirable to ensure taking into account a maximum number of components, which then enables connectivity to emerge from the simulated structures and functions. However, computational constraints and, in many cases, lack of data prevent the representation of all relevant processes and spatial/temporal variability in most models. In most cases, therefore, the level of detail selected for modelling is too coarse to represent the system in a way in which connectivity can emerge; a problem which can be circumvented by representing fine-scale structures and processes within coarser scale models using a variety of approaches. This poster focuses on the results of ongoing discussions on modelling connectivity held during several workshops within COST Action Connecteur. It assesses the current state of the art of incorporating the concept of connectivity in hydrological and sediment models, as well as the attitudes of modellers towards this issue. The discussion will focus on the different approaches through which connectivity

  14. PREDICTIVE MODELS. Enhanced Oil Recovery Model

    SciTech Connect

    Ray, R.M.

    1992-02-26

    PREDICTIVE MODELS is a collection of five models - CFPM, CO2PM, ICPM, PFPM, and SFPM - used in the 1982-1984 National Petroleum Council study of enhanced oil recovery (EOR) potential. Each pertains to a specific EOR process designed to squeeze additional oil from aging or spent oil fields. The processes are: 1 chemical flooding; 2 carbon dioxide miscible flooding; 3 in-situ combustion; 4 polymer flooding; and 5 steamflood. CFPM, the Chemical Flood Predictive Model, models micellar (surfactant)-polymer floods in reservoirs, which have been previously waterflooded to residual oil saturation. Thus, only true tertiary floods are considered. An option allows a rough estimate of oil recovery by caustic or caustic-polymer processes. CO2PM, the Carbon Dioxide miscible flooding Predictive Model, is applicable to both secondary (mobile oil) and tertiary (residual oil) floods, and to either continuous CO2 injection or water-alternating gas processes. ICPM, the In-situ Combustion Predictive Model, computes the recovery and profitability of an in-situ combustion project from generalized performance predictive algorithms. PFPM, the Polymer Flood Predictive Model, is switch-selectable for either polymer or waterflooding, and an option allows the calculation of the incremental oil recovery and economics of polymer relative to waterflooding. SFPM, the Steamflood Predictive Model, is applicable to the steam drive process, but not to cyclic steam injection (steam soak) processes. The IBM PC/AT version includes a plotting capability to produces a graphic picture of the predictive model results.

  15. Biosphere Model Report

    SciTech Connect

    D. W. Wu

    2003-07-16

    The purpose of this report is to document the biosphere model, the Environmental Radiation Model for Yucca Mountain, Nevada (ERMYN), which describes radionuclide transport processes in the biosphere and associated human exposure that may arise as the result of radionuclide release from the geologic repository at Yucca Mountain. The biosphere model is one of the process models that support the Yucca Mountain Project (YMP) Total System Performance Assessment (TSPA) for the license application (LA), the TSPA-LA. The ERMYN model provides the capability of performing human radiation dose assessments. This report documents the biosphere model, which includes: (1) Describing the reference biosphere, human receptor, exposure scenarios, and primary radionuclides for each exposure scenario (Section 6.1); (2) Developing a biosphere conceptual model using site-specific features, events, and processes (FEPs), the reference biosphere, the human receptor, and assumptions (Section 6.2 and Section 6.3); (3) Building a mathematical model using the biosphere conceptual model and published biosphere models (Sections 6.4 and 6.5); (4) Summarizing input parameters for the mathematical model, including the uncertainty associated with input values (Section 6.6); (5) Identifying improvements in the ERMYN model compared with the model used in previous biosphere modeling (Section 6.7); (6) Constructing an ERMYN implementation tool (model) based on the biosphere mathematical model using GoldSim stochastic simulation software (Sections 6.8 and 6.9); (7) Verifying the ERMYN model by comparing output from the software with hand calculations to ensure that the GoldSim implementation is correct (Section 6.10); and (8) Validating the ERMYN model by corroborating it with published biosphere models; comparing conceptual models, mathematical models, and numerical results (Section 7).

  16. Biosphere Model Report

    SciTech Connect

    M. A. Wasiolek

    2003-10-27

    The purpose of this report is to document the biosphere model, the Environmental Radiation Model for Yucca Mountain, Nevada (ERMYN), which describes radionuclide transport processes in the biosphere and associated human exposure that may arise as the result of radionuclide release from the geologic repository at Yucca Mountain. The biosphere model is one of the process models that support the Yucca Mountain Project (YMP) Total System Performance Assessment (TSPA) for the license application (LA), the TSPA-LA. The ERMYN model provides the capability of performing human radiation dose assessments. This report documents the biosphere model, which includes: (1) Describing the reference biosphere, human receptor, exposure scenarios, and primary radionuclides for each exposure scenario (Section 6.1); (2) Developing a biosphere conceptual model using site-specific features, events, and processes (FEPs), the reference biosphere, the human receptor, and assumptions (Section 6.2 and Section 6.3); (3) Building a mathematical model using the biosphere conceptual model and published biosphere models (Sections 6.4 and 6.5); (4) Summarizing input parameters for the mathematical model, including the uncertainty associated with input values (Section 6.6); (5) Identifying improvements in the ERMYN model compared with the model used in previous biosphere modeling (Section 6.7); (6) Constructing an ERMYN implementation tool (model) based on the biosphere mathematical model using GoldSim stochastic simulation software (Sections 6.8 and 6.9); (7) Verifying the ERMYN model by comparing output from the software with hand calculations to ensure that the GoldSim implementation is correct (Section 6.10); and (8) Validating the ERMYN model by corroborating it with published biosphere models; comparing conceptual models, mathematical models, and numerical results (Section 7).

  17. AIDS Epidemiological models

    NASA Astrophysics Data System (ADS)

    Rahmani, Fouad Lazhar

    2010-11-01

    The aim of this paper is to present mathematical modelling of the spread of infection in the context of the transmission of the human immunodeficiency virus (HIV) and the acquired immune deficiency syndrome (AIDS). These models are based in part on the models suggested in the field of th AIDS mathematical modelling as reported by ISHAM [6].

  18. On Multiobjective Evolution Model

    NASA Astrophysics Data System (ADS)

    Ahmed, E.; Elettreby, M. F.

    Self-Organized Criticality (SOC) phenomena could have a significant effect on the dynamics of ecosystems. The Bak-Sneppen (BS) model is a simple and robust model of biological evolution that exhibits punctuated equilibrium behavior. Here, we will introduce random version of BS model. We also generalize the single objective BS model to a multiobjective one.

  19. Biomass Scenario Model

    SciTech Connect

    2015-09-01

    The Biomass Scenario Model (BSM) is a unique, carefully validated, state-of-the-art dynamic model of the domestic biofuels supply chain which explicitly focuses on policy issues, their feasibility, and potential side effects. It integrates resource availability, physical/technological/economic constraints, behavior, and policy. The model uses a system dynamics simulation (not optimization) to model dynamic interactions across the supply chain.

  20. Multimodeling and Model Abstraction

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The multiplicity of models of the same process or phenomenon is the commonplace in environmental modeling. Last 10 years brought marked interest to making use of the variety of conceptual approaches instead of attempting to find the best model or using a single preferred model. Two systematic approa...

  1. Qualitative Student Models.

    ERIC Educational Resources Information Center

    Clancey, William J.

    The concept of a qualitative model is used as the focus of this review of qualitative student models in order to compare alternative computational models and to contrast domain requirements. The report is divided into eight sections: (1) Origins and Goals (adaptive instruction, qualitative models of processes, components of an artificial…

  2. The Instrumental Model

    ERIC Educational Resources Information Center

    Yeates, Devin Rodney

    2011-01-01

    The goal of this dissertation is to enable better predictive models by engaging raw experimental data through the Instrumental Model. The Instrumental Model captures the protocols and procedures of experimental data analysis. The approach is formalized by encoding the Instrumental Model in an XML record. Decoupling the raw experimental data from…

  3. Generative Models of Disfluency

    ERIC Educational Resources Information Center

    Miller, Timothy A.

    2010-01-01

    This thesis describes a generative model for representing disfluent phenomena in human speech. This model makes use of observed syntactic structure present in disfluent speech, and uses a right-corner transform on syntax trees to model this structure in a very natural way. Specifically, the phenomenon of speech repair is modeled by explicitly…

  4. Efficient polarimetric BRDF model.

    PubMed

    Renhorn, Ingmar G E; Hallberg, Tomas; Boreman, Glenn D

    2015-11-30

    The purpose of the present manuscript is to present a polarimetric bidirectional reflectance distribution function (BRDF) model suitable for hyperspectral and polarimetric signature modelling. The model is based on a further development of a previously published four-parameter model that has been generalized in order to account for different types of surface structures (generalized Gaussian distribution). A generalization of the Lambertian diffuse model is presented. The pBRDF-functions are normalized using numerical integration. Using directional-hemispherical reflectance (DHR) measurements, three of the four basic parameters can be determined for any wavelength. This simplifies considerably the development of multispectral polarimetric BRDF applications. The scattering parameter has to be determined from at least one BRDF measurement. The model deals with linear polarized radiation; and in similarity with e.g. the facet model depolarization is not included. The model is very general and can inherently model extreme surfaces such as mirrors and Lambertian surfaces. The complex mixture of sources is described by the sum of two basic models, a generalized Gaussian/Fresnel model and a generalized Lambertian model. Although the physics inspired model has some ad hoc features, the predictive power of the model is impressive over a wide range of angles and scattering magnitudes. The model has been applied successfully to painted surfaces, both dull and glossy and also on metallic bead blasted surfaces. The simple and efficient model should be attractive for polarimetric simulations and polarimetric remote sensing. PMID:26698753

  5. Natural History of Anal Dysplasia in an HIV-Infected Clinical Care Cohort: Estimates Using Multi-State Markov Modeling

    PubMed Central

    Mathews, William C.; Agmas, Wollelaw; Cachay, Edward R.; Cosman, Bard C.; Jackson, Christopher

    2014-01-01

    Objectives (1) To model the natural history of anal neoplasia in HIV-infected patients using a 3-state Markov model of anal cancer pathogenesis, adjusting for cytology misclassification; and (2) to estimate the effects of selected time-varying covariates on transition probabilities. Design A retrospective cytology-based inception screening cohort of HIV-infected adults was analyzed using a 3-state Markov model of clinical pathogenesis of anal neoplasia. Methods Longitudinally ascertained cytology categories were adjusted for misclassification using estimates of cytology accuracy derived from the study cohort. Time-varying covariate effects were estimated as hazard ratios. Results (1) There was a moderate to high probability of regression of the high grade squamous intraepithelial lesion (HSIL) state (27–62%) at 2 years after initial cytology screening; (2) the probability of developing invasive anal cancer (IAC) during the first 2 years after a baseline HSIL cytology is low (1.9–2.8%); (3) infrared coagulation (IRC) ablation of HSIL lesions is associated with a 2.2–4.2 fold increased probability of regression to

  6. Strong decays of excited 1D charmed(-strange) mesons in the covariant oscillator quark model

    NASA Astrophysics Data System (ADS)

    Maeda, Tomohito; Yoshida, Kento; Yamada, Kenji; Ishida, Shin; Oda, Masuho

    2016-05-01

    Recently observed charmed mesons, D1* (2760), D3* (2760) and charmed-strange mesons, Ds1 * (2860), Ds3 * (2860), by BaBar and LHCb collaborations are considered to be plausible candidates for c q ¯ 13 DJ (q = u, d, s) states. We calculate the strong decays with one pion (kaon) emission of these states including well-established 1S and 1P charmed(-strange) mesons within the framework of the covariant oscillator quark model. The results obtained are compared with the experimental data and the typical nonrelativistic quark-model calculations. Concerning the results for 1S and 1P states, we find that, thanks to the relativistic effects of decay form factors, our model parameters take reasonable values, though our relativistic approach and the nonrelativistic quark model give similar decay widths in agreement with experiment. While the results obtained for 13 DJ=1,3 states are roughly consistent with the present data, they should be checked by the future precise measurement.

  7. Calibrated Properties Model

    SciTech Connect

    C.F. Ahlers, H.H. Liu

    2001-12-18

    The purpose of this Analysis/Model Report (AMR) is to document the Calibrated Properties Model that provides calibrated parameter sets for unsaturated zone (UZ) flow and transport process models for the Yucca Mountain Site Characterization Project (YMP). This work was performed in accordance with the AMR Development Plan for U0035 Calibrated Properties Model REV00 (CRWMS M&O 1999c). These calibrated property sets include matrix and fracture parameters for the UZ Flow and Transport Model (UZ Model), drift seepage models, drift-scale and mountain-scale coupled-processes models, and Total System Performance Assessment (TSPA) models as well as Performance Assessment (PA) and other participating national laboratories and government agencies. These process models provide the necessary framework to test conceptual hypotheses of flow and transport at different scales and predict flow and transport behavior under a variety of climatic and thermal-loading conditions.

  8. Calibrated Properties Model

    SciTech Connect

    C. Ahlers; H. Liu

    2000-03-12

    The purpose of this Analysis/Model Report (AMR) is to document the Calibrated Properties Model that provides calibrated parameter sets for unsaturated zone (UZ) flow and transport process models for the Yucca Mountain Site Characterization Project (YMP). This work was performed in accordance with the ''AMR Development Plan for U0035 Calibrated Properties Model REV00. These calibrated property sets include matrix and fracture parameters for the UZ Flow and Transport Model (UZ Model), drift seepage models, drift-scale and mountain-scale coupled-processes models, and Total System Performance Assessment (TSPA) models as well as Performance Assessment (PA) and other participating national laboratories and government agencies. These process models provide the necessary framework to test conceptual hypotheses of flow and transport at different scales and predict flow and transport behavior under a variety of climatic and thermal-loading conditions.

  9. Introduction to Adjoint Models

    NASA Technical Reports Server (NTRS)

    Errico, Ronald M.

    2015-01-01

    In this lecture, some fundamentals of adjoint models will be described. This includes a basic derivation of tangent linear and corresponding adjoint models from a parent nonlinear model, the interpretation of adjoint-derived sensitivity fields, a description of methods of automatic differentiation, and the use of adjoint models to solve various optimization problems, including singular vectors. Concluding remarks will attempt to correct common misconceptions about adjoint models and their utilization.

  10. Stable models of superacceleration

    SciTech Connect

    Kaplinghat, Manoj; Rajaraman, Arvind

    2007-05-15

    We discuss an instability in a large class of models where dark energy is coupled to matter. In these models the mass of the scalar field is much larger than the expansion rate of the Universe. We find models in which this instability is absent, and show that these models generically predict an apparent equation of state for dark energy smaller than -1, i.e., superacceleration. These models have no acausal behavior or ghosts.

  11. ADAPT model: Model use, calibration and validation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This paper presents an overview of the Agricultural Drainage and Pesticide Transport (ADAPT) model and a case study to illustrate the calibration and validation steps for predicting subsurface tile drainage and nitrate-N losses from an agricultural system. The ADAPT model is a daily time step field ...

  12. WASP TRANSPORT MODELING AND WASP ECOLOGICAL MODELING

    EPA Science Inventory

    A combination of lectures, demonstrations, and hands-on excercises will be used to introduce pollutant transport modeling with the U.S. EPA's general water quality model, WASP (Water Quality Analysis Simulation Program). WASP features include a user-friendly Windows-based interfa...

  13. Geochemistry Model Validation Report: External Accumulation Model

    SciTech Connect

    K. Zarrabi

    2001-09-27

    The purpose of this Analysis and Modeling Report (AMR) is to validate the External Accumulation Model that predicts accumulation of fissile materials in fractures and lithophysae in the rock beneath a degrading waste package (WP) in the potential monitored geologic repository at Yucca Mountain. (Lithophysae are voids in the rock having concentric shells of finely crystalline alkali feldspar, quartz, and other materials that were formed due to entrapped gas that later escaped, DOE 1998, p. A-25.) The intended use of this model is to estimate the quantities of external accumulation of fissile material for use in external criticality risk assessments for different types of degrading WPs: U.S. Department of Energy (DOE) Spent Nuclear Fuel (SNF) codisposed with High Level Waste (HLW) glass, commercial SNF, and Immobilized Plutonium Ceramic (Pu-ceramic) codisposed with HLW glass. The scope of the model validation is to (1) describe the model and the parameters used to develop the model, (2) provide rationale for selection of the parameters by comparisons with measured values, and (3) demonstrate that the parameters chosen are the most conservative selection for external criticality risk calculations. To demonstrate the applicability of the model, a Pu-ceramic WP is used as an example. The model begins with a source term from separately documented EQ6 calculations; where the source term is defined as the composition versus time of the water flowing out of a breached waste package (WP). Next, PHREEQC, is used to simulate the transport and interaction of the source term with the resident water and fractured tuff below the repository. In these simulations the primary mechanism for accumulation is mixing of the high pH, actinide-laden source term with resident water; thus lowering the pH values sufficiently for fissile minerals to become insoluble and precipitate. In the final section of the model, the outputs from PHREEQC, are processed to produce mass of accumulation

  14. Trapped Radiation Model Uncertainties: Model-Data and Model-Model Comparisons

    NASA Technical Reports Server (NTRS)

    Armstrong, T. W.; Colborn, B. L.

    2000-01-01

    The standard AP8 and AE8 models for predicting trapped proton and electron environments have been compared with several sets of flight data to evaluate model uncertainties. Model comparisons are made with flux and dose measurements made on various U.S. low-Earth orbit satellites (APEX, CRRES, DMSP, LDEF, NOAA) and Space Shuttle flights, on Russian satellites (Photon-8, Cosmos-1887, Cosmos-2044), and on the Russian Mir Space Station. This report gives the details of the model-data comparisons-summary results in terms of empirical model uncertainty factors that can be applied for spacecraft design applications are given in a combination report. The results of model-model comparisons are also presented from standard AP8 and AE8 model predictions compared with the European Space Agency versions of AP8 and AE8 and with Russian-trapped radiation models.

  15. Model Validation Status Review

    SciTech Connect

    E.L. Hardin

    2001-11-28

    The primary objective for the Model Validation Status Review was to perform a one-time evaluation of model validation associated with the analysis/model reports (AMRs) containing model input to total-system performance assessment (TSPA) for the Yucca Mountain site recommendation (SR). This review was performed in response to Corrective Action Request BSC-01-C-01 (Clark 2001, Krisha 2001) pursuant to Quality Assurance review findings of an adverse trend in model validation deficiency. The review findings in this report provide the following information which defines the extent of model validation deficiency and the corrective action needed: (1) AMRs that contain or support models are identified, and conversely, for each model the supporting documentation is identified. (2) The use for each model is determined based on whether the output is used directly for TSPA-SR, or for screening (exclusion) of features, events, and processes (FEPs), and the nature of the model output. (3) Two approaches are used to evaluate the extent to which the validation for each model is compliant with AP-3.10Q (Analyses and Models). The approaches differ in regard to whether model validation is achieved within individual AMRs as originally intended, or whether model validation could be readily achieved by incorporating information from other sources. (4) Recommendations are presented for changes to the AMRs, and additional model development activities or data collection, that will remedy model validation review findings, in support of licensing activities. The Model Validation Status Review emphasized those AMRs that support TSPA-SR (CRWMS M&O 2000bl and 2000bm). A series of workshops and teleconferences was held to discuss and integrate the review findings. The review encompassed 125 AMRs (Table 1) plus certain other supporting documents and data needed to assess model validity. The AMRs were grouped in 21 model areas representing the modeling of processes affecting the natural and

  16. Trapped Radiation Model Uncertainties: Model-Data and Model-Model Comparisons

    NASA Technical Reports Server (NTRS)

    Armstrong, T. W.; Colborn, B. L.

    2000-01-01

    The standard AP8 and AE8 models for predicting trapped proton and electron environments have been compared with several sets of flight data to evaluate model uncertainties. Model comparisons are made with flux and dose measurements made on various U.S. low-Earth orbit satellites (APEX, CRRES, DMSP. LDEF, NOAA) and Space Shuttle flights, on Russian satellites (Photon-8, Cosmos-1887, Cosmos-2044), and on the Russian Mir space station. This report gives the details of the model-data comparisons -- summary results in terms of empirical model uncertainty factors that can be applied for spacecraft design applications are given in a companion report. The results of model-model comparisons are also presented from standard AP8 and AE8 model predictions compared with the European Space Agency versions of AP8 and AE8 and with Russian trapped radiation models.

  17. Modeling extragalactic bowshocks. I. The model.

    NASA Astrophysics Data System (ADS)

    Ferruit, P.; Binette, L.; Sutherland, R. S.; Pecontal, E.

    1997-06-01

    To probe the effects of the nuclear activity on the host galaxy, it is essential to disentangle the relative contribution of shock excitation from that of photoionization. One milestone towards this goal is the ability to model the bowshock structures created by the interaction of radio ejecta with their surrounding medium. We have built a bowshock model based on TDA's one (Taylor, Dyson & Axon, 1992MNRAS.255..351T) which was itself derived from an earlier work on Herbig-Haro objects. Since TDA's original model supplied the astronomers with only [OIII]λ5007 fluxes and profiles for various models of bowshocks, we undertook to include magnetic fields and to incorporate all of the atomic data tables of the code Mappings Ic for the computation of ionization states, cooling rates and line emissivities of the gas. This new model allows us to map line ratios and profiles of extragalactic bowshocks for all major lines of astrophysical interest. In this first paper, we present our model, analyse the gas behavior along the bowshock and give some examples of model results.

  18. Modeling Hydrothermal Mineralization: Fractal or Multifrcatal Models?

    NASA Astrophysics Data System (ADS)

    Cheng, Q.

    2004-05-01

    Hydrothermal mineralization occurs when the natural geo-processes involve the interaction of ore material-carrying hydrothermal fluids with rocks in the earth's crust in a specific geological environment. Mineralization can cause element concentration enrichment or depletion in the country rocks. Local enrichment may form ore body that can be mined for profit at the current economic and technological conditions. To understand the spatial distribution of element concentration enrichment or depletion caused by mineralization in a mineral district is essential for mineral exploration and mineral prediction. Grade-tonnage model and mineral deposits size distribution model are common models used for characterizing mineral deposits. This paper proposes a non-linear mineralization model on the basis of a modified classical igneous differentiation mineralization model to describe the generation of multifractal distribution of element concentration in the country rocks as well as grade-tonnage fractal/multifractal distribution of ore deposits that have been often observed in hydrothermal mineralization. This work may also lead to a singularity model to explain the common properties of mineralization and mineralization-associated geochemical anomaly diversity and the generalized self-similarity of the anomalies. The model has been applied to a case study of mineral deposits prediction and mineral resource assessment in the Abitibi district, northern Ontario, Canada.

  19. Modeling volatility using state space models.

    PubMed

    Timmer, J; Weigend, A S

    1997-08-01

    In time series problems, noise can be divided into two categories: dynamic noise which drives the process, and observational noise which is added in the measurement process, but does not influence future values of the system. In this framework, we show that empirical volatilities (the squared relative returns of prices) exhibit a significant amount of observational noise. To model and predict their time evolution adequately, we estimate state space models that explicitly include observational noise. We obtain relaxation times for shocks in the logarithm of volatility ranging from three weeks (for foreign exchange) to three to five months (for stock indices). In most cases, a two-dimensional hidden state is required to yield residuals that are consistent with white noise. We compare these results with ordinary autoregressive models (without a hidden state) and find that autoregressive models underestimate the relaxation times by about two orders of magnitude since they do not distinguish between observational and dynamic noise. This new interpretation of the dynamics of volatility in terms of relaxators in a state space model carries over to stochastic volatility models and to GARCH models, and is useful for several problems in finance, including risk management and the pricing of derivative securities. Data sets used: Olsen & Associates high frequency DEM/USD foreign exchange rates (8 years). Nikkei 225 index (40 years). Dow Jones Industrial Average (25 years). PMID:9730016

  20. Energy-consumption modelling

    SciTech Connect

    Reiter, E.R.

    1980-01-01

    A highly sophisticated and accurate approach is described to compute on an hourly or daily basis the energy consumption for space heating by individual buildings, urban sectors, and whole cities. The need for models and specifically weather-sensitive models, composite models, and space-heating models are discussed. Development of the Colorado State University Model, based on heat-transfer equations and on a heuristic, adaptive, self-organizing computation learning approach, is described. Results of modeling energy consumption by the city of Minneapolis and Cheyenne are given. Some data on energy consumption in individual buildings are included.

  1. Holographic twin Higgs model.

    PubMed

    Geller, Michael; Telem, Ofri

    2015-05-15

    We present the first realization of a "twin Higgs" model as a holographic composite Higgs model. Uniquely among composite Higgs models, the Higgs potential is protected by a new standard model (SM) singlet elementary "mirror" sector at the sigma model scale f and not by the composite states at m_{KK}, naturally allowing for m_{KK} beyond the LHC reach. As a result, naturalness in our model cannot be constrained by the LHC, but may be probed by precision Higgs measurements at future lepton colliders, and by direct searches for Kaluza-Klein excitations at a 100 TeV collider. PMID:26024160

  2. Stochastic modeling of rainfall

    SciTech Connect

    Guttorp, P.

    1996-12-31

    We review several approaches in the literature for stochastic modeling of rainfall, and discuss some of their advantages and disadvantages. While stochastic precipitation models have been around at least since the 1850`s, the last two decades have seen an increased development of models based (more or less) on the physical processes involved in precipitation. There are interesting questions of scale and measurement that pertain to these modeling efforts. Recent modeling efforts aim at including meteorological variables, and may be useful for regional down-scaling of general circulation models.

  3. Reliability model generator

    NASA Technical Reports Server (NTRS)

    McMann, Catherine M. (Inventor); Cohen, Gerald C. (Inventor)

    1991-01-01

    An improved method and system for automatically generating reliability models for use with a reliability evaluation tool is described. The reliability model generator of the present invention includes means for storing a plurality of low level reliability models which represent the reliability characteristics for low level system components. In addition, the present invention includes means for defining the interconnection of the low level reliability models via a system architecture description. In accordance with the principles of the present invention, a reliability model for the entire system is automatically generated by aggregating the low level reliability models based on the system architecture description.

  4. Gear mesh compliance modeling

    NASA Technical Reports Server (NTRS)

    Savage, M.; Caldwell, R. J.; Wisor, G. D.; Lewicki, D. G.

    1986-01-01

    A computer model has been constructed to simulate the compliance and load sharing in a spur gear mesh. The model adds the effect of rim deflections to previously developed state-of-the-art gear tooth deflection models. The effects of deflections on mesh compliance and load sharing are examined. The model can treat gear meshes composed to two external gears or an external gear driving an internal gear. The model includes deflection contributions from the bending and shear in the teeth, the Hertzian contact deformations, and primary and secondary rotations of the gear rims. The model shows that rimmed gears increase mesh compliance and, in some cases, improve load sharing.

  5. Gear mesh compliance modeling

    NASA Technical Reports Server (NTRS)

    Savage, M.; Caldwell, R. J.; Wisor, G. D.; Lewicki, D. G.

    1987-01-01

    A computer model has been constructed to simulate the compliance and load sharing in a spur gear mesh. The model adds the effect of rim deflections to previously developed state-of-the-art gear tooth deflection models. The effects of deflections on mesh compliance and load sharing are examined. The model can treat gear meshes composed of two external gears or an external gear driving an internal gear. The model includes deflection contributions from the bending and shear in the teeth, the Hertzian contact deformations, and primary and secondary rotations of the gear rims. The model shows that rimmed gears increase mesh compliance and, in some cases, improve load sharing.

  6. Reduced Vector Preisach Model

    NASA Technical Reports Server (NTRS)

    Patel, Umesh D.; Torre, Edward Della; Day, John H. (Technical Monitor)

    2002-01-01

    A new vector Preisach model, called the Reduced Vector Preisach model (RVPM), was developed for fast computations. This model, derived from the Simplified Vector Preisach model (SVPM), has individual components that like the SVPM are calculated independently using coupled selection rules for the state vector computation. However, the RVPM does not require the rotational correction. Therefore, it provides a practical alternative for computing the magnetic susceptibility using a differential approach. A vector version, using the framework of the DOK model, is implemented. Simulation results for the reduced vector Preisach model are also presented.

  7. Modeling Guru: Knowledge Base for NASA Modelers

    NASA Astrophysics Data System (ADS)

    Seablom, M. S.; Wojcik, G. S.; van Aartsen, B. H.

    2009-05-01

    Modeling Guru is an on-line knowledge-sharing resource for anyone involved with or interested in NASA's scientific models or High End Computing (HEC) systems. Developed and maintained by the NASA's Software Integration and Visualization Office (SIVO) and the NASA Center for Computational Sciences (NCCS), Modeling Guru's combined forums and knowledge base for research and collaboration is becoming a repository for the accumulated expertise of NASA's scientific modeling and HEC communities. All NASA modelers and associates are encouraged to participate and provide knowledge about the models and systems so that other users may benefit from their experience. Modeling Guru is divided into a hierarchy of communities, each with its own set forums and knowledge base documents. Current modeling communities include those for space science, land and atmospheric dynamics, atmospheric chemistry, and oceanography. In addition, there are communities focused on NCCS systems, HEC tools and libraries, and programming and scripting languages. Anyone may view most of the content on Modeling Guru (available at http://modelingguru.nasa.gov/), but you must log in to post messages and subscribe to community postings. The site offers a full range of "Web 2.0" features, including discussion forums, "wiki" document generation, document uploading, RSS feeds, search tools, blogs, email notification, and "breadcrumb" links. A discussion (a.k.a. forum "thread") is used to post comments, solicit feedback, or ask questions. If marked as a question, SIVO will monitor the thread, and normally respond within a day. Discussions can include embedded images, tables, and formatting through the use of the Rich Text Editor. Also, the user can add "Tags" to their thread to facilitate later searches. The "knowledge base" is comprised of documents that are used to capture and share expertise with others. The default "wiki" document lets users edit within the browser so others can easily collaborate on the

  8. A future of the model organism model

    PubMed Central

    Rine, Jasper

    2014-01-01

    Changes in technology are fundamentally reframing our concept of what constitutes a model organism. Nevertheless, research advances in the more traditional model organisms have enabled fresh and exciting opportunities for young scientists to establish new careers and offer the hope of comprehensive understanding of fundamental processes in life. New advances in translational research can be expected to heighten the importance of basic research in model organisms and expand opportunities. However, researchers must take special care and implement new resources to enable the newest members of the community to engage fully with the remarkable legacy of information in these fields. PMID:24577733

  9. 75 FR 39804 - Airworthiness Directives; The Boeing Company Model 757 Airplanes, Model 767 Airplanes, and Model...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-07-13

    ... Model 757 Airplanes, Model 767 Airplanes, and Model 777-200 and -300 Series Airplanes AGENCY: Federal... directive (AD) for certain Model 757 airplanes, Model 767 airplanes, and Model 777-200 and -300 series...) that would apply to certain Model 757 airplanes, Model 767 airplanes, and Model 777-200 and -300...

  10. Adhesion between cells, diffusion of growth factors, and elasticity of the AER produce the paddle shape of the chick limb

    PubMed Central

    Popławski, Nikodem J.; Swat, Maciej; Gens, J. Scott; Glazier, James A.

    2007-01-01

    A central question in developmental biology is how cells interact to organize into tissues? In this paper, we study the role of mesenchyme-ectoderm interaction in the growing chick limb bud using Glazier and Graner's cellular Potts model, a grid-based stochastic framework designed to simulate cell interactions and movement. We simulate cellular mechanisms including cell adhesion, growth, and division and diffusion of morphogens, to show that differential adhesion between the cells, diffusion of growth factors through the extracellular matrix, and the elastic properties of the apical ectodermal ridge together can produce the proper shape of the limb bud. PMID:18167520

  11. Effects of magnetic field on grain growth of non-ferromagnetic metals: A Monte Carlo simulation

    NASA Astrophysics Data System (ADS)

    Lei, H. C.; Zhu, X. B.; Sun, Y. P.; Hu, L.; Song, W. H.

    2009-02-01

    The grain growth kinetics, texture and misorientation distribution function (MDF) evolutions of a non-ferromagnetic metal sheet with isotropic and anisotropic grain boundary under magnetic field are studied using a modified two-dimensions (2D) Potts model, in which the grain boundary migration is driven by the grain boundary energy and the difference in magnetic free energy between grains and their neighbors. Monte Carlo simulation results show that the texture and MDF evolutions of materials intensively depend on the magnetic field and grain boundary anisotropy, whereas the grain boundary growth kinetics is insensitive to the magnetic field.

  12. Graph optimization problems on a Bethe lattice

    NASA Astrophysics Data System (ADS)

    de Oliveira, Mário J.

    1989-01-01

    The p-partitioning and p-coloring problems on a Bethe lattice of coordination number z are analyzed. It is shown that these two NP-complete optimization problems turn out to be equivalent to finding the ground-state energy of p-state Potts models with frustration. Numerical calculation of the cost function of both problems are carried out for several values of z and p. In the case of p=2 the results are identical to those obtained by Mézard and Parisi for the case of the bipartitioning problem. A numerical upper bound to the chromatic number is found for several values of z.

  13. Nested sampling with demons

    NASA Astrophysics Data System (ADS)

    Habeck, Michael

    2015-01-01

    This article looks at Skilling's nested sampling from a physical perspective and interprets it as a microcanonical demon algorithm. Using key quantities of statistical physics we investigate the performance of nested sampling on complex systems such as Ising, Potts and protein models. We show that releasing multiple demons helps to smooth the truncated prior and eases sampling from it because the demons keep the particle off the constraint boundary. For continuous systems it is straightforward to extend this approach and formulate a phase space version of nested sampling that benefits from correlated explorations guided by Hamiltonian dynamics.

  14. Develop a Model Component

    NASA Technical Reports Server (NTRS)

    Ensey, Tyler S.

    2013-01-01

    During my internship at NASA, I was a model developer for Ground Support Equipment (GSE). The purpose of a model developer is to develop and unit test model component libraries (fluid, electrical, gas, etc.). The models are designed to simulate software for GSE (Ground Special Power, Crew Access Arm, Cryo, Fire and Leak Detection System, Environmental Control System (ECS), etc. .) before they are implemented into hardware. These models support verifying local control and remote software for End-Item Software Under Test (SUT). The model simulates the physical behavior (function, state, limits and 110) of each end-item and it's dependencies as defined in the Subsystem Interface Table, Software Requirements & Design Specification (SRDS), Ground Integrated Schematic (GIS), and System Mechanical Schematic.(SMS). The software of each specific model component is simulated through MATLAB's Simulink program. The intensiv model development life cycle is a.s follows: Identify source documents; identify model scope; update schedule; preliminary design review; develop model requirements; update model.. scope; update schedule; detailed design review; create/modify library component; implement library components reference; implement subsystem components; develop a test script; run the test script; develop users guide; send model out for peer review; the model is sent out for verifictionlvalidation; if there is empirical data, a validation data package is generated; if there is not empirical data, a verification package is generated; the test results are then reviewed; and finally, the user. requests accreditation, and a statement of accreditation is prepared. Once each component model is reviewed and approved, they are intertwined together into one integrated model. This integrated model is then tested itself, through a test script and autotest, so that it can be concluded that all models work conjointly, for a single purpose. The component I was assigned, specifically, was a

  15. Biosphere Model Report

    SciTech Connect

    D.W. Wu; A.J. Smith

    2004-11-08

    The purpose of this report is to document the biosphere model, the Environmental Radiation Model for Yucca Mountain, Nevada (ERMYN), which describes radionuclide transport processes in the biosphere and associated human exposure that may arise as the result of radionuclide release from the geologic repository at Yucca Mountain. The biosphere model is one of the process models that support the Yucca Mountain Project (YMP) Total System Performance Assessment (TSPA) for the license application (LA), TSPA-LA. The ERMYN provides the capability of performing human radiation dose assessments. This report documents the biosphere model, which includes: (1) Describing the reference biosphere, human receptor, exposure scenarios, and primary radionuclides for each exposure scenario (Section 6.1); (2) Developing a biosphere conceptual model using site-specific features, events, and processes (FEPs) (Section 6.2), the reference biosphere (Section 6.1.1), the human receptor (Section 6.1.2), and approximations (Sections 6.3.1.4 and 6.3.2.4); (3) Building a mathematical model using the biosphere conceptual model (Section 6.3) and published biosphere models (Sections 6.4 and 6.5); (4) Summarizing input parameters for the mathematical model, including the uncertainty associated with input values (Section 6.6); (5) Identifying improvements in the ERMYN compared with the model used in previous biosphere modeling (Section 6.7); (6) Constructing an ERMYN implementation tool (model) based on the biosphere mathematical model using GoldSim stochastic simulation software (Sections 6.8 and 6.9); (7) Verifying the ERMYN by comparing output from the software with hand calculations to ensure that the GoldSim implementation is correct (Section 6.10); (8) Validating the ERMYN by corroborating it with published biosphere models; comparing conceptual models, mathematical models, and numerical results (Section 7).

  16. [MODELING INFLAMMATORY EDEMA: ARE THE MODELS INTERCHANGEABLE].

    PubMed

    Hanh, Cong Hong; Khaziakhmetova, V N; Ziganshina, L E

    2015-01-01

    Experimental modeling of inflammatory edema by sub-plantar injection of carrageenan and formalin in mice and rats is widely used to evaluate potential anti-inflammatory activity of new drugs. This systematic analysis of published data showed that carrageenan induced paw edema model is used for evaluating the anti-inflammatory activity mostly in rats rather than mice. Formalin induced paw edema in rats and mice is used primarily for evaluation of the analgesic activity of drugs. Taken together, the results of this systematic review of available literature on edema modeling substantiate recommendation to use carrageenan paw edema in rats and formalin paw edema in mice as complementary, but not interchangeable models of inflammation. PMID:26591204

  17. Model documention: Commercial Sector Energy Model. [CSEM

    SciTech Connect

    Not Available

    1984-08-10

    The CSEM forecasts floorspace area and demand for natural gas, electricity and fuel oil for six building categories in four Census regions. Real disposable personal income, population and real fuel prices are the major exogenous drivers of these forecasts. The commercial model uses the coefficients from the three econometric submodules to calculate building floorspace, end-use fuel choices, and utilization (enegy use per square foot) for the three major fuels. Separately from these structural components the model also calculates energy use for the minor fuels liquefied petroleum gas, kerosene, coal and motor gasoline. Through the use of accounting equations, the commercial model combines the structural components to get total commercial energy use over the major fuels. It then adds in the minor fuels, passes the information back to the other models and writes reports.

  18. Aerosol Modeling for the Global Model Initiative

    NASA Technical Reports Server (NTRS)

    Weisenstein, Debra K.; Ko, Malcolm K. W.

    2001-01-01

    The goal of this project is to develop an aerosol module to be used within the framework of the Global Modeling Initiative (GMI). The model development work will be preformed jointly by the University of Michigan and AER, using existing aerosol models at the two institutions as starting points. The GMI aerosol model will be tested, evaluated against observations, and then applied to assessment of the effects of aircraft sulfur emissions as needed by the NASA Subsonic Assessment in 2001. The work includes the following tasks: 1. Implementation of the sulfur cycle within GMI, including sources, sinks, and aqueous conversion of sulfur. Aerosol modules will be added as they are developed and the GMI schedule permits. 2. Addition of aerosol types other than sulfate particles, including dust, soot, organic carbon, and black carbon. 3. Development of new and more efficient parameterizations for treating sulfate aerosol nucleation, condensation, and coagulation among different particle sizes and types.

  19. Nonlinear Modeling by Assembling Piecewise Linear Models

    NASA Technical Reports Server (NTRS)

    Yao, Weigang; Liou, Meng-Sing

    2013-01-01

    To preserve nonlinearity of a full order system over a parameters range of interest, we propose a simple modeling approach by assembling a set of piecewise local solutions, including the first-order Taylor series terms expanded about some sampling states. The work by Rewienski and White inspired our use of piecewise linear local solutions. The assembly of these local approximations is accomplished by assigning nonlinear weights, through radial basis functions in this study. The efficacy of the proposed procedure is validated for a two-dimensional airfoil moving at different Mach numbers and pitching motions, under which the flow exhibits prominent nonlinear behaviors. All results confirm that our nonlinear model is accurate and stable for predicting not only aerodynamic forces but also detailed flowfields. Moreover, the model is robustness-accurate for inputs considerably different from the base trajectory in form and magnitude. This modeling preserves nonlinearity of the problems considered in a rather simple and accurate manner.

  20. Aggregation in ecosystem models and model stability

    NASA Astrophysics Data System (ADS)

    Giricheva, Evgeniya

    2015-05-01

    Using a multimodal approach to research ecosystems improves usage of available information on an object. This study presents several models of the Bering Sea ecosystem. The ecosystem is considered as a closed object, that is, the influence of the environment is not provided. We then add the links with the external medium in the models. The models differ in terms of the degree and method of grouping components. Our method is based on the differences in habitat and food source of groups, which allows us to determine the grouping of species with a greater effect on system dynamics. In particular, we determine whether benthic fish aggregation or pelagic fish aggregation can change the consumption structure of some groups of species, and consequently, the behavior of the entire model system.

  1. PREDICTIVE MODELS. Enhanced Oil Recovery Model

    SciTech Connect

    Ray, R.M.

    1992-02-26

    PREDICTIVE MODELS is a collection of five models - CFPM, CO2PM, ICPM, PFPM, and SFPM - used in the 1982-1984 National Petroleum Council study of enhanced oil recovery (EOR) potential. Each pertains to a specific EOR process designed to squeeze additional oil from aging or spent oil fields. The processes are: 1 chemical flooding, where soap-like surfactants are injected into the reservoir to wash out the oil; 2 carbon dioxide miscible flooding, where carbon dioxide mixes with the lighter hydrocarbons making the oil easier to displace; 3 in-situ combustion, which uses the heat from burning some of the underground oil to thin the product; 4 polymer flooding, where thick, cohesive material is pumped into a reservoir to push the oil through the underground rock; and 5 steamflood, where pressurized steam is injected underground to thin the oil. CFPM, the Chemical Flood Predictive Model, models micellar (surfactant)-polymer floods in reservoirs, which have been previously waterflooded to residual oil saturation. Thus, only true tertiary floods are considered. An option allows a rough estimate of oil recovery by caustic or caustic-polymer processes. CO2PM, the Carbon Dioxide miscible flooding Predictive Model, is applicable to both secondary (mobile oil) and tertiary (residual oil) floods, and to either continuous CO2 injection or water-alternating gas processes. ICPM, the In-situ Combustion Predictive Model, computes the recovery and profitability of an in-situ combustion project from generalized performance predictive algorithms. PFPM, the Polymer Flood Predictive Model, is switch-selectable for either polymer or waterflooding, and an option allows the calculation of the incremental oil recovery and economics of polymer relative to waterflooding. SFPM, the Steamflood Predictive Model, is applicable to the steam drive process, but not to cyclic steam injection (steam soak) processes.

  2. X-33 RCS model

    NASA Technical Reports Server (NTRS)

    1998-01-01

    Model support system and instumentation cabling of the 1% scale X-33 reaction control system model. Installed in the Unitary Plan Wind Tunnel for supersonic testing. In building 1251, test section #2.

  3. Mass modeling for bars

    NASA Technical Reports Server (NTRS)

    Butler, Thomas G.

    1987-01-01

    Methods of modeling mass for bars are surveyed. A method for extending John Archer's concept of consistent mass beyond just translational inertia effects is included. Recommendations are given for various types of modeling situations.

  4. Bounding Species Distribution Models

    NASA Technical Reports Server (NTRS)

    Stohlgren, Thomas J.; Jarnevich, Cahterine S.; Morisette, Jeffrey T.; Esaias, Wayne E.

    2011-01-01

    Species distribution models are increasing in popularity for mapping suitable habitat for species of management concern. Many investigators now recognize that extrapolations of these models with geographic information systems (GIS) might be sensitive to the environmental bounds of the data used in their development, yet there is no recommended best practice for "clamping" model extrapolations. We relied on two commonly used modeling approaches: classification and regression tree (CART) and maximum entropy (Maxent) models, and we tested a simple alteration of the model extrapolations, bounding extrapolations to the maximum and minimum values of primary environmental predictors, to provide a more realistic map of suitable habitat of hybridized Africanized honey bees in the southwestern United States. Findings suggest that multiple models of bounding, and the most conservative bounding of species distribution models, like those presented here, should probably replace the unbounded or loosely bounded techniques currently used [Current Zoology 57 (5): 642-647, 2011].

  5. Bounding species distribution models

    USGS Publications Warehouse

    Stohlgren, T.J.; Jarnevich, C.S.; Esaias, W.E.; Morisette, J.T.

    2011-01-01

    Species distribution models are increasing in popularity for mapping suitable habitat for species of management concern. Many investigators now recognize that extrapolations of these models with geographic information systems (GIS) might be sensitive to the environmental bounds of the data used in their development, yet there is no recommended best practice for "clamping" model extrapolations. We relied on two commonly used modeling approaches: classification and regression tree (CART) and maximum entropy (Maxent) models, and we tested a simple alteration of the model extrapolations, bounding extrapolations to the maximum and minimum values of primary environmental predictors, to provide a more realistic map of suitable habitat of hybridized Africanized honey bees in the southwestern United States. Findings suggest that multiple models of bounding, and the most conservative bounding of species distribution models, like those presented here, should probably replace the unbounded or loosely bounded techniques currently used. ?? 2011 Current Zoology.

  6. SEDIMENT GEOCHEMICAL MODEL

    EPA Science Inventory

    Until recently, sediment geochemical models (diagenetic models) have been only able to explain sedimentary flux and concentration profiles for a few simplified geochemical cycles (e.g., nitrogen, carbon and sulfur). However with advances in numerical methods, increased accuracy ...

  7. Of Molecules and Models.

    ERIC Educational Resources Information Center

    Brinner, Bonnie

    1992-01-01

    Presents an activity in which models help students visualize both the DNA process and transcription. After constructing DNA, RNA messenger, and RNA transfer molecules; students model cells, protein synthesis, codons, and RNA movement. (MDH)

  8. Modeling Infectious Diseases

    MedlinePlus

    ... MIDAS models require a breadth of knowledge, the network draws together an interdisciplinary team of researchers with expertise in epidemiology, infectious diseases, computational biology, statistics, social sciences, physics, computer sciences and informatics. In 2006, MIDAS modelers simulated ...

  9. Modeling DNA Replication.

    ERIC Educational Resources Information Center

    Bennett, Joan

    1998-01-01

    Recommends the use of a model of DNA made out of Velcro to help students visualize the steps of DNA replication. Includes a materials list, construction directions, and details of the demonstration using the model parts. (DDR)

  10. Communication system modeling

    NASA Technical Reports Server (NTRS)

    Holland, L. D.; Walsh, J. R., Jr.; Wetherington, R. D.

    1971-01-01

    This report presents the results of work on communications systems modeling and covers three different areas of modeling. The first of these deals with the modeling of signals in communication systems in the frequency domain and the calculation of spectra for various modulations. These techniques are applied in determining the frequency spectra produced by a unified carrier system, the down-link portion of the Command and Communications System (CCS). The second modeling area covers the modeling of portions of a communication system on a block basis. A detailed analysis and modeling effort based on control theory is presented along with its application to modeling of the automatic frequency control system of an FM transmitter. A third topic discussed is a method for approximate modeling of stiff systems using state variable techniques.

  11. TMDL RUSLE MODEL

    EPA Science Inventory

    We developed a simplified spreadsheet modeling approach for characterizing and prioritizing sources of sediment loadings from watersheds in the United States. A simplified modeling approach was developed to evaluate sediment loadings from watersheds and selected land segments. ...

  12. Modeling EERE deployment programs

    SciTech Connect

    Cort, K. A.; Hostick, D. J.; Belzer, D. B.; Livingston, O. V.

    2007-11-01

    The purpose of the project was to identify and characterize the modeling of deployment programs within the EERE Technology Development (TD) programs, address possible improvements to the modeling process, and note gaps in knowledge for future research.

  13. Consistent model driven architecture

    NASA Astrophysics Data System (ADS)

    Niepostyn, Stanisław J.

    2015-09-01

    The goal of the MDA is to produce software systems from abstract models in a way where human interaction is restricted to a minimum. These abstract models are based on the UML language. However, the semantics of UML models is defined in a natural language. Subsequently the verification of consistency of these diagrams is needed in order to identify errors in requirements at the early stage of the development process. The verification of consistency is difficult due to a semi-formal nature of UML diagrams. We propose automatic verification of consistency of the series of UML diagrams originating from abstract models implemented with our consistency rules. This Consistent Model Driven Architecture approach enables us to generate automatically complete workflow applications from consistent and complete models developed from abstract models (e.g. Business Context Diagram). Therefore, our method can be used to check practicability (feasibility) of software architecture models.

  14. System Advisor Model

    2010-03-01

    The System Advisor Model (SAM) is a performance and economic model designed to facilitate decision making for people involved in the renewable energy industry, ranging from project managers and engineers to incentive program designers, technology developers, and researchers.

  15. Comparison of Decision Models

    NASA Technical Reports Server (NTRS)

    Feinberg, A.; Miles, J. R. F.; Smith, J. H.; Scheuer, E. M.

    1986-01-01

    Two methods of multiattribute decision analysis compared in report. One method employs linear utility model. Other utilizes multiplicative utility model. Report based on interviews with experts in automotive technology to obtain their preferences regarding 10 new types of vehicles.

  16. Protein solubility modeling

    NASA Technical Reports Server (NTRS)

    Agena, S. M.; Pusey, M. L.; Bogle, I. D.

    1999-01-01

    A thermodynamic framework (UNIQUAC model with temperature dependent parameters) is applied to model the salt-induced protein crystallization equilibrium, i.e., protein solubility. The framework introduces a term for the solubility product describing protein transfer between the liquid and solid phase and a term for the solution behavior describing deviation from ideal solution. Protein solubility is modeled as a function of salt concentration and temperature for a four-component system consisting of a protein, pseudo solvent (water and buffer), cation, and anion (salt). Two different systems, lysozyme with sodium chloride and concanavalin A with ammonium sulfate, are investigated. Comparison of the modeled and experimental protein solubility data results in an average root mean square deviation of 5.8%, demonstrating that the model closely follows the experimental behavior. Model calculations and model parameters are reviewed to examine the model and protein crystallization process. Copyright 1999 John Wiley & Sons, Inc.

  17. METEOROLOGICAL AND TRANSPORT MODELING

    EPA Science Inventory

    Advanced air quality simulation models, such as CMAQ, as well as other transport and dispersion models, require accurate and detailed meteorology fields. These meteorology fields include primary 3-dimensional dynamical and thermodynamical variables (e.g., winds, temperature, mo...

  18. Soil moisture modeling review

    NASA Technical Reports Server (NTRS)

    Hildreth, W. W.

    1978-01-01

    A determination of the state of the art in soil moisture transport modeling based on physical or physiological principles was made. It was found that soil moisture models based on physical principles have been under development for more than 10 years. However, these models were shown to represent infiltration and redistribution of soil moisture quite well. Evapotranspiration has not been as adequately incorporated into the models.

  19. Future of groundwater modeling

    USGS Publications Warehouse

    Langevin, Christian D.; Panday, Sorab

    2012-01-01

    With an increasing need to better manage water resources, the future of groundwater modeling is bright and exciting. However, while the past can be described and the present is known, the future of groundwater modeling, just like a groundwater model result, is highly uncertain and any prediction is probably not going to be entirely representative. Thus we acknowledge this as we present our vision of where groundwater modeling may be headed.

  20. Modeling of spacecraft charging

    NASA Technical Reports Server (NTRS)

    Whipple, E. C., Jr.

    1977-01-01

    Three types of modeling of spacecraft charging are discussed: statistical models, parametric models, and physical models. Local time dependence of circuit upset for DoD and communication satellites, and electron current to a sphere with an assumed Debye potential distribution are presented. Four regions were involved in spacecraft charging: (1) undisturbed plasma, (2) plasma sheath region, (3) spacecraft surface, and (4) spacecraft equivalent circuit.

  1. Hierarchical Bass model

    NASA Astrophysics Data System (ADS)

    Tashiro, Tohru

    2014-03-01

    We propose a new model about diffusion of a product which includes a memory of how many adopters or advertisements a non-adopter met, where (non-)adopters mean people (not) possessing the product. This effect is lacking in the Bass model. As an application, we utilize the model to fit the iPod sales data, and so the better agreement is obtained than the Bass model.

  2. Modeling the Pacific Ocean

    SciTech Connect

    Johnson, M.A.; O'Brien, J.J. )

    1990-01-01

    Two numerical models utilizing primitive equations (two momentum equations and a mass continuity equation) simulate the oceanography of the Pacific Ocean from 20{degrees}S to 50{degrees}N. The authors examine the abundant model data through visualization , by animating the appropriate model fields and viewing the time history of each model simulation as a color movie. The animations are used to aid understanding of ocean circulation.

  3. Avionics Architecture Modelling Language

    NASA Astrophysics Data System (ADS)

    Alana, Elena; Naranjo, Hector; Valencia, Raul; Medina, Alberto; Honvault, Christophe; Rugina, Ana; Panunzia, Marco; Dellandrea, Brice; Garcia, Gerald

    2014-08-01

    This paper presents the ESA AAML (Avionics Architecture Modelling Language) study, which aimed at advancing the avionics engineering practices towards a model-based approach by (i) identifying and prioritising the avionics-relevant analyses, (ii) specifying the modelling language features necessary to support the identified analyses, and (iii) recommending/prototyping software tooling to demonstrate the automation of the selected analyses based on a modelling language and compliant with the defined specification.

  4. Current sheet model

    NASA Technical Reports Server (NTRS)

    1981-01-01

    The model of a rectenna based on the current sheet equivalency of a large planar array is described. The model is mathematically characterized by expression for the fraction of the incident plane wave that is reflected from the sheet. The model is conceptually justified for normal incidence by comparing it to the waveguide model in which evanescent modes, present as beyond and cutoff, correspond to the near field components which become negligible at any significant distance from the antenna array.

  5. Modeling Complex Calorimeters

    NASA Technical Reports Server (NTRS)

    Figueroa-Feliciano, Enectali

    2004-01-01

    We have developed a software suite that models complex calorimeters in the time and frequency domain. These models can reproduce all measurements that we currently do in a lab setting, like IV curves, impedance measurements, noise measurements, and pulse generation. Since all these measurements are modeled from one set of parameters, we can fully describe a detector and characterize its behavior. This leads to a model than can be used effectively for engineering and design of detectors for particular applications.

  6. Mathematical circulatory system model

    NASA Technical Reports Server (NTRS)

    Lakin, William D. (Inventor); Stevens, Scott A. (Inventor)

    2010-01-01

    A system and method of modeling a circulatory system including a regulatory mechanism parameter. In one embodiment, a regulatory mechanism parameter in a lumped parameter model is represented as a logistic function. In another embodiment, the circulatory system model includes a compliant vessel, the model having a parameter representing a change in pressure due to contraction of smooth muscles of a wall of the vessel.

  7. Campus Energy Modeling Platform

    2014-09-19

    NREL's Campus Energy Modeling project provides a suite of simulation tools for integrated, data driven energy modeling of commercial buildings and campuses using Simulink. The tools enable development of fully interconnected models for commercial campus energy infrastructure, including electrical distribution systems, district heating and cooling, onsite generation (both conventional and renewable), building loads, energy storage, and control systems.

  8. Models, Norms and Sharing.

    ERIC Educational Resources Information Center

    Harris, Mary B.

    To investigate the effect of modeling on altruism, 156 third and fifth grade children were exposed to a model who either shared with them, gave to a charity, or refused to share. The test apparatus, identified as a game, consisted of a box with signal lights and a chute through which marbles were dispensed. Subjects and the model played the game…

  9. Biophysical and spectral modeling

    NASA Technical Reports Server (NTRS)

    Goel, N. S. (Principal Investigator)

    1982-01-01

    Activities and results of a project to develop strategies for modeling vegetative canopy reflectance are reported. Specific tasks included the inversion of canopy reflectance models to estimate agronomic variables (particularly leaf area index) from in-situ reflectance measurements, and a study of possible uses of ecological models in analyzing temporal profiles of greenness.

  10. A Model Chemistry Class.

    ERIC Educational Resources Information Center

    Summerlin, Lee; Borgford, Christie

    1989-01-01

    Described is an activity which uses a 96-well reaction plate and soda straws to construct a model of the periodic table of the elements. The model illustrates the ionization energies of the various elements. Construction of the model and related concepts are discussed. (CW)

  11. What Is a Model?

    ERIC Educational Resources Information Center

    McNamara, James F.

    1996-01-01

    Uses R.A. Ackoff's connotations to define "model" as noun, adjective, and verb. Researchers should use various types of models (iconic, analogue, or symbolic) for three purposes: to reveal reality, to explain the past and present, and to predict and control the future. Herbert Simon's process model for administrative decision making has widespread…

  12. Crushed Salt Constitutive Model

    SciTech Connect

    Callahan, G.D.

    1999-02-01

    The constitutive model used to describe the deformation of crushed salt is presented in this report. Two mechanisms -- dislocation creep and grain boundary diffusional pressure solution -- are combined to form the basis for the constitutive model governing the deformation of crushed salt. The constitutive model is generalized to represent three-dimensional states of stress. Upon complete consolidation, the crushed-salt model reproduces the Multimechanism Deformation (M-D) model typically used for the Waste Isolation Pilot Plant (WIPP) host geological formation salt. New shear consolidation tests are combined with an existing database that includes hydrostatic consolidation and shear consolidation tests conducted on WIPP and southeastern New Mexico salt. Nonlinear least-squares model fitting to the database produced two sets of material parameter values for the model -- one for the shear consolidation tests and one for a combination of the shear and hydrostatic consolidation tests. Using the parameter values determined from the fitted database, the constitutive model is validated against constant strain-rate tests. Shaft seal problems are analyzed to demonstrate model-predicted consolidation of the shaft seal crushed-salt component. Based on the fitting statistics, the ability of the model to predict the test data, and the ability of the model to predict load paths and test data outside of the fitted database, the model appears to capture the creep consolidation behavior of crushed salt reasonably well.

  13. Modeling rapidly rotating stars

    NASA Astrophysics Data System (ADS)

    Rieutord, M.

    2006-06-01

    We review the quest of modeling rapidly rotating stars during the past 40 years and detail the challenges to be taken up by models facing new data from interferometry, seismology, spectroscopy... We then present the progress of the ESTER project aimed at giving a physically self-consistent model for the structure and evolution of rapidly rotating stars.

  14. Retrofitted supersymmetric models

    NASA Astrophysics Data System (ADS)

    Bose, Manatosh

    This thesis explores several models of metastable dynamic supersymmetry breaking (MDSB) and a supersymmetric model of hybrid inflation. All of these models possess discrete R-symmetries. We specially focus on the retrofitted models for supersymmetry breaking models. At first we construct retrofitted models of gravity mediation. In these models we explore the genericity of the so-called "split supersymmetry." We show that with the simplest models, where the goldstino multiplet is neutral under the discrete R-symmetry, a split spectrum is not generic. However if the goldstino superfield is charged under some symmetry other than the R-symmetry, then a split spectrum is achievable but not generic. We also present a gravity mediated model where the fine tuning of the Z-boson mass is dictated by a discrete choice rather than a continuous tuning. Then we construct retrofitted models of gauge mediated SUSY breaking. We show that, in these models, if the approximate R-symmetry of the theory is spontaneously broken, the messenger scale is fixed; if explicitly broken by retrofitted couplings, a very small dimensionless number is required; if supergravity corrections are responsible for the symmetry breaking, at least two moderately small couplings are required, and that there is a large range of possible messenger scales. Finally we switch our attention to small field hybrid inflation. We construct a model that yields a spectral index ns = 0.96. Here, we also briefly discuss the possibility of relating the scale of inflation with the dynamics responsible for supersymmetry breaking.

  15. Modeling Natural Selection

    ERIC Educational Resources Information Center

    Bogiages, Christopher A.; Lotter, Christine

    2011-01-01

    In their research, scientists generate, test, and modify scientific models. These models can be shared with others and demonstrate a scientist's understanding of how the natural world works. Similarly, students can generate and modify models to gain a better understanding of the content, process, and nature of science (Kenyon, Schwarz, and Hug…

  16. A Model Performance

    ERIC Educational Resources Information Center

    Thornton, Bradley D.; Smalley, Robert A.

    2008-01-01

    Building information modeling (BIM) uses three-dimensional modeling concepts, information technology and interoperable software to design, construct and operate a facility. However, BIM can be more than a tool for virtual modeling--it can provide schools with a 3-D walkthrough of a project while it still is on the electronic drawing board. BIM can…

  17. Impact-GMI Model

    2007-03-22

    IMPACT-GMI is an atmospheric chemical transport model designed to run on massively parallel computers. It is designed to model trace pollutants in the atmosphere. It includes models for emission, chemistry and deposition of pollutants. It can be used to assess air quality and its impact on future climate change.

  18. Surface complexation modeling

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Adsorption-desorption reactions are important processes that affect the transport of contaminants in the environment. Surface complexation models are chemical models that can account for the effects of variable chemical conditions, such as pH, on adsorption reactions. These models define specific ...

  19. SECOND GENERATION MODEL

    EPA Science Inventory

    One of the environmental and economic models that the U.S. EPA uses to assess climate change policies is the Second Generation Model (SGM). SGM is a 13 region, 24 sector computable general equilibrium (CGE) model of the world that can be used to estimate the domestic and intern...

  20. Progress in mix modeling

    SciTech Connect

    Harrison, A.K.

    1997-03-14

    We have identified the Cranfill multifluid turbulence model (Cranfill, 1992) as a starting point for development of subgrid models of instability, turbulent and mixing processes. We have differenced the closed system of equations in conservation form, and coded them in the object-oriented hydrodynamics code FLAG, which is to be used as a testbed for such models.

  1. Modeling EERE Deployment Programs

    SciTech Connect

    Cort, K. A.; Hostick, D. J.; Belzer, D. B.; Livingston, O. V.

    2007-11-01

    This report compiles information and conclusions gathered as part of the “Modeling EERE Deployment Programs” project. The purpose of the project was to identify and characterize the modeling of deployment programs within the EERE Technology Development (TD) programs, address possible improvements to the modeling process, and note gaps in knowledge in which future research is needed.

  2. Modern Media Education Models

    ERIC Educational Resources Information Center

    Fedorov, Alexander

    2011-01-01

    The author supposed that media education models can be divided into the following groups: (1) educational-information models (the study of the theory, history, language of media culture, etc.), based on the cultural, aesthetic, semiotic, socio-cultural theories of media education; (2) educational-ethical models (the study of moral, religions,…

  3. Rock Properties Model

    SciTech Connect

    C. Lum

    2004-09-16

    The purpose of this model report is to document the Rock Properties Model version 3.1 with regard to input data, model methods, assumptions, uncertainties and limitations of model results, and qualification status of the model. The report also documents the differences between the current and previous versions and validation of the model. The rock properties model provides mean matrix and lithophysae porosity, and the cross-correlated mean bulk density as direct input to the ''Saturated Zone Flow and Transport Model Abstraction'', MDL-NBS-HS-000021, REV 02 (BSC 2004 [DIRS 170042]). The constraints, caveats, and limitations associated with this model are discussed in Section 6.6 and 8.2. Model validation accomplished by corroboration with data not cited as direct input is discussed in Section 7. The revision of this model report was performed as part of activities being conducted under the ''Technical Work Plan for: The Integrated Site Model, Revision 05'' (BSC 2004 [DIRS 169635]). The purpose of this revision is to bring the report up to current procedural requirements and address the Regulatory Integration Team evaluation comments. The work plan describes the scope, objectives, tasks, methodology, and procedures for this process.

  4. Modeling Climate Dynamically

    ERIC Educational Resources Information Center

    Walsh, Jim; McGehee, Richard

    2013-01-01

    A dynamical systems approach to energy balance models of climate is presented, focusing on low order, or conceptual, models. Included are global average and latitude-dependent, surface temperature models. The development and analysis of the differential equations and corresponding bifurcation diagrams provides a host of appropriate material for…

  5. Model Breaking Points Conceptualized

    ERIC Educational Resources Information Center

    Vig, Rozy; Murray, Eileen; Star, Jon R.

    2014-01-01

    Current curriculum initiatives (e.g., National Governors Association Center for Best Practices and Council of Chief State School Officers 2010) advocate that models be used in the mathematics classroom. However, despite their apparent promise, there comes a point when models break, a point in the mathematical problem space where the model cannot,…

  6. URBAN AIRSHED MODEL (UAM)

    EPA Science Inventory

    The Urban Airshed Model (UAM) is an urban scale, three-dimensional, grid type, numerical simulation model. The model incorporates a condensed photochemical kinetics mechanism for urban atmospheres. The UAM is designed for computing ozone (O3) concentrations under short-term, epis...

  7. Model Rockets and Microchips.

    ERIC Educational Resources Information Center

    Fitzsimmons, Charles P.

    1986-01-01

    Points out the instructional applications and program possibilities of a unit on model rocketry. Describes the ways that microcomputers can assist in model rocket design and in problem calculations. Provides a descriptive listing of model rocket software for the Apple II microcomputer. (ML)

  8. New Directions for Modeling?

    ERIC Educational Resources Information Center

    Mason, Thomas R.

    1976-01-01

    Noting the disappointing results of past experimentation with computer modeling technology in higher education, the author discusses developments which promise potential: communication between model builders and users, interaction between large- and small-scale models, interface with operating data systems, emphasis on outcomes, and continued…

  9. General Graded Response Model.

    ERIC Educational Resources Information Center

    Samejima, Fumiko

    This paper describes the graded response model. The graded response model represents a family of mathematical models that deal with ordered polytomous categories, such as: (1) letter grading; (2) an attitude survey with "strongly disagree, disagree, agree, and strongly agree" choices; (3) partial credit given in accord with an individual's degree…

  10. Models for Products

    ERIC Educational Resources Information Center

    Speiser, Bob; Walter, Chuck

    2011-01-01

    This paper explores how models can support productive thinking. For us a model is a "thing", a tool to help make sense of something. We restrict attention to specific models for whole-number multiplication, hence the wording of the title. They support evolving thinking in large measure through the ways their users redesign them. They assume new…

  11. REGULATORY AIR QUALITY MODELS

    EPA Science Inventory

    Appendix W to 40CFR Part 51 (Guideline on Air Quality Models) specifies the models to be used for purposes of permitting, PSD, and SIPs. Through a formal regulatory process this modeling guidance is periodically updated to reflect current science. In the most recent action, thr...

  12. Molecular Models in Biology

    ERIC Educational Resources Information Center

    Goodman, Richard E.

    1970-01-01

    Describes types of molecular models (ball-and-stick, framework, and space-filling) and evaluates commercially available kits. Gives instructions for constructive models from polystyrene balls and pipe-cleaners. Models are useful for class demonstrations although not sufficiently accurate for research use. Illustrations show biologically important…

  13. Modeling and Remodeling Writing

    ERIC Educational Resources Information Center

    Hayes, John R.

    2012-01-01

    In Section 1 of this article, the author discusses the succession of models of adult writing that he and his colleagues have proposed from 1980 to the present. He notes the most important changes that differentiate earlier and later models and discusses reasons for the changes. In Section 2, he describes his recent efforts to model young…

  14. IR DIAL performance modeling

    SciTech Connect

    Sharlemann, E.T.

    1994-07-01

    We are developing a DIAL performance model for CALIOPE at LLNL. The intent of the model is to provide quick and interactive parameter sensitivity calculations with immediate graphical output. A brief overview of the features of the performance model is given, along with an example of performance calculations for a non-CALIOPE application.

  15. Global Timber Model (GTM)

    EPA Science Inventory

    GTM is an economic model capable of examining global forestry land-use, management, and trade responses to policies. In responding to a policy, the model captures afforestation, forest management, and avoided deforestation behavior. The model estimates harvests in industrial fore...

  16. Hierarchical Models of Attitude.

    ERIC Educational Resources Information Center

    Reddy, Srinivas K.; LaBarbera, Priscilla A.

    1985-01-01

    The application and use of hierarchical models is illustrated, using the example of the structure of attitudes toward a new product and a print advertisement. Subjects were college students who responded to seven-point bipolar scales. Hierarchical models were better than nonhierarchical models in conceptualizing attitude but not intention. (GDC)

  17. Generalized Latent Trait Models.

    ERIC Educational Resources Information Center

    Moustaki, Irini; Knott, Martin

    2000-01-01

    Discusses a general model framework within which manifest variables with different distributions in the exponential family can be analyzed with a latent trait model. Presents a unified maximum likelihood method for estimating the parameters of the generalized latent trait model and discusses the scoring of individuals on the latent dimensions.…

  18. Modelling Vocabulary Loss

    ERIC Educational Resources Information Center

    Meara, Paul

    2004-01-01

    This paper describes some simple simulation models of vocabulary attrition. The attrition process is modelled using a random autonomous Boolean network model, and some parallels with real attrition data are drawn. The paper argues that applying a complex systems approach to attrition can provide some important insights, which suggest that real…

  19. Modelling MIZ dynamics in a global model

    NASA Astrophysics Data System (ADS)

    Rynders, Stefanie; Aksenov, Yevgeny; Feltham, Daniel; Nurser, George; Naveira Garabato, Alberto

    2016-04-01

    Exposure of large, previously ice-covered areas of the Arctic Ocean to the wind and surface ocean waves results in the Arctic pack ice cover becoming more fragmented and mobile, with large regions of ice cover evolving into the Marginal Ice Zone (MIZ). The need for better climate predictions, along with growing economic activity in the Polar Oceans, necessitates climate and forecasting models that can simulate fragmented sea ice with a greater fidelity. Current models are not fully fit for the purpose, since they neither model surface ocean waves in the MIZ, nor account for the effect of floe fragmentation on drag, nor include sea ice rheology that represents both the now thinner pack ice and MIZ ice dynamics. All these processes affect the momentum transfer to the ocean. We present initial results from a global ocean model NEMO (Nucleus for European Modelling of the Ocean) coupled to the Los Alamos sea ice model CICE. The model setup implements a novel rheological formulation for sea ice dynamics, accounting for ice floe collisions, thus offering a seamless framework for pack ice and MIZ simulations. The effect of surface waves on ice motion is included through wave pressure and the turbulent kinetic energy of ice floes. In the multidecadal model integrations we examine MIZ and basin scale sea ice and oceanic responses to the changes in ice dynamics. We analyse model sensitivities and attribute them to key sea ice and ocean dynamical mechanisms. The results suggest that the effect of the new ice rheology is confined to the MIZ. However with the current increase in summer MIZ area, which is projected to continue and may become the dominant type of sea ice in the Arctic, we argue that the effects of the combined sea ice rheology will be noticeable in large areas of the Arctic Ocean, affecting sea ice and ocean. With this study we assert that to make more accurate sea ice predictions in the changing Arctic, models need to include MIZ dynamics and physics.

  20. Advances in Watershed Models and Modeling

    NASA Astrophysics Data System (ADS)

    Yeh, G. T.; Zhang, F.

    2015-12-01

    The development of watershed models and their applications to real-world problems has evolved significantly since 1960's. Watershed models can be classified based on what media are included, what processes are dealt with, and what approaches are taken. In term of media, a watershed may include segregated overland regime, river-canal-open channel networks, ponds-reservoirs-small lakes, and subsurface media. It may also include integrated media of all these or a partial set of these as well as man-made control structures. In term of processes, a watershed model may deal with coupled or decoupled hydrological and biogeochemical cycles. These processes include fluid flow, thermal transport, salinity transport, sediment transport, reactive transport, and biota and microbe kinetics. In terms of approaches, either parametric or physics-based approach can be taken. This talk discusses the evolution of watershed models in the past sixty years. The advances of watershed models center around their increasing design capability to foster these segregated or integrated media and coupled or decoupled processes. Widely used models developed by academia, research institutes, government agencies, and private industries will be reviewed in terms of the media and processes included as well as approaches taken. Many types of potential benchmark problems in general can be proposed and will be discussed. This presentation will focus on three benchmark problems of biogeochemical cycles. These three problems, dealing with water quality transport, will be formulated in terms of reactive transport. Simulation results will be illustrated using WASH123D, a watershed model developed and continuously updated by the author and his PhD graduates. Keywords: Hydrological Cycles, Biogeochemical Cycles, Biota Kinetics, Parametric Approach, Physics-based Approach, Reactive Transport.

  1. Modeling agriculture in the Community Land Model

    NASA Astrophysics Data System (ADS)

    Drewniak, B.; Song, J.; Prell, J.; Kotamarthi, V. R.; Jacob, R.

    2013-04-01

    The potential impact of climate change on agriculture is uncertain. In addition, agriculture could influence above- and below-ground carbon storage. Development of models that represent agriculture is necessary to address these impacts. We have developed an approach to integrate agriculture representations for three crop types - maize, soybean, and spring wheat - into the coupled carbon-nitrogen version of the Community Land Model (CLM), to help address these questions. Here we present the new model, CLM-Crop, validated against observations from two AmeriFlux sites in the United States, planted with maize and soybean. Seasonal carbon fluxes compared well with field measurements for soybean, but not as well for maize. CLM-Crop yields were comparable with observations in countries such as the United States, Argentina, and China, although the generality of the crop model and its lack of technology and irrigation made direct comparison difficult. CLM-Crop was compared against the standard CLM3.5, which simulates crops as grass. The comparison showed improvement in gross primary productivity in regions where crops are the dominant vegetation cover. Crop yields and productivity were negatively correlated with temperature and positively correlated with precipitation, in agreement with other modeling studies. In case studies with the new crop model looking at impacts of residue management and planting date on crop yield, we found that increased residue returned to the litter pool increased crop yield, while reduced residue returns resulted in yield decreases. Using climate controls to signal planting date caused different responses in different crops. Maize and soybean had opposite reactions: when low temperature threshold resulted in early planting, maize responded with a loss of yield, but soybean yields increased. Our improvements in CLM demonstrate a new capability in the model - simulating agriculture in a realistic way, complete with fertilizer and residue management

  2. Influence of satellite-derived photolysis rates and NOx emissions on Texas ozone modeling

    NASA Astrophysics Data System (ADS)

    Tang, W.; Cohan, D. S.; Pour-Biazar, A.; Lamsal, L. N.; White, A. T.; Xiao, X.; Zhou, W.; Henderson, B. H.; Lash, B. F.

    2015-02-01

    Uncertain photolysis rates and emission inventory impair the accuracy of state-level ozone (O3) regulatory modeling. Past studies have separately used satellite-observed clouds to correct the model-predicted photolysis rates, or satellite-constrained top-down NOx emissions to identify and reduce uncertainties in bottom-up NOx emissions. However, the joint application of multiple satellite-derived model inputs to improve O3 state implementation plan (SIP) modeling has rarely been explored. In this study, Geostationary Operational Environmental Satellite (GOES) observations of clouds are applied to derive the photolysis rates, replacing those used in Texas SIP modeling. This changes modeled O3 concentrations by up to 80 ppb and improves O3 simulations by reducing modeled normalized mean bias (NMB) and normalized mean error (NME) by up to 0.1. A sector-based discrete Kalman filter (DKF) inversion approach is incorporated with the Comprehensive Air Quality Model with extensions (CAMx)-decoupled direct method (DDM) model to adjust Texas NOx emissions using a high-resolution Ozone Monitoring Instrument (OMI) NO2 product. The discrepancy between OMI and CAMx NO2 vertical column densities (VCDs) is further reduced by increasing modeled NOx lifetime and adding an artificial amount of NO2 in the upper troposphere. The region-based DKF inversion suggests increasing NOx emissions by 10-50% in most regions, deteriorating the model performance in predicting ground NO2 and O3, while the sector-based DKF inversion tends to scale down area and nonroad NOx emissions by 50%, leading to a 2-5 ppb decrease in ground 8 h O3 predictions. Model performance in simulating ground NO2 and O3 are improved using sector-based inversion-constrained NOx emissions, with 0.25 and 0.04 reductions in NMBs and 0.13 and 0.04 reductions in NMEs, respectively. Using both GOES-derived photolysis rates and OMI-constrained NOx emissions together reduces modeled NMB and NME by 0.05, increases the model

  3. Pediatric Computational Models

    NASA Astrophysics Data System (ADS)

    Soni, Bharat K.; Kim, Jong-Eun; Ito, Yasushi; Wagner, Christina D.; Yang, King-Hay

    A computational model is a computer program that attempts to simulate a behavior of a complex system by solving mathematical equations associated with principles and laws of physics. Computational models can be used to predict the body's response to injury-producing conditions that cannot be simulated experimentally or measured in surrogate/animal experiments. Computational modeling also provides means by which valid experimental animal and cadaveric data can be extrapolated to a living person. Widely used computational models for injury biomechanics include multibody dynamics and finite element (FE) models. Both multibody and FE methods have been used extensively to study adult impact biomechanics in the past couple of decades.

  4. UZ Colloid Transport Model

    SciTech Connect

    M. McGraw

    2000-04-13

    The UZ Colloid Transport model development plan states that the objective of this Analysis/Model Report (AMR) is to document the development of a model for simulating unsaturated colloid transport. This objective includes the following: (1) use of a process level model to evaluate the potential mechanisms for colloid transport at Yucca Mountain; (2) Provide ranges of parameters for significant colloid transport processes to Performance Assessment (PA) for the unsaturated zone (UZ); (3) Provide a basis for development of an abstracted model for use in PA calculations.

  5. Pilot model hypothesis testing

    NASA Technical Reports Server (NTRS)

    Broussard, J. R.; Berry, P. W.

    1982-01-01

    The aircraft control time history predicted by the optimal control pilot model and actual pilot tracking data obtained from NASA Langley's differential maneuvering simulator (DMS) are analyzed. The analysis is performed using a hypothesis testing scheme modified to allow for changes in the true hypothesis. A finite number of pilot models, each with different hypothesized internal model representations of the aircraft dynamics, are constructed. The hypothesis testing scheme determines the relative probability that each pilot model best matches the DMS data. By observing the changes in probabilities, it is possible to determine when the pilot changes control strategy and which hypothesized pilot model best represent's the pilot's control behavior.

  6. Models of Goldstone gauginos

    NASA Astrophysics Data System (ADS)

    Alves, Daniele S. M.; Galloway, Jamison; McCullough, Matthew; Weiner, Neal

    2016-04-01

    Models with Dirac gauginos are appealing scenarios for physics beyond the Standard Model. They have smaller radiative corrections to scalar soft masses, a suppression of certain supersymmetry (SUSY) production processes at the LHC, and ameliorated flavor constraints. Unfortunately, they are generically plagued by tachyons charged under the Standard Model, and attempts to eliminate such states typically spoil the positive features. The recently proposed "Goldstone gaugino" mechanism provides a simple realization of Dirac gauginos that is automatically free of dangerous tachyonic states. We provide details on this mechanism and explore models for its origin. In particular, we find SUSY QCD models that realize this idea simply and discuss scenarios for unification.

  7. The FREZCHEM Model

    NASA Astrophysics Data System (ADS)

    Marion, Giles M.; Kargel, Jeffrey S.

    Implementation of the Pitzer approach is through the FREZCHEM (FREEZING CHEMISTRY) model, which is at the core of this work. This model was originally designed to simulate salt chemistries and freezing processes at low temperatures (-54 to 25°C) and 1 atm pressure. Over the years, this model has been broadened to include more chemistries (from 16 to 58 solid phases), a broader temperature range for some chemistries (to 113°C), and incorporation of a pressure dependence (1 to 1000 bars) into the model. Implementation, parameterization, validation, and limitations of the FREZCHEM model are extensively discussed in Chapter 3.

  8. Surrogate waveform models

    NASA Astrophysics Data System (ADS)

    Blackman, Jonathan; Field, Scott; Galley, Chad; Scheel, Mark; Szilagyi, Bela; Tiglio, Manuel

    2015-04-01

    With the advanced detector era just around the corner, there is a strong need for fast and accurate models of gravitational waveforms from compact binary coalescence. Fast surrogate models can be built out of an accurate but slow waveform model with minimal to no loss in accuracy, but may require a large number of evaluations of the underlying model. This may be prohibitively expensive if the underlying is extremely slow, for example if we wish to build a surrogate for numerical relativity. We examine alternate choices to building surrogate models which allow for a more sparse set of input waveforms. Research supported in part by NSERC.

  9. CRAC2 model description

    SciTech Connect

    Ritchie, L.T.; Alpert, D.J.; Burke, R.P.; Johnson, J.D.; Ostmeyer, R.M.; Aldrich, D.C.; Blond, R.M.

    1984-03-01

    The CRAC2 computer code is a revised version of CRAC (Calculation of Reactor Accident Consequences) which was developed for the Reactor Safety Study. This document provides an overview of the CRAC2 code and a description of each of the models used. Significant improvements incorporated into CRAC2 include an improved weather sequence sampling technique, a new evacuation model, and new output capabilities. In addition, refinements have been made to the atmospheric transport and deposition model. Details of the modeling differences between CRAC2 and CRAC are emphasized in the model descriptions.

  10. Adaptive background model

    NASA Astrophysics Data System (ADS)

    Lu, Xiaochun; Xiao, Yijun; Chai, Zhi; Wang, Bangping

    2007-11-01

    An adaptive background model aiming at outdoor vehicle detection is presented in this paper. This model is an improved model of PICA (pixel intensity classification algorithm), it classifies pixels into K-distributions by color similarity, and then a hypothesis that the background pixel color appears in image sequence with a high frequency is used to evaluate all the distributions to determine which presents the current background color. As experiments show, the model presented in this paper is a robust, adaptive and flexible model, which can deal with situations like camera motions, lighting changes and so on.

  11. Complex matrix model duality

    SciTech Connect

    Brown, T. W.

    2011-04-15

    The same complex matrix model calculates both tachyon scattering for the c=1 noncritical string at the self-dual radius and certain correlation functions of operators which preserve half the supersymmetry in N=4 super-Yang-Mills theory. It is dual to another complex matrix model where the couplings of the first model are encoded in the Kontsevich-like variables of the second. The duality between the theories is mirrored by the duality of their Feynman diagrams. Analogously to the Hermitian Kontsevich-Penner model, the correlation functions of the second model can be written as sums over discrete points in subspaces of the moduli space of punctured Riemann surfaces.

  12. How the Whole School, Whole Community, Whole Child Model Works: Creating Greater Alignment, Integration, and Collaboration Between Health and Education

    PubMed Central

    Chiang, Rachelle Johnsson; Meagher, Whitney; Slade, Sean

    2015-01-01

    BACKGROUND The Whole School, Whole Community, Whole Child (WSCC) model calls for greater collaboration across the community, school, and health sectors to meet the needs and support the full potential of each child. This article reports on how 3 states and 2 local school districts have implemented aspects of the WSCC model through collaboration, leadership and policy creation, alignment, and implementation. METHODS We searched state health and education department websites, local school district websites, state legislative databases, and sources of peer-reviewed and gray literature to identify materials demonstrating adoption and implementation of coordinated school health, the WSCC model, and associated policies and practices in identified states and districts. We conducted informal interviews in each state and district to reinforce the document review. RESULTS States and local school districts have been able to strategically increase collaboration, integration, and alignment of health and education through the adoption and implementation of policy and practice supporting the WSCC model. Successful utilization of the WSCC model has led to substantial positive changes in school health environments, policies, and practices. CONCLUSIONS Collaboration among health and education sectors to integrate and align services may lead to improved efficiencies and better health and education outcomes for students. PMID:26440819

  13. Modelling Farm Animal Welfare

    PubMed Central

    Collins, Lisa M.; Part, Chérie E.

    2013-01-01

    Simple Summary In this review paper we discuss the different modeling techniques that have been used in animal welfare research to date. We look at what questions they have been used to answer, the advantages and pitfalls of the methods, and how future research can best use these approaches to answer some of the most important upcoming questions in farm animal welfare. Abstract The use of models in the life sciences has greatly expanded in scope and advanced in technique in recent decades. However, the range, type and complexity of models used in farm animal welfare is comparatively poor, despite the great scope for use of modeling in this field of research. In this paper, we review the different modeling approaches used in farm animal welfare science to date, discussing the types of questions they have been used to answer, the merits and problems associated with the method, and possible future applications of each technique. We find that the most frequently published types of model used in farm animal welfare are conceptual and assessment models; two types of model that are frequently (though not exclusively) based on expert opinion. Simulation, optimization, scenario, and systems modeling approaches are rarer in animal welfare, despite being commonly used in other related fields. Finally, common issues such as a lack of quantitative data to parameterize models, and model selection and validation are discussed throughout the review, with possible solutions and alternative approaches suggested. PMID:26487411

  14. TEAMS Model Analyzer

    NASA Technical Reports Server (NTRS)

    Tijidjian, Raffi P.

    2010-01-01

    The TEAMS model analyzer is a supporting tool developed to work with models created with TEAMS (Testability, Engineering, and Maintenance System), which was developed by QSI. In an effort to reduce the time spent in the manual process that each TEAMS modeler must perform in the preparation of reporting for model reviews, a new tool has been developed as an aid to models developed in TEAMS. The software allows for the viewing, reporting, and checking of TEAMS models that are checked into the TEAMS model database. The software allows the user to selectively model in a hierarchical tree outline view that displays the components, failure modes, and ports. The reporting features allow the user to quickly gather statistics about the model, and generate an input/output report pertaining to all of the components. Rules can be automatically validated against the model, with a report generated containing resulting inconsistencies. In addition to reducing manual effort, this software also provides an automated process framework for the Verification and Validation (V&V) effort that will follow development of these models. The aid of such an automated tool would have a significant impact on the V&V process.

  15. Animal models of atherosclerosis

    PubMed Central

    Kapourchali, Fatemeh Ramezani; Surendiran, Gangadaran; Chen, Li; Uitz, Elisabeth; Bahadori, Babak; Moghadasian, Mohammed H

    2014-01-01

    In this mini-review several commonly used animal models of atherosclerosis have been discussed. Among them, emphasis has been made on mice, rabbits, pigs and non-human primates. Although these animal models have played a significant role in our understanding of induction of atherosclerotic lesions, we still lack a reliable animal model for regression of the disease. Researchers have reported several genetically modified and transgenic animal models that replicate human atherosclerosis, however each of current animal models have some limitations. Among these animal models, the apolipoprotein (apo) E-knockout (KO) mice have been used extensively because they develop spontaneous atherosclerosis. Furthermore, atherosclerotic lesions developed in this model depending on experimental design may resemble humans’ stable and unstable atherosclerotic lesions. This mouse model of hypercholesterolemia and atherosclerosis has been also used to investigate the impact of oxidative stress and inflammation on atherogenesis. Low density lipoprotein (LDL)-r-KO mice are a model of human familial hypercholesterolemia. However, unlike apo E-KO mice, the LDL-r-KO mice do not develop spontaneous atherosclerosis. Both apo E-KO and LDL-r-KO mice have been employed to generate other relevant mouse models of cardiovascular disease through breeding strategies. In addition to mice, rabbits have been used extensively particularly to understand the mechanisms of cholesterol-induced atherosclerosis. The present review paper details the characteristics of animal models that are used in atherosclerosis research. PMID:24868511

  16. Calibrated Properties Model

    SciTech Connect

    T. Ghezzehej

    2004-10-04

    The purpose of this model report is to document the calibrated properties model that provides calibrated property sets for unsaturated zone (UZ) flow and transport process models (UZ models). The calibration of the property sets is performed through inverse modeling. This work followed, and was planned in, ''Technical Work Plan (TWP) for: Unsaturated Zone Flow Analysis and Model Report Integration'' (BSC 2004 [DIRS 169654], Sections 1.2.6 and 2.1.1.6). Direct inputs to this model report were derived from the following upstream analysis and model reports: ''Analysis of Hydrologic Properties Data'' (BSC 2004 [DIRS 170038]); ''Development of Numerical Grids for UZ Flow and Transport Modeling'' (BSC 2004 [DIRS 169855]); ''Simulation of Net Infiltration for Present-Day and Potential Future Climates'' (BSC 2004 [DIRS 170007]); ''Geologic Framework Model'' (GFM2000) (BSC 2004 [DIRS 170029]). Additionally, this model report incorporates errata of the previous version and closure of the Key Technical Issue agreement TSPAI 3.26 (Section 6.2.2 and Appendix B), and it is revised for improved transparency.

  17. A model of strength

    USGS Publications Warehouse

    Johnson, Douglas H.; Cook, R.D.

    2013-01-01

    In her AAAS News & Notes piece "Can the Southwest manage its thirst?" (26 July, p. 362), K. Wren quotes Ajay Kalra, who advocates a particular method for predicting Colorado River streamflow "because it eschews complex physical climate models for a statistical data-driven modeling approach." A preference for data-driven models may be appropriate in this individual situation, but it is not so generally, Data-driven models often come with a warning against extrapolating beyond the range of the data used to develop the models. When the future is like the past, data-driven models can work well for prediction, but it is easy to over-model local or transient phenomena, often leading to predictive inaccuracy (1). Mechanistic models are built on established knowledge of the process that connects the response variables with the predictors, using information obtained outside of an extant data set. One may shy away from a mechanistic approach when the underlying process is judged to be too complicated, but good predictive models can be constructed with statistical components that account for ingredients missing in the mechanistic analysis. Models with sound mechanistic components are more generally applicable and robust than data-driven models.

  18. Titan atmospheric models intercomparison

    NASA Astrophysics Data System (ADS)

    Pernot, P.

    2008-09-01

    Several groups over the world have developed independently models of the photochemistry of Titan. The Cassini mission reveals daily that the chemical complexity is beyond our expectations e. g. observation of heavy positive and negative ions..., and the models are updated accordingly. At this stage, there is no consensus on the various input parameters, and it becomes increasingly difficult to compare outputs form different models. An ISSI team of experts of those models will be gathered shortly to proceed to an intercomparison, i.e. to assess how the models behave, given identical sets of inputs (collectively defined). Expected discrepancies will have to be elucidated and reduced. This intercomparison will also be an occasion to estimate explicitly the importance of various physicalchemical processes on model predictions versus observations. More robust and validated models are expected from this study for the interpretation of Titanrelated data.

  19. Multiscale Modeling of Recrystallization

    SciTech Connect

    Godfrey, A.W.; Holm, E.A.; Hughes, D.A.; Lesar, R.; Miodownik, M.A.

    1998-12-07

    We propose a multi length scale approach to modeling recrystallization which links a dislocation model, a cell growth model and a macroscopic model. Although this methodology and linking framework will be applied to recrystallization, it is also applicable to other types of phase transformations in bulk and layered materials. Critical processes such as the dislocation structure evolution, nucleation, the evolution of crystal orientations into a preferred texture, and grain size evolution all operate at different length scales. In this paper we focus on incorporating experimental measurements of dislocation substructures, rnisorientation measurements of dislocation boundaries, and dislocation simulations into a mesoscopic model of cell growth. In particular, we show how feeding information from the dislocation model into the cell growth model can create realistic initial microstructure.

  20. Toward Scientific Numerical Modeling

    NASA Technical Reports Server (NTRS)

    Kleb, Bil

    2007-01-01

    Ultimately, scientific numerical models need quantified output uncertainties so that modeling can evolve to better match reality. Documenting model input uncertainties and verifying that numerical models are translated into code correctly, however, are necessary first steps toward that goal. Without known input parameter uncertainties, model sensitivities are all one can determine, and without code verification, output uncertainties are simply not reliable. To address these two shortcomings, two proposals are offered: (1) an unobtrusive mechanism to document input parameter uncertainties in situ and (2) an adaptation of the Scientific Method to numerical model development and deployment. Because these two steps require changes in the computational simulation community to bear fruit, they are presented in terms of the Beckhard-Harris-Gleicher change model.

  1. Foam process models.

    SciTech Connect

    Moffat, Harry K.; Noble, David R.; Baer, Thomas A.; Adolf, Douglas Brian; Rao, Rekha Ranjana; Mondy, Lisa Ann

    2008-09-01

    In this report, we summarize our work on developing a production level foam processing computational model suitable for predicting the self-expansion of foam in complex geometries. The model is based on a finite element representation of the equations of motion, with the movement of the free surface represented using the level set method, and has been implemented in SIERRA/ARIA. An empirically based time- and temperature-dependent density model is used to encapsulate the complex physics of foam nucleation and growth in a numerically tractable model. The change in density with time is at the heart of the foam self-expansion as it creates the motion of the foam. This continuum-level model uses an homogenized description of foam, which does not include the gas explicitly. Results from the model are compared to temperature-instrumented flow visualization experiments giving the location of the foam front as a function of time for our EFAR model system.

  2. Minimal quiver standard model

    SciTech Connect

    Berenstein, David; Pinansky, Samuel

    2007-05-01

    This paper discusses the minimal quiver gauge theory embedding of the standard model that could arise from brane world type string theory constructions. It is based on the low energy effective field theory of D branes in the perturbative regime. The model differs from the standard model by the addition of one extra massive gauge boson, and contains only one additional parameter to the standard model: the mass of this new particle. The coupling of this new particle to the standard model is uniquely determined by input from the standard model and consistency conditions of perturbative string theory. We also study some aspects of the phenomenology of this model and bounds on its possible observation at the Large Hadron Collider.

  3. Modelling structured data with Probabilistic Graphical Models

    NASA Astrophysics Data System (ADS)

    Forbes, F.

    2016-05-01

    Most clustering and classification methods are based on the assumption that the objects to be clustered are independent. However, in more and more modern applications, data are structured in a way that makes this assumption not realistic and potentially misleading. A typical example that can be viewed as a clustering task is image segmentation where the objects are the pixels on a regular grid and depend on neighbouring pixels on this grid. Also, when data are geographically located, it is of interest to cluster data with an underlying dependence structure accounting for some spatial localisation. These spatial interactions can be naturally encoded via a graph not necessarily regular as a grid. Data sets can then be modelled via Markov random fields and mixture models (e.g. the so-called MRF and Hidden MRF). More generally, probabilistic graphical models are tools that can be used to represent and manipulate data in a structured way while modeling uncertainty. This chapter introduces the basic concepts. The two main classes of probabilistic graphical models are considered: Bayesian networks and Markov networks. The key concept of conditional independence and its link to Markov properties is presented. The main problems that can be solved with such tools are described. Some illustrations are given associated with some practical work.

  4. Ventilation Model Report

    SciTech Connect

    V. Chipman; J. Case

    2002-12-20

    The purpose of the Ventilation Model is to simulate the heat transfer processes in and around waste emplacement drifts during periods of forced ventilation. The model evaluates the effects of emplacement drift ventilation on the thermal conditions in the emplacement drifts and surrounding rock mass, and calculates the heat removal by ventilation as a measure of the viability of ventilation to delay the onset of peak repository temperature and reduce its magnitude. The heat removal by ventilation is temporally and spatially dependent, and is expressed as the fraction of heat carried away by the ventilation air compared to the fraction of heat produced by radionuclide decay. One minus the heat removal is called the wall heat fraction, or the remaining amount of heat that is transferred via conduction to the surrounding rock mass. Downstream models, such as the ''Multiscale Thermohydrologic Model'' (BSC 2001), use the wall heat fractions as outputted from the Ventilation Model to initialize their post-closure analyses. The Ventilation Model report was initially developed to analyze the effects of preclosure continuous ventilation in the Engineered Barrier System (EBS) emplacement drifts, and to provide heat removal data to support EBS design. Revision 00 of the Ventilation Model included documentation of the modeling results from the ANSYS-based heat transfer model. Revision 01 ICN 01 included the results of the unqualified software code MULTIFLUX to assess the influence of moisture on the ventilation efficiency. The purposes of Revision 02 of the Ventilation Model are: (1) To validate the conceptual model for preclosure ventilation of emplacement drifts and verify its numerical application in accordance with new procedural requirements as outlined in AP-SIII-10Q, Models (Section 7.0). (2) To satisfy technical issues posed in KTI agreement RDTME 3.14 (Reamer and Williams 2001a). Specifically to demonstrate, with respect to the ANSYS ventilation model, the adequacy of

  5. Thermal phase transitions in a honeycomb lattice gas with three-body interactions.

    PubMed

    Lohöfer, Maximilian; Bonnes, Lars; Wessel, Stefan

    2013-11-01

    We study the thermal phase transitions in a classical (hard-core) lattice gas model with nearest-neighbor three-body interactions on the honeycomb lattice, based on parallel tempering Monte Carlo simulations. This system realizes incompressible low-temperature phases at fractional fillings of 9/16, 5/8, and 3/4 that were identified in a previous study of a related quantum model. In particular, both the 9/16 and the 5/8 phase exhibit an extensive ground-state degeneracy reflecting the frustrated nature of the three-body interactions on the honeycomb lattice. The thermal melting of the 9/16 phase is found to be a first-order, discontinuous phase transition. On the other hand, from the thermodynamic behavior we obtain indications for a four-states Potts-model thermal transition out of the 5/8 phase. We find that this thermal Potts-model transition relates to the selection of one out of four extensive sectors within the low-energy manifold of the 5/8 phase, which we obtain via an exact mapping of the ground-state manifold to a hard-core dimer model on an embedded honeycomb superlattice. PMID:24329242

  6. Integrated modeling, data transfers, and physical models

    NASA Astrophysics Data System (ADS)

    Brookshire, D. S.; Chermak, J. M.

    2003-04-01

    Difficulties in developing precise economic policy models for water reallocation and re-regulation in various regional and transboundary settings has been exacerbated not only by climate issues but also by institutional changes reflected in the promulgation of environmental laws, changing regional populations, and an increased focus on water quality standards. As complexity of the water issues have increased, model development at a micro-policy level is necessary to capture difficult institutional nuances and represent the differing national, regional and stakeholders' viewpoints. More often than not, adequate "local" or specific micro-data are not available in all settings for modeling and policy decisions. Economic policy analysis increasingly deals with this problem through data transfers (transferring results from one study area to another) and significant progress has been made in understanding the issue of the dimensionality of data transfers. This paper explores the conceptual and empirical dimensions of data transfers in the context of integrated modeling when the transfers are not only from the behavioral, but also from the hard sciences. We begin by exploring the domain of transfer issues associated with policy analyses that directly consider uncertainty in both the behavioral and physical science settings. We then, through a stylized, hybrid, economic-engineering model of water supply and demand in the Middle Rio Grand Valley of New Mexico (USA) analyze the impacts of; (1) the relative uncertainty of data transfers methods, (2) the uncertainty of climate data and, (3) the uncertainly of population growth. These efforts are motivated by the need to address the relative importance of more accurate data both from the physical sciences as well as from demography and economics for policy analyses. We evaluate the impacts by empirically addressing (within the Middle Rio Grand model): (1) How much does the surrounding uncertainty of the benefit transfer

  7. Phyloclimatic modeling: combining phylogenetics and bioclimatic modeling.

    PubMed

    Yesson, C; Culham, A

    2006-10-01

    We investigate the impact of past climates on plant diversification by tracking the "footprint" of climate change on a phylogenetic tree. Diversity within the cosmopolitan carnivorous plant genus Drosera (Droseraceae) is focused within Mediterranean climate regions. We explore whether this diversity is temporally linked to Mediterranean-type climatic shifts of the mid-Miocene and whether climate preferences are conservative over phylogenetic timescales. Phyloclimatic modeling combines environmental niche (bioclimatic) modeling with phylogenetics in order to study evolutionary patterns in relation to climate change. We present the largest and most complete such example to date using Drosera. The bioclimatic models of extant species demonstrate clear phylogenetic patterns; this is particularly evident for the tuberous sundews from southwestern Australia (subgenus Ergaleium). We employ a method for establishing confidence intervals of node ages on a phylogeny using replicates from a Bayesian phylogenetic analysis. This chronogram shows that many clades, including subgenus Ergaleium and section Bryastrum, diversified during the establishment of the Mediterranean-type climate. Ancestral reconstructions of bioclimatic models demonstrate a pattern of preference for this climate type within these groups. Ancestral bioclimatic models are projected into palaeo-climate reconstructions for the time periods indicated by the chronogram. We present two such examples that each generate plausible estimates of ancestral lineage distribution, which are similar to their current distributions. This is the first study to attempt bioclimatic projections on evolutionary time scales. The sundews appear to have diversified in response to local climate development. Some groups are specialized for Mediterranean climates, others show wide-ranging generalism. This demonstrates that Phyloclimatic modeling could be repeated for other plant groups and is fundamental to the understanding of

  8. Modeling agriculture in the Community Land Model

    NASA Astrophysics Data System (ADS)

    Drewniak, B.; Song, J.; Prell, J.; Kotamarthi, V. R.; Jacob, R.

    2012-12-01

    The potential impact of climate change on agriculture is uncertain. In addition, agriculture could influence above- and below-ground carbon storage. Development of models that represent agriculture is necessary to address these impacts. We have developed an approach to integrate agriculture representations for three crop types - maize, soybean, and spring wheat - into the coupled carbon-nitrogen version of the Community Land Model (CLM), to help address these questions. Here we present the new model, CLM-Crop, validated against observations from two AmeriFlux sites in the United States, planted with maize and soybean. Seasonal carbon fluxes compared well with field measurements. CLM-Crop yields were comparable with observations in some regions, although the generality of the crop model and its lack of technology and irrigation made direct comparison difficult. CLM-Crop was compared against the standard CLM3.5, which simulates crops as grass. The comparison showed improvement in gross primary productivity in regions where crops are the dominant vegetation cover. Crop yields and productivity were negatively correlated with temperature and positively correlated with precipitation. In case studies with the new crop model looking at impacts of residue management and planting date on crop yield, we found that increased residue returned to the litter pool increased crop yield, while reduced residue returns resulted in yield decreases. Using climate controls to signal planting date caused different responses in different crops. Maize and soybean had opposite reactions: when low temperature threshold resulted in early planting, maize responded with a loss of yield, but soybean yields increased. Our improvements in CLM demonstrate a new capability in the model - simulating agriculture in a realistic way, complete with fertilizer and residue management practices. Results are encouraging, with improved representation of human influences on the land surface and the potentially

  9. Loehlin's original models and model contributions.

    PubMed

    McArdle, John J

    2014-11-01

    This is a short story about John C. Loehlin who is now at the University of Texas at Austin, dealing with his original simulation models and developments, which led to his current latent variable models. This talk was initially presented at a special meeting for John before the BGA in Rhode Island, and I was very pleased to contribute. It probably goes without saying, but John helped create this important society, has been a key contributor to this journal for several decades, and he deserves a lot for this leadership. PMID:25367673

  10. Modeling local dependence in longitudinal IRT models.

    PubMed

    Olsbjerg, Maja; Christensen, Karl Bang

    2015-12-01

    Measuring change in a latent variable over time is often done using the same instrument at several time points. This can lead to dependence between responses across time points for the same person yielding within person correlations that are stronger than what can be attributed to the latent variable. Ignoring this can lead to biased estimates of changes in the latent variable. In this paper we propose a method for modeling local dependence in the longitudinal 2PL model. It is based on the concept of item splitting, and makes it possible to correctly estimate change in the latent variable. PMID:25552424

  11. Constitutive models in LAME.

    SciTech Connect

    Hammerand, Daniel Carl; Scherzinger, William Mark

    2007-09-01

    The Library of Advanced Materials for Engineering (LAME) provides a common repository for constitutive models that can be used in computational solid mechanics codes. A number of models including both hypoelastic (rate) and hyperelastic (total strain) constitutive forms have been implemented in LAME. The structure and testing of LAME is described in Scherzinger and Hammerand ([3] and [4]). The purpose of the present report is to describe the material models which have already been implemented into LAME. The descriptions are designed to give useful information to both analysts and code developers. Thus far, 33 non-ITAR/non-CRADA protected material models have been incorporated. These include everything from the simple isotropic linear elastic models to a number of elastic-plastic models for metals to models for honeycomb, foams, potting epoxies and rubber. A complete description of each model is outside the scope of the current report. Rather, the aim here is to delineate the properties, state variables, functions, and methods for each model. However, a brief description of some of the constitutive details is provided for a number of the material models. Where appropriate, the SAND reports available for each model have been cited. Many models have state variable aliases for some or all of their state variables. These alias names can be used for outputting desired quantities. The state variable aliases available for results output have been listed in this report. However, not all models use these aliases. For those models, no state variable names are listed. Nevertheless, the number of state variables employed by each model is always given. Currently, there are four possible functions for a material model. This report lists which of these four methods are employed in each material model. As far as analysts are concerned, this information is included only for the awareness purposes. The analyst can take confidence in the fact that model has been properly implemented

  12. A reductionist mechanistic model for bioconcentration of neutral and weakly polar organic compounds in fish.

    PubMed

    Kuo, Dave T F; Di Toro, Dominic M

    2013-09-01

    The bioconcentration factor (BCF) of neutral and weakly polar organic chemicals in fish is modeled using independently calibrated models of chemical partitioning (freely dissolved fraction of chemical in the aqueous phase [φsys ] and wet-weight fish-water partition coefficient [KFW ]), respiratory exchange (respiratory update rate constant [k1 ], and respiratory elimination rate constant [k2  = k1 /KFW ]), and biotransformation (whole-body biotransformation rate constant [kM ]) as BCF = φsys KFW /(1 + kM /k2 ). Existing k1 models tend to overestimate for chemicals with log KOW  < 3.5, which constituted 30% to 50% of the examined chemicals. A revised k1 model covering a wider log KOW range (0-8.5) is presented k1  = (5.46 × 10(-6) MW + 0.261/KOW )(-1) , where MW is the molecular weight. The biotransformation rate constant kM is modeled using biota internal partitioning and Abraham parameters as reactivity descriptors. The reductionist model was tested using 3 different BCF data sets (US Environmental Protection Agency's Estimation Programs Interface [EPI], n = 548; Hertfordshire, n = 210; Arnot-Gobas, n = 1855) and compared with the following 3 state-of-the-art models: 1) the EPI Suite BCFBAF module, 2) the European Commision's Computer Assisted Evaluation of industrial chemical Substances According to Regulations (CAESAR), and 3) the EPI/Arnot mechanistic kinetic model. The reductionist model performed comparably with the alternative models (root mean square errors [RMSEs] = 0.72-0.77), with only 5 fitting parameters and no training against experimental BCFs. Respiratory elimination and biotransformation dominate the total depuration (i.e., [k2  + kM ]/kT  ≥ 0.8) for approximately 98% of the data entries, thus validating the reductionist approximation. Mechanistic models provide greater insights into bioaccumulation and are more sensitive to biological variation. All three BCF data sets and relevant

  13. Influence of satellite-derived photolysis rates and NOx emissions on Texas ozone modeling

    NASA Astrophysics Data System (ADS)

    Tang, W.; Cohan, D. S.; Pour-Biazar, A.; Lamsal, L. N.; White, A.; Xiao, X.; Zhou, W.; Henderson, B. H.; Lash, B.

    2014-09-01

    Uncertain photolysis rates and emission inventory impair the accuracy of state-level ozone (O3) regulatory modeling. Past studies have separately used satellite-observed clouds to correct the model-predicted photolysis rates, or satellite-constrained top-down NOx emissions to identify and reduce uncertainties in bottom-up NOx emissions. However, the joint application of multiple satellite-derived model inputs to improve O3 State Implementation Plan (SIP) modeling has rarely been explored. In this study, Geostationary Operational Environmental Satellite (GOES) observations of clouds are applied to derive the photolysis rates, replacing those used in Texas SIP modeling. This changes modeled O3 concentrations by up to 80 ppb and improves O3 simulations by reducing modeled normalized mean bias (NMB) and normalized mean error (NME) by up to 0.1. A sector-based discrete Kalman filter (DKF) inversion approach is incorporated with the Comprehensive Air Quality Model with extensions (CAMx)-Decoupled Direct Method (DDM) model to adjust Texas NOx emissions using a high resolution Ozone Monitoring Instrument (OMI) NO2 product. The discrepancy between OMI and CAMx NO2 vertical column densities (VCD) is further reduced by increasing modeled NOx lifetime and adding an artificial amount of NO2 in the upper troposphere. The sector-based DKF inversion tends to scale down area and non-road NOx emissions by 50%, leading to a 2-5 ppb decrease in ground 8 h O3 predictions. Model performance in simulating ground NO2 and O3 are improved using inverted NOx emissions, with 0.25 and 0.04 reductions in NMBs and 0.13 and 0.04 reductions in NMEs, respectively. Using both GOES-derived photolysis rates and OMI-constrained NOx emissions together reduces modeled NMB and NME by 0.05 and increases the model correlation with ground measurement in O3 simulations and makes O3 more sensitive to NOx emissions in the O3 non-attainment areas.

  14. Quantitative Rheological Model Selection

    NASA Astrophysics Data System (ADS)

    Freund, Jonathan; Ewoldt, Randy

    2014-11-01

    The more parameters in a rheological the better it will reproduce available data, though this does not mean that it is necessarily a better justified model. Good fits are only part of model selection. We employ a Bayesian inference approach that quantifies model suitability by balancing closeness to data against both the number of model parameters and their a priori uncertainty. The penalty depends upon prior-to-calibration expectation of the viable range of values that model parameters might take, which we discuss as an essential aspect of the selection criterion. Models that are physically grounded are usually accompanied by tighter physical constraints on their respective parameters. The analysis reflects a basic principle: models grounded in physics can be expected to enjoy greater generality and perform better away from where they are calibrated. In contrast, purely empirical models can provide comparable fits, but the model selection framework penalizes their a priori uncertainty. We demonstrate the approach by selecting the best-justified number of modes in a Multi-mode Maxwell description of PVA-Borax. We also quantify relative merits of the Maxwell model relative to powerlaw fits and purely empirical fits for PVA-Borax, a viscoelastic liquid, and gluten.

  15. Geochemical modeling: a review

    SciTech Connect

    Jenne, E.A.

    1981-06-01

    Two general families of geochemical models presently exist. The ion speciation-solubility group of geochemical models contain submodels to first calculate a distribution of aqueous species and to secondly test the hypothesis that the water is near equilibrium with particular solid phases. These models may or may not calculate the adsorption of dissolved constituents and simulate the dissolution and precipitation (mass transfer) of solid phases. Another family of geochemical models, the reaction path models, simulates the stepwise precipitation of solid phases as a result of reacting specified amounts of water and rock. Reaction path models first perform an aqueous speciation of the dissolved constituents of the water, test solubility hypotheses, then perform the reaction path modeling. Certain improvements in the present versions of these models would enhance their value and usefulness to applications in nuclear-waste isolation, etc. Mass-transfer calculations of limited extent are certainly within the capabilities of state-of-the-art models. However, the reaction path models require an expansion of their thermodynamic data bases and systematic validation before they are generally accepted.

  16. Differential Topic Models.

    PubMed

    Chen, Changyou; Buntine, Wray; Ding, Nan; Xie, Lexing; Du, Lan

    2015-02-01

    In applications we may want to compare different document collections: they could have shared content but also different and unique aspects in particular collections. This task has been called comparative text mining or cross-collection modeling. We present a differential topic model for this application that models both topic differences and similarities. For this we use hierarchical Bayesian nonparametric models. Moreover, we found it was important to properly model power-law phenomena in topic-word distributions and thus we used the full Pitman-Yor process rather than just a Dirichlet process. Furthermore, we propose the transformed Pitman-Yor process (TPYP) to incorporate prior knowledge such as vocabulary variations in different collections into the model. To deal with the non-conjugate issue between model prior and likelihood in the TPYP, we thus propose an efficient sampling algorithm using a data augmentation technique based on the multinomial theorem. Experimental results show the model discovers interesting aspects of different collections. We also show the proposed MCMC based algorithm achieves a dramatically reduced test perplexity compared to some existing topic models. Finally, we show our model outperforms the state-of-the-art for document classification/ideology prediction on a number of text collections. PMID:26353238

  17. The Earth System Model

    NASA Technical Reports Server (NTRS)

    Schoeberl, Mark; Rood, Richard B.; Hildebrand, Peter; Raymond, Carol

    2003-01-01

    The Earth System Model is the natural evolution of current climate models and will be the ultimate embodiment of our geophysical understanding of the planet. These models are constructed from components - atmosphere, ocean, ice, land, chemistry, solid earth, etc. models and merged together through a coupling program which is responsible for the exchange of data from the components. Climate models and future earth system models will have standardized modules, and these standards are now being developed by the ESMF project funded by NASA. The Earth System Model will have a variety of uses beyond climate prediction. The model can be used to build climate data records making it the core of an assimilation system, and it can be used in OSSE experiments to evaluate. The computing and storage requirements for the ESM appear to be daunting. However, the Japanese ES theoretical computing capability is already within 20% of the minimum requirements needed for some 2010 climate model applications. Thus it seems very possible that a focused effort to build an Earth System Model will achieve succcss.

  18. Kp forecast models

    NASA Astrophysics Data System (ADS)

    Meng, C.; Wing, S.; Johnson, J. R.; Jen, J.; Carr, S.; Sibeck, D. G.; Costello, K.; Freeman, J.; Balikhin, M.; Bechtold, K.; Vandegriff, J.

    2004-12-01

    Magnetically active times, e.g., Kp > 5, are notoriously difficult to predict, precisely when the predictions are crucial to the space weather users. Taking advantage of the routinely available solar wind measurements at Langrangian point (L1) and nowcast Kps, Kp forecast models based on neural networks were developed with the focus on improving the forecast for active times. In order to satisfy different needs and operational constraints, three models were developed: (1) model that inputs nowcast Kp, solar wind parameters, and predict Kp 1 hr ahead; (2) model with the same input as (1) and predict Kp 4 hr ahead; and (3) model that inputs only solar wind parameters and predict Kp 1 hr ahead (the exact prediction lead time depends on the solar wind speed and the location of the solar wind monitor). Extensive evaluations of these models and other major operational Kp forecast models show that while the new models can predict Kps more accurately for all activities, the most dramatic improvements occur for moderate and active times. The evaluations of the models over 2 solar cycles, 1975-2001, show that solar wind driven models predict Kp more accurately during solar maximum than solar minimum. This result, as well as information dynamics analysis of Kp, suggests that geospace is more dominated by internal dynamics during solar minimum than solar maximum, when it is more directly driven by external inputs, namely solar wind and IMF.

  19. Preliminary DIAL model

    SciTech Connect

    Gentry, S.; Taylor, J.; Stephenson, D.

    1994-06-01

    A unique end-to-end LIDAR sensor model has been developed supporting the concept development stage of the CALIOPE UV DIAL and UV laser-induced-fluorescence (LIF) efforts. The model focuses on preserving the temporal and spectral nature of signals as they pass through the atmosphere, are collected by the optics, detected by the sensor, and processed by the sensor electronics and algorithms. This is done by developing accurate component sub-models with realistic inputs and outputs, as well as internal noise sources and operating parameters. These sub-models are then configured using data-flow diagrams to operate together to reflect the performance of the entire DIAL system. This modeling philosophy allows the developer to have a realistic indication of the nature of signals throughout the system and to design components and processing in a realistic environment. Current component models include atmospheric absorption and scattering losses, plume absorption and scattering losses, background, telescope and optical filter models, PMT (photomultiplier tube) with realistic noise sources, amplifier operation and noise, A/D converter operation, noise and distortion, pulse averaging, and DIAL computation. Preliminary results of the model will be presented indicating the expected model operation depicting the October field test at the NTS spill test facility. Indications will be given concerning near-term upgrades to the model.

  20. Turbulence modeling and experiments

    NASA Technical Reports Server (NTRS)

    Shabbir, Aamir

    1992-01-01

    The best way of verifying turbulence is to do a direct comparison between the various terms and their models. The success of this approach depends upon the availability of the data for the exact correlations (both experimental and DNS). The other approach involves numerically solving the differential equations and then comparing the results with the data. The results of such a computation will depend upon the accuracy of all the modeled terms and constants. Because of this it is sometimes difficult to find the cause of a poor performance by a model. However, such a calculation is still meaningful in other ways as it shows how a complete Reynolds stress model performs. Thirteen homogeneous flows are numerically computed using the second order closure models. We concentrate only on those models which use a linear (or quasi-linear) model for the rapid term. This, therefore, includes the Launder, Reece and Rodi (LRR) model; the isotropization of production (IP) model; and the Speziale, Sarkar, and Gatski (SSG) model. Which of the three models performs better is examined along with what are their weaknesses, if any. The other work reported deal with the experimental balances of the second moment equations for a buoyant plume. Despite the tremendous amount of activity toward the second order closure modeling of turbulence, very little experimental information is available about the budgets of the second moment equations. Part of the problem stems from our inability to measure the pressure correlations. However, if everything else appearing in these equations is known from the experiment, pressure correlations can be obtained as the closing terms. This is the closest we can come to in obtaining these terms from experiment, and despite the measurement errors which might be present in such balances, the resulting information will be extremely useful for the turbulence modelers. The purpose of this part of the work was to provide such balances of the Reynolds stress and heat