A hybrid parallel framework for the cellular Potts model simulations
Energy Technology Data Exchange (ETDEWEB)
Jiang, Yi [Los Alamos National Laboratory; He, Kejing [SOUTH CHINA UNIV; Dong, Shoubin [SOUTH CHINA UNIV
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}).
Multiscale Model of Colorectal Cancer Using the Cellular Potts Framework
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
Reconstruction of symmetric Potts Models
Sly, Allan
2008-01-01
The reconstruction problem on the tree has been studied in numerous contexts including statistical physics, information theory and computational biology. However, rigorous reconstruction thresholds have only been established in a small number of models. We prove the first exact reconstruction threshold in a non-binary model establishing the Kesten-Stigum bound for the 3-state Potts model on regular trees of large degree. We further establish that the Kesten-Stigum bound is not tight for the $...
Nested sampling for Potts models
Murray, Iain; MacKay, David J. C.; Ghahramani, Zoubin; Skilling, John
2006-01-01
Nested sampling is a new Monte Carlo method by Skilling intended for general Bayesian computation. Nested sampling provides a robust alternative to annealing-based methods for computing normalizing constants. It can also generate estimates of other quantities such as posterior expectations. The key technical requirement is an ability to draw samples uniformly from the prior subject to a constraint on the likelihood. We provide a demonstration with the Potts model, an undirected graphical model.
BTF Potts compound texture model
Czech Academy of Sciences Publication Activity Database
Haindl, Michal; Remeš, Václav; Havlíček, Vojtěch
Bellingham: SPIE-IS&T, 2015, 939807-1-939807-11. (Proceedings of SPIE. 9398). ISBN 978-1-62841-488-2. ISSN 0277-786X. [Electronic Imaging 2015. San Francisco (US), 08.02.2015-12.02.2015] R&D Projects: GA ČR(CZ) GA14-10911S; GA ČR(CZ) GA14-02652S Keywords : Texture * texture synthesis * compound Markov random field model * CAR model * Potts MRF * Voronoi mosaic Subject RIV: BD - Theory of Information http://library.utia.cas.cz/separaty/21015/RO/haindl-0443580.pdf
Potts Compound Markovian Texture Model
Czech Academy of Sciences Publication Activity Database
Haindl, Michal; Remeš, Václav; Havlíček, Vojtěch
Piscataway : IEEE Press, 2012, s. 29-32. ISBN 978-1-4673-2216-4. [21st International Conference on Pattern Recognition (ICPR 2012). Tsukuba (JP), 11.11.2012-15.11.2012] R&D Projects: GA ČR GAP103/11/0335; GA ČR GA102/08/0593 Grant ostatní: CESNET(CZ) 409/2011 Institutional support: RVO:67985556 Keywords : texture * Markov random field Subject RIV: BD - Theory of Information http://library.utia.cas.cz/separaty/2012/RO/haindl-potts compound markov ian texture model.pdf
Dilute Potts model in two dimensions
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 q1 . The updates for q>1 use a number of operations per site independent of the system size.
Phase Transitions in Delaunay Potts Models
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.
Non compact continuum limit of two coupled Potts models
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 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.
High-temperature series expansions for random Potts models
Directory of Open Access Journals (Sweden)
M.Hellmund
2005-01-01
Full Text Available We discuss recently generated high-temperature series expansions for the free energy and the susceptibility of random-bond q-state Potts models on hypercubic lattices. Using the star-graph expansion technique, quenched disorder averages can be calculated exactly for arbitrary uncorrelated coupling distributions while keeping the disorder strength p as well as the dimension d as symbolic parameters. We present analyses of the new series for the susceptibility of the Ising (q=2 and 4-state Potts model in three dimensions up to the order 19 and 18, respectively, and compare our findings with results from field-theoretical renormalization group studies and Monte Carlo simulations.
The Many Faces of the Chiral Potts Model
Au-Yang, H; Au-Yang, Helen; Perk, Jacques H.H.
1996-01-01
In this talk, we give a brief overview of several aspects of the theory of the chiral Potts model, including higher-genus solutions of the star-triangle and tetrahedron equations, cyclic representations of affine quantum groups, basic hypergeometric functions at root of unity, and possible applications.
Phase transition in Potts model with invisible states
International Nuclear Information System (INIS)
We study phase transition in the ferromagnetic Potts model with invisible states that are added as redundant states by mean-field calculation and Monte Carlo simulation. Invisible states affect the entropy and free energy, although they do not contribute to the internal energy. A second-order phase transition takes place at finite temperature in the standard q-state ferromagnetic Potts model on two-dimensional lattice for q=2,3, and 4. However, our present model on two-dimensional lattice undergoes a first-order phase transition with spontaneous q-fold symmetry breaking (q=2,3, and 4) due to entropy effect of invisible states. The model is fundamental for the analysis of a first-order phase transition with spontaneous discrete symmetry breaking. (author)
Potts models with invisible states on general Bethe lattices
International Nuclear Information System (INIS)
The number of so-called invisible states which need to be added to the q-state Potts model to transmute its phase transition from continuous to first order has attracted recent attention. In the q = 2 case, a Bragg–Williams (mean-field) approach necessitates four such invisible states while a 3-regular random graph formalism requires seventeen. In both of these cases, the changeover from second- to first-order behaviour induced by the invisible states is identified through the tricritical point of an equivalent Blume–Emery–Griffiths model. Here we investigate the generalized Potts model on a Bethe lattice with z neighbours. We show that, in the q = 2 case, invisible states are required to manifest the equivalent Blume–Emery–Griffiths tricriticality. When z = 3, the 3-regular random graph result is recovered, while z → ∞ delivers the Bragg–Williams (mean-field) result. (paper)
Application of nested sampling in statistical physics: the Potts model
Pfeifenberger, Manuel J
2016-01-01
We present a systematic benchmark study of the nested sampling algorithm on the basis of the Potts model. This model exhibits a first order phase transition for $q>4$ at the critical temperature. The numerical evaluation of the partition function and thermodynamic observables, which involves high dimensional sums of sharply structured multi-modal density functions, represents a major challenge to most standard numerical techniques, such as Markov Chain Monte Carlo. Nested sampling, on the other hand, is particularly suited for such problems. In this paper we will employ both, nested sampling and thermodynamic integration to evaluate the partition function of the Potts model. In both cases individual moves are based on Swendsen-Wang updates. A autocorrelation time analysis of both algorithms shows that the severe slowing down of thermodynamic integration around the critical temperature does not occur in nested sampling. In addition we show, how thermodynamic variables can be computed with high accuracy from th...
Gibbs properties of the fuzzy Potts model on trees and in mean field
Haeggstroem, Olle; Kuelske, Christof
2003-01-01
We study Gibbs properties of the fuzzy Potts model in the mean field case (i.e on a complete graph) and on trees. For the mean field case, a complete characterization of the set of temperatures for which non-Gibbsianness happens is given. The results for trees are somewhat less explicit, but we do show for general trees that non-Gibbsianness of the fuzzy Potts model happens exactly for those temperatures where the underlying Potts model has multiple Gibbs measures.
Gibbs Properties of the Fuzzy Potts Model on Trees and in Mean Field
Häggström, O.; Külske, C.
2004-01-01
We study Gibbs properties of the fuzzy Potts model in the mean field case (i.e. on a complete graph) and on trees. For the mean field case, a complete characterization of the set of temperatures for which non-Gibbsianness happens is given. The results for trees are somewhat less explicit, but we do show for general trees that non-Gibbsianness of the fuzzy Potts model happens exactly for those temperatures where the underlying Potts model has multiple Gibbs measures.
Potts models with (17) invisible states on thin graphs
International Nuclear Information System (INIS)
The order of a phase transition is usually determined by the nature of the symmetry breaking at the phase transition point and the dimension of the model under consideration. For instance, q-state Potts models in two dimensions display a second order, continuous transition for q = 2, 3, 4 and first order for higher q. Tamura et al recently introduced Potts models with ‘invisible’ states which contribute to the entropy but not the internal energy and noted that adding such invisible states could transmute continuous transitions into first order transitions (Tamura et al 2010 Prog. Theor. Phys. 124 381; 2011 J. Phys: Conf. Ser. 297 012022; 2012 Interface Between Quantum Information and Statistical Physics; Tanaka and Tamura 2011 J. Phys.: Conf. Ser. 320 012025). This was observed both in a Bragg–Williams type mean-field calculation and 2D Monte-Carlo simulations. It was suggested that the invisible state mechanism for transmuting the order of a transition might play a role where transition orders inconsistent with the usual scheme had been observed. In this paper we note that an alternative mean-field approach employing 3-regular random (‘thin’) graphs also displays this change in the order of the transition as the number of invisible states is varied, although the number of states required to effect the transmutation, 17 invisible states when there are 2 visible states, is much higher than in the Bragg–Williams case. The calculation proceeds by using the equivalence of the Potts model with two visible and r invisible states to the Blume–Emery–Griffiths (BEG) model, so a by-product is the solution of the BEG model on thin random graphs. (paper)
Parallel family trees for transfer matrices in the Potts model
Navarro, Cristobal A; Kahler, Nancy Hitschfeld; Navarro, Gonzalo
2013-01-01
The computational cost of transfer matrix methods for the Potts model is directly related to the problem of \\textit{into how many ways can two adjacent blocks of a lattice be connected}. Answering this question leads to the generation of a combinatorial set of lattice configurations. This set defines the \\textit{configuration space} of the problem, and the smaller it is, the faster the transfer matrix method can be. The configuration space of generic transfer matrix methods for strip lattices in the Potts model is in the order of the Catalan numbers, leading to an asymptotic cost of $O(4^m)$ with $m$ being the width of the strip. Transfer matrix methods with a smaller configuration space indeed exist but they make assumptions on the temperature, number of spin states, or restrict the topology of the lattice in order to work. In this paper we propose a general and parallel transfer matrix method, based on family trees, that uses a sub-Catalan configuration space of size $O(3^m)$. The improvement is achieved by...
Dynamical Properties of Potts Model with Invisible States
International Nuclear Information System (INIS)
We study dynamic behavior of Potts model with invisible states near the first-order phase transition temperature. This model is regarded as a standard model to analyse nature of phase transition. We can control the energy barrier between the ordered state and disordered state without changing the symmetry which breaks at the transition point. We focus on melting process starting from the perfect ordered state. We calculate time-dependency of the order parameter, density of invisible state, and internal energy. All of them show two-step relaxation behavior. We also analyze the relationship between the characteristic melting time and characteristic scale of the energy barrier by changing the number of invisible states. We find that characteristic melting time increases as the energy barrier enlarges in this model. This model is regarded as a fundamental model to analyze dynamic behavior near the first-order phase transition point.
Coupled Potts models: Self-duality and fixed point structure
International Nuclear Information System (INIS)
We consider q-state Potts models coupled by their energy operators. Restricting our study to self-dual couplings, numerical simulations demonstrate the existence of non-trivial fixed points for 2 ≤ q ≤ 4. These fixed points were first predicted by perturbative renormalisation group calculations. Accurate values for the central charge and the multiscaling exponents of the spin and energy operators are calculated using a series of novel transfer matrix algorithms employing clusters and loops. These results compare well with those of the perturbative expansion, in the range of parameter values where the latter is valid. The criticality of the fixed-point models is independently verified by examining higher eigenvalues in the even sector, and by demonstrating the existence of scaling laws from Monte Carlo simulations. This might be a first step towards the identification of the conformal field theories describing the critical behaviour of this class of models
Evolution of scale-free random graphs: Potts model formulation
International Nuclear Information System (INIS)
We study the bond percolation problem in random graphs of N weighted vertices, where each vertex i has a prescribed weight Pi and an edge can connect vertices i and j with rate PiPj. The problem is solved by the q→1 limit of the q-state Potts model with inhomogeneous interactions for all pairs of spins. We apply this approach to the static model having Pi∝i-μ (03 and 2<λ<3. While for the former, the giant cluster forms abruptly at the percolation transition, for the latter, however, the formation of the giant cluster is gradual and the mean cluster size for finite N shows double peaks
Generalized Potts-Models and their Relevance for Gauge Theories
Directory of Open Access Journals (Sweden)
Andreas Wipf
2007-01-01
Full Text Available We study the Polyakov loop dynamics originating from finite-temperature Yang-Mills theory. The effective actions contain center-symmetric terms involving powers of the Polyakov loop, each with its own coupling. For a subclass with two couplings we perform a detailed analysis of the statistical mechanics involved. To this end we employ a modified mean field approximation and Monte Carlo simulations based on a novel cluster algorithm. We find excellent agreement of both approaches. The phase diagram exhibits both first and second order transitions between symmetric, ferromagnetic and antiferromagnetic phases with phase boundaries merging at three tricritical points. The critical exponents ν and γ at the continuous transition between symmetric and antiferromagnetic phases are the same as for the 3-state spin Potts model.
Glauber Dynamics for the mean-field Potts Model
Cuff, Paul; Louidor, Oren; Lubetzky, Eyal; Peres, Yuval; Sly, Allan
2012-01-01
We study Glauber dynamics for the mean-field (Curie-Weiss) Potts model with $q\\geq 3$ states and show that it undergoes a critical slowdown at an inverse-temperature $\\beta_s(q)$ strictly lower than the critical $\\beta_c(q)$ for uniqueness of the thermodynamic limit. The dynamical critical $\\beta_s(q)$ is the spinodal point marking the onset of metastability. We prove that when $\\beta\\beta_s(q)$ the mixing time is exponentially large in $n$. Furthermore, as $\\beta \\uparrow \\beta_s$ with $n$, the mixing time interpolates smoothly from subcritical to critical behavior, with the latter reached at a scaling window of $O(n^{-2/3})$ around $\\beta_s$. These results form the first complete analysis of the critical slowdown of a dynamics with a first order phase transition.
Interplay between sign problem and Z_3 symmetry in three-dimensional Potts model
Hirakida, Takehiro; Takahashi, Junichi; Yahiro, Masanobu
2016-01-01
We construct four kinds of Z3-symmetric three-dimentional (3-d) Potts models, each with different number of states at each site on a 3-d lattice, by extending the 3-d three-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 $\\mu-\\kappa$ plane as the number of states increases, where $\\mu$ $(\\kappa)$ 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 $\\mu$-dependence with respect to increasing the number of states.
Nishimori point in random-bond Ising and Potts models in 2D
A. Honecker; Jacobsen, J. L.; Picco, M.; Pujol, P.
2001-01-01
We study the universality class of the fixed points of the 2D random bond q-state Potts model by means of numerical transfer matrix methods. In particular, we determine the critical exponents associated with the fixed point on the Nishimori line. Precise measurements show that the universality class of this fixed point is inconsistent with percolation on Potts clusters for q=2, corresponding to the Ising model, and q=3
Double Potts chain and exact results for some two-dimensional models
International Nuclear Information System (INIS)
A closed-form exact analytical solution for the q-state Potts model on a ladder 2x∞ with arbitrary two-, three-, and four-site interactions in a unit cell is presented. Using the obtained solution it is shown that the finite-size internal energy equation [J. Wosiek, Phys. Rev. B 49, 15 023 (1994)] yields an accurate value of the critical temperature for the triangular Potts lattice with three-site interactions in alternate triangular faces. (author)
Ising and Potts models: binding disorder-and dimension effects
International Nuclear Information System (INIS)
Within the real space renormalization group framework, some thermal equilibrium properties of pure and disordered insulating systems are calculated. In the pure hypercubic lattice system, the Ising model surface tension and the correlation length of the q-state Potts model, which generalizes the former are analyzed. Several asymptotic behaviors are obtained (for the first time as far as we know) for both functions and the influence of dimension over them can be observed. Accurate numerical proposals for the surface tension are made in several dimensions, and the effect of the number of states (q) on the correlation lenght is shown. In disordered systems, attention is focused essentiall on those which can be theoretically represented by pure sistem Hamiltonians where probability distributions are assumed for the coupling constants (disorder in the bonds). It is obtained with high precision several approximate critical surfaces for the quenched square-lattice Ising model, whose probability distribution can assume two positive values (hence there is no frustration). These aproximate surfaces contain all the exact known points. In the cases where the coupling constant probability distribution can also assume negative values (allowing disordered and frustrated systems), a theoretical treatment which distinguishes the frustration effect from the dilution one is proposed. This distinction can be seen by the different ways in which the bonds of any series-parallel topological array combine. (Author)
Roughness exponent in two-dimensional percolation, Potts model, and clock model
International Nuclear Information System (INIS)
We present a numerical study of the self-affine profiles obtained from configurations of the q-state Potts (with q=2,3, and 7) and p=10 clock models as well as from the occupation states for site percolation on the square lattice. The first and second order static phase transitions of the Potts model are located by a sharp change in the value of the roughness exponent α characterizing those profiles. The low temperature phase of the Potts model corresponds to flat (α≅1) profiles, whereas its high temperature phase is associated with rough (α≅0.5) ones. For the p=10 clock model, in addition to the flat (ferromagnetic) and rough (paramagnetic) profiles, an intermediate rough (0.5<α<1) phase-associated with a soft spin-wave one-is observed. Our results for the transition temperatures in the Potts and clock models are in agreement with the static values, showing that this approach is able to detect the phase transitions in these models directly from the spin configurations, without any reference to thermodynamical potentials, order parameters, or response functions. Finally, we show that the roughness exponent α is insensitive to geometric critical phenomena
Scale-free random graphs and Potts model
Indian Academy of Sciences (India)
D-S Lee; K-I Goh; B Kahng; D Kim
2005-06-01
We introduce a simple algorithm that constructs scale-free random graphs efficiently: each vertex has a prescribed weight − (0 < < 1) and an edge can connect vertices and with rate . Corresponding equilibrium ensemble is identified and the problem is solved by the → 1 limit of the -state Potts model with inhomogeneous interactions for all pairs of spins. The number of loops as well as the giant cluster size and the mean cluster size are obtained in the thermodynamic limit as a function of the edge density. Various critical exponents associated with the percolation transition are also obtained together with finite-size scaling forms. The process of forming the giant cluster is qualitatively different between the cases of > 3 and 2 < < 3, where = 1 + -1 is the degree distribution exponent. While for the former, the giant cluster forms abruptly at the percolation transition, for the latter, however, the formation of the giant cluster is gradual and the mean cluster size for finite shows double peaks.
Potts models with magnetic field: Arithmetic, geometry, and computation
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.
Optimal region of latching activity in an adaptive Potts model for networks of neurons
International Nuclear Information System (INIS)
In statistical mechanics, the Potts model is a model for interacting spins with more than two discrete states. Neural networks which exhibit features of learning and associative memory can also be modeled by a system of Potts spins. A spontaneous behavior of hopping from one discrete attractor state to another (referred to as latching) has been proposed to be associated with higher cognitive functions. Here we propose a model in which both the stochastic dynamics of Potts models and an adaptive potential function are present. A latching dynamics is observed in a limited region of the noise(temperature)–adaptation parameter space. We hence suggest noise as a fundamental factor in such alternations alongside adaptation. From a dynamical systems point of view, the noise–adaptation alternations may be the underlying mechanism for multi-stability in attractor-based models. An optimality criterion for realistic models is finally inferred
Marginal dimensions of the Potts model with invisible states
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.
Dotsenko, V S; Pujol, P; Dotsenko, Vladimir; Picco, Marco; Pujol, Pierre
1995-01-01
We find the cross-over behavior for the spin-spin correlation function for the 2D Ising and 3-states Potts model with random bonds at the critical point. The procedure employed is the renormalisation approach of the perturbation series around the conformal field theories representing the pure models. We obtain a crossover in the amplitude for the correlation function for the Ising model which doesn't change the critical exponent, and a shift in the critical exponent produced by randomness in the case of the Potts model. A comparison with numerical data is discussed briefly.
Phase Transition of Generalized Ferromagnetic Potts Model - Effect of Invisible States -
International Nuclear Information System (INIS)
We investigate the nature of the phase transition of the ferromagnetic Potts model with invisible states. The ferromagnetic Potts model with invisible states can be regarded as a straightforward extension of the standard ferromagnetic Potts model. The invisible states contribute the entropy, however they do not affect the internal energy. They also do not change the symmetry which breaks at the transition temperature. The invisible states stimulate a first-order phase transition. We confirm that the first-order phase transition with spontaneous q-fold symmetry breaking for q = 2,3, and 4 takes place even on two-dimensional lattice by Monte Carlo simulation. We also find that the transition temperature decreases and the latent heat increases as the number of invisible states increases.
Potts Model on Maple Leaf Lattice with Pure Three-Site Interaction
Institute of Scientific and Technical Information of China (English)
WANG Zhou-Fei; CHEN Li
2005-01-01
We use Monte Carlo method to study three-state Potts model on maple leaf lattice with pure three-site interaction. The critical behavior of both ferromagnetic and antiferromagnetic cases is studied. Our results confirm that the critical behavior of the ferromagnetic model is independent of the lattice details and lies in the universality class of the three-state ferromagnetic Potts model. For the antiferromagnetic case the transition is of the first order. We have calculated the energy jump and critical temperature in this area. We find there is a tricritical point separating the first order and second order phases for this system.
Potts model on directed small-world Voronoi-Delaunay lattices
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).
International Nuclear Information System (INIS)
We employ the second renormalization group method of tensor-network states to investigate thermodynamic properties of the ferromagnetic and antiferromagnetic Potts model on triangular lattices. From the temperature dependence of the internal energy and the specific heat, both the critical temperatures and critical exponents are evaluated. For the q = 3 antiferromagnetic Potts model, the critical temperature is found to be Tc = 0.627163±0.000003, which is at least one order of magnitude more accurate than that obtained by other methods. (condensed matter: structure, mechanical and thermal properties)
Random matrix theory and higher genus integrability: the quantum chiral Potts model
International Nuclear Information System (INIS)
We perform a random matrix theory (RMT) analysis of the quantum four-state chiral Potts chain for different sizes of the chain up to size L 8. Our analysis gives clear evidence of a Gaussian orthogonal ensemble (GOE) statistics, suggesting the existence of a generalized time-reversal invariance. Furthermore, a change from the (generic) GOE distribution to a Poisson distribution occurs when the integrability conditions are met. The chiral Potts model is known to correspond to a (star-triangle) integrability associated with curves of genus higher than zero or one. Therefore, the RMT analysis can also be seen as a detector of 'higher genus integrability'. (author)
Softening of Phase Transition in 2D Potts Model Under Quenched Bond Randomness
Yaşar, Fatih; Gündüç, Yiğit; Çelik, Tarık
1997-01-01
We have simulated, by using cluster algorithm, the $q=8$ state Potts model in two-dimension with varying amount of quenched bond randomness. We have shown that there exist a finite size dependent threshold value of the introduced quenched bond randomness for rounding the first-order phase transition and this threshold value becomes smaller as the system size increased.
Susceptibility of the Potts model in an hierarchical lattice: renormalisation group approach
International Nuclear Information System (INIS)
Using a real space renormalization group method, the thermal dependence of the susceptibility of the q-state Potts model (ferro-and antiferromagnet) on self-dual Wheatstone-bridge-like hierarchical lattices is calculated. The influence of external fields on the antiferromagnetic phase diagram is discussed as well. (author)
An improvement of extremality regions for Gibbs measures of the Potts model on a Cayley tree
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.
Positive association in the fractional fuzzy Potts model
Kahn, Jeff; Weininger, Nicholas
2007-01-01
A fractional fuzzy Potts measure is a probability distribution on spin configurations of a finite graph $G$ obtained in two steps: first a subgraph of $G$ is chosen according to a random cluster measure $\\phi_{p,q}$, and then a spin ($\\pm1$) is chosen independently for each component of the subgraph and assigned to all vertices of that component. We show that whenever $q\\geq1$, such a measure is positively associated, meaning that any two increasing events are positively correlated. This gene...
Joint Image Reconstruction and Segmentation Using the Potts Model
Storath, Martin; Frikel, Jürgen; Unser, Michael
2014-01-01
We propose a new algorithmic approach to the non-smooth and non-convex Potts problem (also called piecewise-constant Mumford-Shah problem) for inverse imaging problems. We derive a suitable splitting into specific subproblems that can all be solved efficiently. Our method does not require a priori knowledge on the gray levels nor on the number of segments of the reconstruction. Further, it avoids anisotropic artifacts such as geometric staircasing. We demonstrate the suitability of our method for joint image reconstruction and segmentation from limited data in x-ray and photoacoustic tomography. For instance, our method is able to reconstruct the Shepp-Logan phantom from $7$ angular views only. We demonstrate the practical applicability in an experiment with real PET data.
Dotsenko, V S; Picco, M; Pujol, P; Dotsenko, Viktor; Dotsenko, Vladimir; Picco, Marco; Pujol, Pierre
1995-01-01
We find a new solution of the renormalization group for the Potts model with ferromagnetic random valued coupling constants. The solution exhibits universality and broken replica symmetry. It is argued that the model reaches this universality class if the replica symmetry is broken initially. Otherwise the model stays with the replica symmetric renormalization group flow and reaches the fixed point which has been considered before.
The number of link and cluster states: the core of the 2D q state Potts model
International Nuclear Information System (INIS)
Due to Fortuin and Kastelyin the q state Potts model has a representation as a sum over random graphs, generalizing the Potts model to arbitrary q is based on this representation. A key element of the random cluster representation is the combinatorial factor Γg(C,E), which is the number of ways to form C distinct clusters, consisting of totally E edges. We have devised a method to calculate Γg(C,E) from Monte Carlo simulations
Critical dynamics of the Potts model: short-time Monte Carlo simulations
International Nuclear Information System (INIS)
We calculate the new dynamic exponent θ of the 4-state Potts model, using short-time simulations. Our estimates θ1=-0.0471(33) and θ2=-0.0429(11) obtained by following the behavior of the magnetization or measuring the evolution of the time correlation function of the magnetization corroborate the conjecture by Okano et al. [Nucl. Phys. B 485 (1997) 727]. In addition, these values agree with previous estimate of the same dynamic exponent for the two-dimensional Ising model with three-spin interactions in one direction, that is known to belong to the same universality class as the 4-state Potts model. The anomalous dimension of initial magnetization x0=zθ+β/ν is calculated by an alternative way that mixes two different initial conditions. We have also estimated the values of the static exponents β and ν. They are in complete agreement with the pertinent results of the literature
Uniqueness of Gibbs measure for Potts model with countable set of spin values
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We consider a nearest-neighbor Potts model with countable spin values 0,1,..., and non zero external field, on a Cayley tree of order k (with k+1 neighbors). We study translation-invariant 'splitting' Gibbs measures. We reduce the problem to the description of the solutions of some infinite system of equations. For any k≥1 and any fixed probability measure ν with ν(i)>0 on the set of all non negative integer numbers Φ={0,1,...} we show that the set of translation-invariant splitting Gibbs measures contains at most one point, independently on parameters of the Potts model with countable set of spin values on Cayley tree. Also we give a full description of the class of measures ν on Φ such that wit respect to each element of this class our infinite system of equations has unique solution {ai=1,2,...}, where a is an element of (0,1). (author)
FERRIMAGNETIC PHASES OF THE BLUME-EMERY-GRIFFITHS MODEL AND THE POTTS MODEL ON THE DIAMOND LATTICE
Institute of Scientific and Technical Information of China (English)
Ni Jun; Gu Bing-lin
2000-01-01
The phase transitions in the Blume-Emery-Griffiths (BEG) model andantiferromagnetic Potts model on the diamond lattice are investigatedusing the cluster-variation method in the pair approximation. Theferrimagnetic phases are found to be different from those on thesimple-cubic lattice. The phase diagrams of the BEG model are alsocalculated. In the vicinity of the parameter line where the BEG modelreduces to the three-state antiferromagnetic Potts model, new types ofphase diagram are obtained. The results are different from those of themean-field theory, which is a good approximation only for largecoordination number of the lattice.
Topological aspects of Potts gauge models and their 1/Q expansion
International Nuclear Information System (INIS)
In the d-dimensional Potts gauge model the summation over field variables in the partition function is replaced by that over hyper graphs where the topological invariants (Betty numbers) are essentially used, that take into account both oriented and non oriented surfaces. 1/Q expansion in three - and four - dimensions is carried out. A critical temperature and latent heat are obtained by the Pade approximation
Entropy-driven phase transition in low-temperature antiferromagnetic Potts models
Czech Academy of Sciences Publication Activity Database
Kotecký, R.; Sokal, A.D.; Swart, Jan M.
2014-01-01
Roč. 330, č. 3 (2014), s. 1339-1394. ISSN 0010-3616 R&D Projects: GA ČR GA201/09/1931; GA ČR GAP201/12/2613 Institutional support: RVO:67985556 Keywords : Antiferromagnetic Potts model * proper coloring * plane quadrangulation * phase transition * diced lattice Subject RIV: BA - General Mathematics Impact factor: 2.086, year: 2014 http://library.utia.cas.cz/separaty/2014/SI/swart-0429507.pdf
Dynamic Scaling and Universality of the Two-Dimensional Random-Bond Potts Model
Institute of Scientific and Technical Information of China (English)
YING He-Ping; BIAN Bao-Jun; JI Da-Ren; Lothar Schiilke
2001-01-01
Short-time dynamics and universality are investigated for the random-bond Potts model with a trinary distribu tion of quenched randomness on a two-dimensional triangular lattice. The universal power-law scaling behaviour is applied to estimate the exponents z and β/v. Emphasis is placed on dynamic Monte Carlo evolutions for different multi-disorder amplitudes. Our results indicate that the quenched impurities cause a change of the critical universality.
Julia sets and complex singularities in diamond-like hierarchical Potts models
Institute of Scientific and Technical Information of China (English)
QIAO; Jianyong
2005-01-01
We study the phase transition of the Potts model on diamond-like hierarchical lattices. It is shown that the set of the complex singularities is the Julia set of a rational mapping. An interesting problem is how are these singularities continued to the complex plane. In this paper, by the method of complex dynamics, we give a complete description about the connectivity of the set of the complex singularities.
Efficient Monte Carlo Methods for the Potts Model at Low Temperature
Molkaraie, Mehdi
2015-01-01
We consider the problem of estimating the partition function of the ferromagnetic $q$-state Potts model. We propose an importance sampling algorithm in the dual of the normal factor graph representing the model. The algorithm can efficiently compute an estimate of the partition function in a wide range of parameters; in particular, when the coupling parameters of the model are strong (corresponding to models at low temperature) or when the model contains a mixture of strong and weak couplings. We show that, in this setting, the proposed algorithm significantly outperforms the state of the art methods in the primal and in the dual domains.
CSOS models descending from chiral Potts models: degeneracy of the eigenspace and loop algebra
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.
Shaken, but not stirred—Potts model coupled to quantum gravity
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.
Nogawa, Tomoaki
2011-12-05
The evaporation-condensation transition of the Potts model on a square lattice is numerically investigated by the Wang-Landau sampling method. An intrinsically system-size-dependent discrete transition between supersaturation state and phase-separation state is observed in the microcanonical ensemble by changing constrained internal energy. We calculate the microcanonical temperature, as a derivative of microcanonical entropy, and condensation ratio, and perform a finite-size scaling of them to indicate the clear tendency of numerical data to converge to the infinite-size limit predicted by phenomenological theory for the isotherm lattice gas model. © 2011 American Physical Society.
The early history of the integrable chiral Potts model and the odd-even problem
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.
Spin-spin critical point correlation functions for the 2D random bond Ising and Potts models
Dotsenko, V S; Pujol, P; Vladimir Dotsenko; Marco Picco; Pierre Pujol
1994-01-01
We compute the combined two and three loop order correction to the spin-spin correlation functions for the 2D Ising and q-states Potts model with random bonds at the critical point. The procedure employed is the renormalisation group approach for the perturbation series around the conformal field theories representing the pure models. We obtain corrections for the correlations functions which produce crossover in the amplitude but don't change the critical exponent in the case of the Ising model and which produce a shift in the critical exponent, due to randomness, in the case of the Potts model. Comparison with numerical data is discussed briefly.
First order phase transition of the q-state Potts model in two dimensions
Arisue, H
2000-01-01
We have calculated the large-$q$ series of the energy cumulants, the magnetization cumulants and the correlation length at the first order phase transition point both in the ordered and disordered phases for the $q$-state Potts model in two dimensions. The series enables us to estimate the numerical values of the quantities more precisely by a factor of $10^2 - 10^4$ than the Monte Carlo simulations. From the large-$q$ series of the eigenvalues of the transfer matrix, we also find that the excited states form a continuum spectrum and there is no particle state at the first order phase transition point.
High-precision percolation thresholds and Potts-model critical manifolds from graph polynomials
Jacobsen, Jesper Lykke
2014-01-01
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. Jacobsen and Scullard have defined a graph polynomial P_B(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 = e^K - 1 provide increasingly accurate approximations to the critical manifolds upon increasing ...
Potts Model Partition Functions for Self-Dual Families of Strip Graphs
Chang, Shu-Chiuan; Shrock, Robert
2001-01-01
We consider the $q$-state Potts model on families of self-dual strip graphs $G_D$ of the square lattice of width $L_y$ and arbitrarily great length $L_x$, with periodic longitudinal boundary conditions. The general partition function $Z$ and the T=0 antiferromagnetic special case $P$ (chromatic polynomial) have the respective forms $\\sum_{j=1}^{N_{F,L_y,\\lambda}} c_{F,L_y,j} (\\lambda_{F,L_y,j})^{L_x}$, with $F=Z,P$. For arbitrary $L_y$, we determine (i) the general coefficient $c_{F,L_y,j}$ i...
Chang, Shu-Chiuan; Shrock, Robert
2000-01-01
partial abstract: The $q$-state Potts model partition function (equivalent to the Tutte polynomial) for a lattice strip of fixed width $L_y$ and arbitrary length $L_x$ has the form $Z(G,q,v)=\\sum_{j=1}^{N_{Z,G,\\lambda}}c_{Z,G,j}(\\lambda_{Z,G,j})^{L_x}$, 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}=\\sum_{j=1}...
Interface tension of the 3d 4-state Potts model using the Wang-Landau algorithm
Hietanen, A
2011-01-01
We study the interface tension of the 4-state Potts model in three dimensions using the Wang- Landau algorithm. The interface tension is given by the ratio of the partition function with a twisted boundary condition in one direction and periodic boundary conditions in all other directions over the partition function with periodic boundary conditions in all directions. With the Wang-Landau algorithm we can explicitly calculate both partition functions and obtain the result for all temperatures. We find solid numerical evidence for perfect wetting. Our algorithm is tested by calculating thermodynamic quantities at the phase transition point.
High-precision percolation thresholds and Potts-model critical manifolds from graph polynomials
International Nuclear Information System (INIS)
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 B(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. (paper)
Dynamics of Phase Transitions: The 3D 3-state Potts model
Berg, B A; Velytsky, A; Berg, Bernd A.; Meyer-Ortmanns, Hildegard; Velytsky, Alexander
2004-01-01
In studies of the QCD deconfining phase transition or cross-over by means of heavy ion experiments, one ought to be concerned about non-equilibrium effects due to heating and cooling of the system. In this paper we extend our previous study of Glauber dynamics of 2D Potts models to the 3D 3-state Potts model, which serves as an effective model for some QCD properties. We investigate the linear theory of spinodal decomposition in some detail. It describes the early time evolution of the 3D model under a quench from the disordered into the ordered phase well, but fails in 2D. Further, the quench leads to competing vacuum domains, which are difficult to equilibrate, even in the presence of a small external magnetic field. From our hysteresis study we find, as before, a dynamics dominated by spinodal decomposition. There is evidence that some effects survive in the case of a cross-over. But the infinite volume extrapolation is difficult to control, even with lattices as large as 120^3.
International Nuclear Information System (INIS)
Critical behaviour of the dynamical Potts model, subjected to vivid turbulent mixing, is studied by means of the renormalization group. The advecting velocity field is modelled by Kraichnan’s rapid-change ensemble: Gaussian statistics with a given pair correlator 〈vv〉∝δ(t − t′) k−d−ξ, where k is the wave number, d is the dimension of space and 0 < ξ < 2 is an arbitrary exponent. The system exhibits different types of infrared scaling behaviour, associated with four infrared attractors of the renormalization group equations. In addition to the known asymptotic regimes (equilibrium Potts model and passive scalar field), the existence of a new, strongly non-equilibrium type of critical behaviour (universality class) is established, where the self-interaction of the order parameter and the turbulent mixing are equally important. The corresponding critical dimensions and the regions of stability for all the regimes are calculated in the leading order of the double expansion in ξ and ε = 6 − d. Special attention is paid to the effects of compressibility of the fluid, because they lead to interesting crossover phenomena. (paper)
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.
Cumulants of the three-state Potts model and of nonequilibrium models with C{sub 3v} symmetry
Energy Technology Data Exchange (ETDEWEB)
Tome, Tania [Instituto de Fisica, Universidade de Sao Paulo, Sao Paulo, SP (Brazil); Petri, Alberto [Istituto di Acustica O M Corbino, Consiglio Nazionale delle Ricerche, Via del Fosso del Cavaliere, Rome (Italy)
2002-07-05
The critical behaviour of two-dimensional stochastic lattice gas models with C{sub 3v} symmetry is analysed. We study the cumulants of the order parameter for the three-state (equilibrium) Potts model and for two irreversible models whose dynamic rules are invariant under the symmetry operations of the point group C{sub 3v}. By means of extensive numerical analysis of the phase transition we show that irreversibility does not affect the critical behaviour of the systems. In particular, we find that the Binder reduced fourth-order cumulant takes a universal value U* which is the same for the three-state Potts model and for the irreversible models. The same universal behaviour is observed for the reduced third-order cumulant. (author)
Application of simulated tempering and magnetizing to a two-dimensional Potts model
International Nuclear Information System (INIS)
We apply the simulated tempering and magnetizing (STM) method to the two-dimensional three-state Potts model in an external magnetic field in order to investigate STM’s applicability further. The temperature and the external field are treated as dynamical variables updated during the STM simulations. On the basis of adequate information obtained by STM for several lattice sizes L × L (up to 160×160), we also perform a number of conventional canonical simulations of larger lattices in order to illustrate the crossover behavior of the Potts model in an external field with increasing L. The temperature and external field for the larger lattice size simulations are chosen by extrapolation of the detailed information obtained by STM. We present a careful analysis of the crossover-scaling behavior at the phase transitions with respect to the lattice size as well as the temperature and external field. The crossover behavior is clearly observed in the simulations in agreement with theoretical predictions. (paper)
Integrable aspects of the scaling q-state Potts models II: finite-size effects
International Nuclear Information System (INIS)
We continue our discussion of the q-state Potts models for q≤4, in the scaling regimes close to their critical and tricritical points. In a previous paper, the spectrum and full S-matrix of the models on an infinite line were elucidated; here, we consider finite-size behaviour. TBA equations are proposed for all cases related to phi21 and phi12 perturbations of unitary minimal models. These are subjected to a variety of checks in the ultraviolet and infrared limits, and compared with results from a recently-proposed non-linear integral equation. A non-linear integral equation is also used to study the flows from tricritical to critical models, over the full range of q. Our results should also be of relevance to the study of the off-critical dilute A models in regimes 1 and 2
Exact S-matrices for supersymmetric sigma models and the Potts model
International Nuclear Information System (INIS)
We study the algebraic formulation of exact factorizable S-matrices for integrable two-dimensional field theories. We show that different formulations of the S-matrices for the Potts field theory are essentially equivalent, in the sense that they can be expressed in the same way as elements of the Temperley-Lieb algebra, in various representations. This enables us to construct the S-matrices for certain nonlinear sigma models that are invariant under the Lie 'supersymmetry' algebras sl(m+n|n) (m=1, 2, n>0), both for the bulk and for the boundary, simply by using another representation of the same algebra. These S-matrices represent the perturbation of the conformal theory at θ=π by a small change in the topological angle θ. The m=1, n=1 theory has applications to the spin quantum Hall transition in disordered fermion systems. We also find S-matrices describing the flow from weak to strong coupling, both for θ=0 and θ=π, in certain other supersymmetric sigma models
Fermat Surface and Group Theory in Symmetry of Rapidity Family in Chiral Potts Model
Roan, Shi-shyr
2013-01-01
The present paper discusses various mathematical aspects about the rapidity symmetry in chiral Potts model (CPM) in the context of algebraic geometry and group theory . We re-analyze the symmetry group of a rapidity curve in $N$-state CPM, explore the universal group structure for all $N$, and further enlarge it to modular symmetries of the complete rapidity family in CPM. As will be shown in the article that all rapidity curves in $N$-state CPM constitute a Fermat hypersurface in $\\PZ^3$ of degree 2N as the natural generalization of the Fermat K3 elliptic surface $(N=2)$, we conduct a thorough algebraic geometry study about the rapidity fibration of Fermat surface and its reduced hyperelliptic fibration via techniques in algebraic surface theory. Symmetries of rapidity family in CPM and hyperelliptic family in $\\tau^{(2)}$-model are exhibited through the geometrical representation of the universal structural group in mathematics.
Yang-Lee zeros for a Potts model of helix-coil transition with nontrivial topology
International Nuclear Information System (INIS)
The Yang-Lee partition function zeros of the Q-state Potts model on a zigzag ladder are studied by a transfer-matrix approach. This Q-state model has a non-trivial topology induced by three-site interactions on a zigzag ladder and is proposed as a description of helix-coil transition in homo-polymers. The Yang-Lee zeros are associated to complex values of the solvent-related coupling constant K (magnetic field) and they are exactly derived for arbitrary values of the system parameters: Q, J (coupling constant of hydrogen binding) and temperature. It is shown that there is only a quasi-phase transition for all temperatures. The densities of the Yang-Lee zeros are singular at the edge singularity points and the critical exponent σ = -1/2. (author)
Au-Yang, Helen; Perk, Jacques H. H.
2016-01-01
In this paper we discuss the integrable chiral Potts model, as it clearly relates to how we got befriended with Vaughan Jones, whose birthday we celebrated at the Qinhuangdao meeting. Remarkably we can also celebrate the birthday of the model, as it has been introduced about 30 years ago as the first solution of the star-triangle equations parametrized in terms of higher genus functions. After introducing the most general checkerboard Yang--Baxter equation, we specialize to the star-triangle ...
Random-field Potts model for the polar domains of lead magnesium niobate and lead scandium tantalate
Energy Technology Data Exchange (ETDEWEB)
Qian, H.; Bursill, L.A
1997-06-01
A random filed Potts model is used to establish the spatial relationship between the nanoscale distribution of charges chemical defects and nanoscale polar domains for the perovskite-based relaxor materials lead magnesium niobate (PMN) and lead scandium tantalate (PST). The random fields are not set stochastically but are determined initially by the distribution of B-site cations (Mg, Nb) or (Sc, Ta) generated by Monte Carlo NNNI-model simulations for the chemical defects. An appropriate random field Potts model is derived and algorithms developed for a 2D lattice. It is shown that the local fields are strongly correlated with the chemical domain walls and that polar domains as a function of decreasing temperature is simulated for the two cases of PMN and PST. The dynamics of the polar clusters is also discussed. 33 refs., 9 figs.
Random-field Potts model for the polar domains of lead magnesium niobate and lead scandium tantalate
International Nuclear Information System (INIS)
A random filed Potts model is used to establish the spatial relationship between the nanoscale distribution of charges chemical defects and nanoscale polar domains for the perovskite-based relaxor materials lead magnesium niobate (PMN) and lead scandium tantalate (PST). The random fields are not set stochastically but are determined initially by the distribution of B-site cations (Mg, Nb) or (Sc, Ta) generated by Monte Carlo NNNI-model simulations for the chemical defects. An appropriate random field Potts model is derived and algorithms developed for a 2D lattice. It is shown that the local fields are strongly correlated with the chemical domain walls and that polar domains as a function of decreasing temperature is simulated for the two cases of PMN and PST. The dynamics of the polar clusters is also discussed. 33 refs., 9 figs
International Nuclear Information System (INIS)
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
Cluster-size distribution and the magnetic property of a Potts model
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 T
Nature of phase transitions in Axelrod-like coupled Potts models in two dimensions
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.
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.
Improved contact prediction in proteins: Using pseudolikelihoods to infer Potts models
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/.
Reconstruction of a real world social network using the Potts model and Loopy Belief Propagation
Directory of Open Access Journals (Sweden)
Cristian eBisconti
2015-11-01
Full Text Available The scope of this paper is to test the adoption of a statistical model derived from Condensed Matter Physics, aiming at the reconstruction of a networked structure from observations of the states of the nodes in the network.The inverse Potts model, normally applied to observations of quantum states, is here addressed to observations of the node states in a network and their (anticorrelations, thus inferring interactions as links connecting the nodes. Adopting the Bethe approximation, such an inverse problem is known to be tractable.Within this operational framework, we discuss and apply this network-reconstruction method to a small real-world social network, where it is easy to track statuses of its members: the Italian parliament, adopted as a case study. The dataset is made of (cosponsorships of law proposals by parliament members. 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 standard methods, outlining discrepancies and advantages.
Phase transitions for p-adic Potts model on the Cayley tree of order three
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In the present paper, we study a phase transition problem for the q-state p-adic Potts model over the Cayley tree of order three. We consider a more general notion of p-adic Gibbs measure which depends on parameter ρ∈Qp. Such a measure is called generalized p-adic quasi Gibbs measure. When ρ equals the p-adic exponent, then it coincides with the p-adic Gibbs measure. When ρ = p, then it coincides with the p-adic quasi Gibbs measure. Therefore, we investigate two regimes with respect to the value of |ρ|p. Namely, in the first regime, one takes ρ = expp(J) for some J∈Qp, in the second one |ρ|p p,|q|p ≤ p−2 we prove the existence of a quasi phase transition. It turns out that if |ρ|pp2p, then one finds the existence of the strong phase transition. (paper)
The surface expoents of the Quantum XXZ, Ashkin-Teller, and Potts models
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The eigen-spectrum of both the quantum Ashkin-Teller and Potts chains with free boundaries can be respectively obtained from that of the XXZ chain with free boundaries and a complex surface field. By solving numerically the recently introduced Bethe ansatz equations for such boundaries, eigen-energies are obtained for chains of up to L=256. The conformal anomaly and surface exponents of the quantum XXZ, Ashkin-Teller, and Potts chains are calculated by exploiting their relations with the mass gap amplitudes predicted by conformal invariance. (Author)
Chang, Shu-Chiuan; Shrock, Robert
2015-11-01
We calculate the partition function of the q-state Potts model on arbitrary-length cyclic ladder graphs of the square and triangular lattices, with a generalized external magnetic field that favors or disfavors a subset of spin values {1,ldots ,s} with s ≤ q. For the case of antiferromagnet spin-spin coupling, these provide exactly solved models that exhibit an onset of frustration and competing interactions in the context of a novel type of tensor-product S_s ⊗ S_{q-s} global symmetry, where S_s is the permutation group on s objects.
Ding, Chengxiang; Fu, Zhe; Guo, Wenan; Wu, F Y
2010-01-01
In a recent paper (arXiv:0911.2514), one of us (FYW) 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 two-fo...
Potts model partition functions for self-dual families of strip graphs
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.
Large-$q$ expansion of the two-dimensional $q$-state Potts model by the finite lattice method
Arisue, H
1999-01-01
We have calculated the large-$q$ expansion for the energy and magnetization cumulants at the first order phase transition point in the two-dimensional $q$-state Potts model to the 21st or 23rd order in $1/\\sqrt{q}$ using the finite lattice method. The obtained series allow us to give highly convergent estimates of the cumulants for $q>4$. The results confirm us the correctness of the conjecture by Bhattacharya {\\em et al.} on the asymptotic behavior of the energy cumulants for $q \\to 4_+$ and a similar new conjecture on the magnetization cumulants.
Arisue, H
1999-01-01
We have calculated the large-$q$ expansion for the energy cumulants and the magnetization cumulants at the phase transition point in the two-dimensional $q$-state Potts model to the 21st or 23rd order in $1/\\sqrt{q}$ using the finite lattice method. The obtained series allow us to give very precise estimates of the cumulants for $q>4$ on the first order transition point. The result confirms us the correctness of the conjecture by Bhattacharya et al. on the asymptotic behavior not only of the energy cumulants but also of the magnetization cumulants for $q \\to 4_+$.
Large-$q$ expansion of the specific heat for the two-dimensional $q$-state Potts model
Arisue, H
1999-01-01
We have calculated the large-$q$ expansion for the specific heat at the phase transition point in the two-dimensional $q$-state Potts model to the 23rd order in $1/\\sqrt{q}$ using the finite lattice method. The obtained series allows us to give highly convergent estimates of the specific heat for $q>4$ on the first order transition point. The result confirm us the correctness of the conjecture by Bhattacharya et al. on the asymptotic behavior of the specific heat for $q
Large-$q$ expansion of the energy cumulants for the two-dimensional $q$-state Potts model
Arisue, H
1998-01-01
We have calculated the large-q expansion for the energy cumulants at the phase transition point in the two-dimensional q-state Potts model to the 23rd order in $1/\\sqrt{q}$ using the finite lattice method. The obtained series allow us to give very precise estimates of the cumulants for $q>4$ on the first order transition point. The result confirm us the correctness of the conjecture by Bhattacharya et al. on the asymptotic behavior of the cumulants for $q \\to 4_+$.
Jacobsen, Jesper Lykke
2015-01-01
In previous work with Scullard, we defined a graph polynomial P_B(q,T) that gives access to the critical temperature T_c of the q-state Potts model on a general two-dimensional lattice L. It depends on a basis B, containing n x m unit cells of L, and the relevant root of P_B(q,T) was observed to converge quickly to T_c in the limit n,m to infinity. Moreover, in exactly solvable cases there is no finite-size dependence at all. We reformulate this method as an eigenvalue problem within the peri...
Non-trivial exponents in the zero temperature dynamics of the 1D Ising and Potts models
Derrida, B.; Bray, A. J.; Godrèche, C.
1994-01-01
We consider the Glauber dynamics of the $ q $-state Potts model in one dimension at zero temperature. Starting with a random initial configuration, we measure the density $ r_t $ of spins which have never flipped from the beginning of the simulation until time $ t. $ We find that for large $ t, $ the density $ r_t $ has a power law decay $ \\left(r_t \\sim t^{-\\theta} \\right) $ where the exponent $ \\theta $ varies with $ q. $ Our simulations lead to $ \\theta \\simeq .37 $ for $ q=2, $ $ \\theta \\...
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The renormalization and the critical and tricritical behavior of the three-state Potts model with broken symmetry between the state vectors and with a external field is studied in a field theory. As an extension of Landau phase-transition theory, renormalization group transformations, to first order in ε =dc-d, are applyied, generating recursion relations. These differential equations are solved in two cases: (a) dc = 6 the φ3-field critical dimension; (b) dc = 4 the φ4-field (XY model) critical dimension. In both cases, non-universal ratios of temperaturestt/tc, magnetizationsmt/ mc and external fieldsht/ hc tricritical and critical are obtained. Such results are applyied to the structural phase transition of SrTiO3 stressed along p->//[1+δ, 1+δ, 1-2δ] yielding a non-universal ratioδt/ δc. Finally, the susceptibility, the magnetization and the singular part of the free energy are calculated in d = 4 - ε dimension at the critical region, showing the crossover from XY model to Potts model behavior. Universal ratio of susceptibilities calculated above and bellow the critical point is obtained too. (author)
The Potts glass on the Bethe lattice
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It is considered the nearest-neighbor p-state random Potts model on a Cayley tree of infinite coordination. The problem is formulated as a discrete mapping whose fixed points correspond to solutions deep inside the tree. The introduction of an ansatz which allows for the breaking of the Potts symmetry leads to an instability of the spin glass fixed point for p > 4. (author)
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We obtain long series expansions for the bulk, surface and corner free energies for several two-dimensional statistical models, by combining Enting’s finite lattice method (FLM) with exact transfer matrix enumerations. The models encompass all integrable curves of the Q-state Potts model on the square and triangular lattices, including the antiferromagnetic transition curves and the Ising model (Q = 2) at temperature T, as well as a fully packed O(n) type loop model on the square lattice. The expansions are around the trivial fixed points at infinite Q, n or 1/T. By using a carefully chosen expansion parameter, q ≪ 1, all expansions turn out to be of the form Πk=1∞(1-qk)αk+kβk, where the coefficients αk and βk are periodic functions of k. Thanks to this periodicity property, we can conjecture the form of the expansions to all orders (except in a few cases where the periodicity is too large). These expressions are then valid for all 0 ⩽ q − limit in which the models become critical. In this limit the divergence of the corner free energy defines a universal term which can be compared with the conformal field theory (CFT) predictions of Cardy and Peschel. This allows us to deduce the asymptotic expressions for the correlation length in several cases. Finally we work out the FLM formulae for the case where some of the system’s boundaries are endowed with particular (non-free) boundary conditions. We apply this in particular to the square-lattice Potts model with Jacobsen–Saleur boundary conditions, conjecturing the expansions of the surface and corner free energies to arbitrary order for any integer value of the boundary interaction parameter r. These results are in turn compared with CFT predictions. (paper)
Large-q expansion of the correlation length in the two-dimensional q-state Potts model
Arisue, H
2000-01-01
The large-q expansions of the exponential correlation length and the second moment correlation length for the q-state Potts model in two dimensions are calculated at the first order phase transition point both in the ordered and disordered phases. The expansion coefficients in the ordered and disordered phases coincide in lower orders for both of the two types of the correlation lengths, but they differ a little from each other in higher orders for the second moment correlation length. The second largest eigenvalues of the transfer matrix have the continuum spectrum both in the ordered and disordered phases in the large-q region, which is suggested to be maintained even in the limit of $q\\to 4$ from the analysis of the expansion series.
Arisue, H
2000-01-01
We calculate the large-q expansion of the second moment correlation length at the first order phase transition point of the q-state Potts model in two dimensions both in the ordered and disordered phases to order 21 in $1/\\sqrt{q}$. They coincide with each other to the third term of the series but differ a little in higher orders. Numerically the ratio of the second moment correlation length in the two phases is not far from unity in all region of q>4. The ratio of the second moment correlation length to the standard correlation length in the disordered phase is far from unity, which suggests that the second largest and smaller eigenvalues of the transfer matrix form a continuum spectrum not only in the large-q region but also in all the region of q>4.
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.
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 .
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Testing the applicability of mathematical models with carefully designed experiments is a powerful tool in the investigations of the effects of ionizing radiation on cells. The modeling and cellular studies complement each other, for modeling provides guidance for designing critical experiments which must provide definitive results, while the experiments themselves provide new input to the model. Based on previous experimental results the model for the accumulation of damage in Chlamydomonas reinhardi has been extended to include various multiple two-event combinations. Split dose survival experiments have shown that models tested to date predict most but not all the observed behavior. Stationary-phase mammalian cells, required for tests of other aspects of the model, have been shown to be at different points in the cell cycle depending on how they were forced to stop proliferating. These cultures also demonstrate different capacities for repair of sublethal radiation damage
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.
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The geometrical critical behaviour of the two-dimensional Q-state Potts model is usually studied in terms of the Fortuin–Kasteleyn (FK) clusters, or their surrounding loops. In this paper we study a quite different geometrical object: the spin clusters, defined as connected domains where the spin takes a constant value. Unlike the usual loops, the domain walls separating different spin clusters can cross and branch. Moreover, they come in two versions, 'thin' or 'thick', depending on whether they separate spin clusters of different or identical colours. For these reasons their critical behaviour is different from, and richer than, those of FK clusters. 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. We study the critical behaviour both in the bulk, and at a boundary with free, fixed, or mixed boundary conditions. This leads to infinite series of fundamental critical exponents, hl1-l2,2l1 in the bulk and h1+2(l1-l2),1+4l1 at the boundary, valid for 0 ≤ Q ≤ 4, that describe the insertion of l1 thin and l2 thick domain walls. We argue that these exponents imply that the domain walls are 'thin' and 'thick' also in the continuum limit. A special case of the bulk exponents is derived analytically from a massless scattering approach
Statics and dynamics of the ten-state mean-field Potts glass model: a Monte Carlo study
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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 -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). (author)
Endy, Drew; Brent, Roger
2001-01-01
Representations of cellular processes that can be used to compute their future behaviour would be of general scientific and practical value. But past attempts to construct such representations have been disappointing. This is now changing. Increases in biological understanding combined with advances in computational methods and in computer power make it possible to foresee construction of useful and predictive simulations of cellular processes.
Modelling the phase diagram of Ni-Mn-X(X=In,Sn,Sb) alloys: A q-state Potts model monte Carlo study
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On the basis of Monte Carlo simulations using Heisenberg and Potts model Hamiltonians, we investigate the complex temperature dependence of the phase diagram of Ni-Mn-X (X=In,Sn,Sb) Heusler alloys. For Mn excess concentration, we find Mn atoms on the X sites, whose magnetic moments interact antiferromagnetically with the Mn spin moments on the Mn sublattice. Using ab initio data for the magnetic exchange interactions, it is shown that this antiferromagnetic exchange is responsible for metamagnetic behavior and a series of magnetic phase transitions, which compete or act in favor of the martensitic transformation being present in the Heusler alloys. This scenario is finally responsible for the occurrence of magneto-structural phase transitions in this class of ferromagnetic Heusler alloys.
Energy Technology Data Exchange (ETDEWEB)
Andrade, Pedro H.A. de; Cabral, Manuela O.M., E-mail: andrade.pha@gmail.com [Universidade Federal de Pernambuco (DEN/UFPE), Recife, PE (Brazil). Departamento de Engenharia Nuclear; Vieira, Jose W.; Correia, Filipe L. de B., E-mail: jose.wilson59@uol.com.br [Instituto Federal de Educacao, Ciencia e Tecnologia de Pernambuco (IFPE), Recife, PE (Brazil); Lima, Fernando R. De A., E-mail: falima@cnen.gov.br [Centro Regional de Ciencias Nucleares do Nordeste (CRCN-NE/CNEN-PE), Recife, PE (brazil)
2015-07-01
Exposure Computational Models are composed basically of an anthropomorphic phantom, a Monte Carlo (MC) code, and an algorithm simulator of the radioactive source. Tomographic phantoms are developed from medical images and must be pre-processed and segmented before being coupled to a MC code (which simulates the interaction of radiation with matter). This work presents a methodology used for treatment of micro-CT images stack of a femur, obtained from a 30 year old female skeleton provided by the Imaging Laboratory for Anthropology of the University of Bristol, UK. These images contain resolution of 60 micrometers and from these a block containing only 160 x 60 x 160 pixels of trabecular tissues and bone marrow was cut and saved as ⁎.sgi file (header + ⁎.raw file). The Grupo de Dosimetria Numerica (Recife-PE, Brazil) developed a software named Digital Image Processing (DIP), in which a method for segmentation based on a physical model for particle interaction known as Potts Model (or q-Ising) was implemented. This model analyzes the statistical dependence between sites in a network. In Potts Model, when the values of spin variables at neighboring sites are identical, it is assigned an 'energy of interaction' between them. Otherwise, it is said that the sites do not interact. Making an analogy between network sites and the pixels of a digital image and, moreover, between the spins variables and the intensity of the gray scale, it was possible to apply this model to obtain texture descriptors and segment the image. (author)
International Nuclear Information System (INIS)
Exposure Computational Models are composed basically of an anthropomorphic phantom, a Monte Carlo (MC) code, and an algorithm simulator of the radioactive source. Tomographic phantoms are developed from medical images and must be pre-processed and segmented before being coupled to a MC code (which simulates the interaction of radiation with matter). This work presents a methodology used for treatment of micro-CT images stack of a femur, obtained from a 30 year old female skeleton provided by the Imaging Laboratory for Anthropology of the University of Bristol, UK. These images contain resolution of 60 micrometers and from these a block containing only 160 x 60 x 160 pixels of trabecular tissues and bone marrow was cut and saved as ⁎.sgi file (header + ⁎.raw file). The Grupo de Dosimetria Numerica (Recife-PE, Brazil) developed a software named Digital Image Processing (DIP), in which a method for segmentation based on a physical model for particle interaction known as Potts Model (or q-Ising) was implemented. This model analyzes the statistical dependence between sites in a network. In Potts Model, when the values of spin variables at neighboring sites are identical, it is assigned an 'energy of interaction' between them. Otherwise, it is said that the sites do not interact. Making an analogy between network sites and the pixels of a digital image and, moreover, between the spins variables and the intensity of the gray scale, it was possible to apply this model to obtain texture descriptors and segment the image. (author)
Predictive Modelling of Cellular Load
Carolan, Emmett; McLoone, Seamus; Farrell, Ronan
2015-01-01
This work examines the temporal dynamics of cellular load in four Irish regions. Large scale underutilisation of network resources is identified both at the regional level and at the level of individual cells. Cellular load is modeled and prediction intervals are generated. These prediction intervals are used to put an upper bound on usage in a particular cell at a particular time. Opportunities for improvements in network utilization by incorporating these upper bounds on usage are identifie...
Xtoys cellular automata on xwindows
Creutz, M
1995-01-01
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.
Vernier, Eric
2011-01-01
We obtain long series expansions for the bulk, surface and corner free energies for several two-dimensional statistical models, by combining Enting's finite lattice method (FLM) with exact transfer matrix enumerations. The models encompass all integrable curves of the Q-state Potts model on the square and triangular lattices, including the antiferromagnetic transition curves and the Ising model (Q=2) at temperature T, as well as a fully-packed O(n) type loop model on the square lattice. The expansions are around the trivial fixed points at infinite Q, n or 1/T. By using a carefully chosen expansion parameter, q << 1, all expansions turn out to be of the form \\prod_{k=1}^\\infty (1-q^k)^{\\alpha_k + k \\beta_k}, where the coefficients \\alpha_k and \\beta_k are periodic functions of k. Thanks to this periodicity property we can conjecture the form of the expansions to all orders (except in a few cases where the periodicity is too large). These expressions are then valid for all 0 <= q < 1. We analyse in...
Pott's disease: radioisotope scanning findings
International Nuclear Information System (INIS)
The study is aim was to describe findings in bone scan in patients with Pott's disease. Eight patients had a bone scan with 99mTc . The findings included: a spindle image due to increased uptake in vertebrae and intervertebral uptake in three cases, increased uptake in vertebrae in three cases, paravertebral uptake in one case and vertebral compression with diminished uptake in one case. Bone scan is a useful tool in evaluating spinal tuberculosis (Pott's disease) as an indicator of activity within the lesion. (authors)
Cellular automata a parallel model
Mazoyer, J
1999-01-01
Cellular automata can be viewed both as computational models and modelling systems of real processes. This volume emphasises the first aspect. In articles written by leading researchers, sophisticated massive parallel algorithms (firing squad, life, Fischer's primes recognition) are treated. Their computational power and the specific complexity classes they determine are surveyed, while some recent results in relation to chaos from a new dynamic systems point of view are also presented. Audience: This book will be of interest to specialists of theoretical computer science and the parallelism challenge.
The potts chain in a random field: an exact solution
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An exact solution is presented for the one-dimensional q-state Potts model in a quenched random field. The ferromagnetic phase is unstable against any small random field perturbation. The correlation function and the Edwards-Anderson order parameter Q are discussed. For finite q only the phase with Q ≠ 0 is present. (Author)
Potts critical frontiers of inhomogeneous and asymmetric bow-tie lattices
Scullard, Christian R.; Jacobsen, Jesper Lykke
2012-01-01
We study the critical frontiers of the Potts model on two-dimensional bow-tie lattices with fully inhomogeneous coupling constants. Generally, for the Potts critical frontier to be found exactly, the underlying lattice must be a 3-uniform hypergraph. A more general class of lattices are the 4-uniform ones, with unit cells contained within four boundary vertices. We demonstrate that in some cases, such lattices can be decomposed into triangular cells, and solved using a modification of standar...
Influence of lattice defects on criticality of Potts ferromagnet
International Nuclear Information System (INIS)
The critical properties of the q-state Potts ferromagnet and the anisotropic Heisenberg model on hypercubic lattices (d = 2,3); emphasis is given to the free surface and the interface effects, the Real Space Renormalization Group approach. The criticality of the quenched bond-mixed q-state Potts ferromagnet on square lattice is discussed. It is shown that, the crossover from the pure fixed point to the random one occurs, while q increases, through a pitchfork bifurcation; the relation-ship with the Harris criterion is analyzed. High precision numerical values for the critical temperatures corresponding to arbitrary concentrations of the coupling constants J sub(1) and J sub(2), and arbitrary ratios J sub(1)/J sub(2) are presented.(author)
Understanding cisplatin resistance using cellular models.
STORDAL, BRITTA KRISTINA
2007-01-01
PUBLISHED Many mechanisms of cisplatin resistance have been proposed from studies of cellular models of resistance including changes in cellular drug accumulation, detoxification of the drug, inhibition of apoptosis and repair of the DNA adducts. A series of resistant models were developed from CCRF-CEM leukaemia cells with increasing doses of cisplatin from 100 ng/ml. This produced increasing resistance up to 7-fold with a treatment dose of 1.6 ?g/ml. Cisplatin resistance i...
Understanding cisplatin resistance using cellular models
Stordal, Britta; Davey, Mary
2007-01-01
Many mechanisms of cisplatin resistance have been proposed from studies of cellular models of resistance including changes in cellular drug accumulation, detoxification of the drug, inhibition of apoptosis and repair of the DNA adducts. A series of resistant models were developed from CCRF-CEM leukaemia cells with increasing doses of cisplatin from 100 ng/ml. This produced increasing resistance up to 7-fold with a treatment dose of 1.6 microg/ml. Cisplatin resistance in these cells correlated...
Animal and cellular models of human disease
Arends, Mark; White, Eric; Whitelaw, Christopher
2016-01-01
In this eighteenth (2016) Annual Review Issue of The Journal of Pathology, we present a collection of 19 invited review articles that cover different aspects of cellular and animal models of disease. These include genetically-engineered models, chemically-induced models, naturally-occurring models, and combinations thereof, with the focus on recent methodological and conceptual developments across a wide range of human diseases.
A Modified Sensitive Driving Cellular Automaton Model
Institute of Scientific and Technical Information of China (English)
GE Hong-Xia; DAI Shi-Qiang; DONG Li-Yun; LEI Li
2005-01-01
A modified cellular automaton model for traffic flow on highway is proposed with a novel concept about the variable security gap. The concept is first introduced into the original Nagel-Schreckenberg model, which is called the non-sensitive driving cellular automaton model. And then it is incorporated with a sensitive driving NaSch model,in which the randomization brake is arranged before the deterministic deceleration. A parameter related to the variable security gap is determined through simulation. Comparison of the simulation results indicates that the variable security gap has different influence on the two models. The fundamental diagram obtained by simulation with the modified sensitive driving NaSch model shows that the maximumflow are in good agreement with the observed data, indicating that the presented model is more reasonable and realistic.
Potts disease: Diagnosis with magnetic resonance imaging
International Nuclear Information System (INIS)
The eponymously named Potts disease is a relatively rare form of Tuberculosis (TB) which affects the spine. TB of the spine is one of the earliest diseases known to man and in the 20th century was thought to be a disease which had been defeated by the advent of antitubercular drugs. Over the last two decades there have been several reports which indicate a revival of TB in both the developing and developed world. Factors which may be contributing to this are the spread of the HIV virus, increased immigration and the emergence of drug resistant strains of the TB bacteria. Potts disease has an insidious onset and often the radiographic findings are far advanced when a diagnosis is finally reached. MRI is able to detect changes to the vertebrae in Potts disease earlier than radiographs. This case report outlines the clinical presentation of a young male with Potts disease who was HIV negative, and the important role that MRI plays in diagnosis and therefore in appropriate and timely intervention. The typical magnetic resonance (MR) imaging features and the radiographic hallmarks of the disease will also be discussed.
Potts disease: Diagnosis with magnetic resonance imaging
Energy Technology Data Exchange (ETDEWEB)
Pursey, Jacqueline [MRI Department, Gartnavel General Hospitial, 1053 Great Western road, Glasgow G12 0YN (United Kingdom)], E-mail: Jacqueline.pursey@ggc.scot.nhs.uk; Stewart, Sharon [School of Health and Social Care, Caledonian University, Glasgow (United Kingdom)
2010-02-15
The eponymously named Potts disease is a relatively rare form of Tuberculosis (TB) which affects the spine. TB of the spine is one of the earliest diseases known to man and in the 20th century was thought to be a disease which had been defeated by the advent of antitubercular drugs. Over the last two decades there have been several reports which indicate a revival of TB in both the developing and developed world. Factors which may be contributing to this are the spread of the HIV virus, increased immigration and the emergence of drug resistant strains of the TB bacteria. Potts disease has an insidious onset and often the radiographic findings are far advanced when a diagnosis is finally reached. MRI is able to detect changes to the vertebrae in Potts disease earlier than radiographs. This case report outlines the clinical presentation of a young male with Potts disease who was HIV negative, and the important role that MRI plays in diagnosis and therefore in appropriate and timely intervention. The typical magnetic resonance (MR) imaging features and the radiographic hallmarks of the disease will also be discussed.
Segmenting images into four classes of magnetism: A linear-time Potts method
Bentrem, Frank W
2009-01-01
A computational method is presented which efficiently segments digital grayscale images by directly applying the Potts (or Q-state Ising) model. Since the Potts model was first proposed in 1952, physicists have studied lattice models to gain deep insights into magnetism and other disordered systems. For some time, researchers have realized that digital images may be modeled in much the same way as these physical systems (i.e., as a square lattice of numerical values). A major drawback in using Potts model methods for image segmentation is that, with conventional methods, it processes in exponential time. Advances have been made via certain approximations to reduce the segmentation process to power-law time. However, in many applications (such as for sonar imagery), real-time processing requires much greater efficiency. This article contains a description of an energy minimization technique that applies four Potts (Q-Ising) models directly to the image and processes in linear time. The result is analogous to p...
A Mathematical Model for Cisplatin Cellular Pharmacodynamics
Directory of Open Access Journals (Sweden)
Ardith W. El-Kareh
2003-03-01
Full Text Available A simple theoretical model for the cellular pharmacodynamics of cisplatin is presented. The model, which takes into account the kinetics of cisplatin uptake by cells and the intracellular binding of the drug, can be used to predict the dependence of survival (relative to controls on the time course of extracellular exposure. Cellular pharmacokinetic parameters are derived from uptake data for human ovarian and head and neck cancer cell lines. Survival relative to controls is assumed to depend on the peak concentration of DNA-bound intracellular platinum. Model predictions agree well with published data on cisplatin cytotoxicity for three different cancer cell lines, over a wide range of exposure times. In comparison with previously published mathematical models for anticancer drug pharmacodynamics, the present model provides a better fit to experimental data sets including long exposure times (∼100 hours. The model provides a possible explanation for the fact that cell kill correlates well with area under the extracellular concentration-time curve in some data sets, but not in others. The model may be useful for optimizing delivery schedules and for the dosing of cisplatin for cancer therapy.
Cellular automata modelling of hantarvirus infection
International Nuclear Information System (INIS)
Hantaviruses are a group of viruses which have been identified as being responsible for the outbreak of diseases such as the hantavirus pulmonary syndrome. In an effort to understand the characteristics and dynamics of hantavirus infection, mathematical models based on differential equations have been developed and widely studied. However, such models neglect the local characteristics of the spreading process and do not include variable susceptibility of individuals. In this paper, we develop an alternative approach based on cellular automata to analyze and study the spatiotemporal patterns of hantavirus infection.
Cellular automata modelling of hantarvirus infection
Energy Technology Data Exchange (ETDEWEB)
Abdul Karim, Mohamad Faisal [School of Distance Education, Universiti Sains Malaysia, Minden 11800, Penang (Malaysia)], E-mail: faisal@usm.my; Md Ismail, Ahmad Izani [School of Mathematical Sciences, Universiti Sains Malaysia, Minden 11800, Penang (Malaysia)], E-mail: izani@cs.usm.my; Ching, Hoe Bee [School of Mathematical Sciences, Universiti Sains Malaysia, Minden 11800, Penang (Malaysia)], E-mail: Bee_Ching_Janice_Hoe@dell.com
2009-09-15
Hantaviruses are a group of viruses which have been identified as being responsible for the outbreak of diseases such as the hantavirus pulmonary syndrome. In an effort to understand the characteristics and dynamics of hantavirus infection, mathematical models based on differential equations have been developed and widely studied. However, such models neglect the local characteristics of the spreading process and do not include variable susceptibility of individuals. In this paper, we develop an alternative approach based on cellular automata to analyze and study the spatiotemporal patterns of hantavirus infection.
Spatial game in cellular automaton evacuation model
von Schantz, Anton; Ehtamo, Harri
2015-11-01
For numerical simulations of crowd dynamics in an evacuation we need a computationally light environment, such as the cellular automaton model (CA). By choosing the right model parameters, different types of crowd behavior and collective effects can be produced. But the CA does not answer why, when, and how these different behaviors and collective effects occur. In this article, we present a model, where we couple a spatial evacuation game to the CA. In the game, an agent chooses its strategy by observing its neighbors' strategies. The game matrix changes with the distance to the exit as the evacuation conditions develop. In the resulting model, an agent's strategy choice alters the parameters that govern its behavior in the CA. Thus, with our model, we are able to simulate how evacuation conditions affect the behavior of the crowd. Also, we show that some of the collective effects observed in evacuations are a result of the simple game the agents play.
John Potts, The New Time and Space
Jean-Christophe MURAT
2016-01-01
John Potts, Professor of Media at Macquarie University, Australia, is no newcomer to the domain of media studies. Some of his outstanding publications, like Radio in Australia (New South Wales University Press, 1989), Culture and Technology (with Andrew Murphie, Palgrave Macmillan, 2002) and Technologies of Magic (co-edited with Edward Scheer, Sydney: Power Publications, 2011), have established his credentials and revealed the versatility of his knowledge in the field. The New Time and Space,...
A cellular automata model for ant trails
Indian Academy of Sciences (India)
Sibel Gokce; Ozhan Kayacan
2013-05-01
In this study, the unidirectional ant traffic flow with U-turn in an ant trail was investigated using one-dimensional cellular automata model. It is known that ants communicate with each other by dropping a chemical, called pheromone, on the substrate. Apart from the studies in the literature, it was considered in the model that (i) ant colony consists of two kinds of ants, goodand poor-smelling ants, (ii) ants might make U-turn for some special reasons. For some values of densities of good- and poor-smelling ants, the flux and mean velocity of the colony were studied as a function of density and evaporation rate of pheromone.
Modeling the topological organization of cellular processes.
Giavitto, Jean-Louis; Michel, Olivier
2003-07-01
The cell as a dynamical system presents the characteristics of having a dynamical structure. That is, the exact phase space of the system cannot be fixed before the evolution and integrative cell models must state the evolution of the structure jointly with the evolution of the cell state. This kind of dynamical systems is very challenging to model and simulate. New programming concepts must be developed to ease their modeling and simulation. In this context, the goal of the MGS project is to develop an experimental programming language dedicated to the simulation of this kind of systems. MGS proposes a unified view on several computational mechanisms (CHAM, Lindenmayer systems, Paun systems, cellular automata) enabling the specification of spatially localized computations on heterogeneous entities. The evolution of a dynamical structure is handled through the concept of transformation which relies on the topological organization of the system components. An example based on the modeling of spatially distributed biochemical networks is used to illustrate how these notions can be used to model the spatial and temporal organization of intracellular processes. PMID:12915272
Cellular automata modelling of biomolecular networks dynamics.
Bonchev, D; Thomas, S; Apte, A; Kier, L B
2010-01-01
The modelling of biological systems dynamics is traditionally performed by ordinary differential equations (ODEs). When dealing with intracellular networks of genes, proteins and metabolites, however, this approach is hindered by network complexity and the lack of experimental kinetic parameters. This opened the field for other modelling techniques, such as cellular automata (CA) and agent-based modelling (ABM). This article reviews this emerging field of studies on network dynamics in molecular biology. The basics of the CA technique are discussed along with an extensive list of related software and websites. The application of CA to networks of biochemical reactions is exemplified in detail by the case studies of the mitogen-activated protein kinase (MAPK) signalling pathway, the FAS-ligand (FASL)-induced and Bcl-2-related apoptosis. The potential of the CA method to model basic pathways patterns, to identify ways to control pathway dynamics and to help in generating strategies to fight with cancer is demonstrated. The different line of CA applications presented includes the search for the best-performing network motifs, an analysis of importance for effective intracellular signalling and pathway cross-talk. PMID:20373215
Cellular automata modeling of cooperative eutectic growth
Directory of Open Access Journals (Sweden)
E. Olejnik
2010-01-01
Full Text Available The model and results of the 2D simulation of the cooperative growth of two phases in the lamellar eutectic are presented. The pro-posed model takes into account heat transfer, components diffusion and nonstationary concentration distribution in the liquid and solid phases, non-equlibrium nature of the phase transformation and kinetics of the growth, influence of the surface energy and interface curva-ture on the conditions of the thermodynamic equilibrium. For the determination of the phase interface shape the Cellular Automata tech-nique (CA was used. For the calculation of temperature and concentration distribution the numerical solution of the Fourier equation was used. The partial differential equations were solved by Finite Differences Method (FDM. The spatial position and cell sizes of CA lattice and FDM mesh are equal.Proposed model can predict the steady state growth with a constant interlamellar spacing in the regular plate eutectic, as well as some transient processes that bring to the changes of that parameters. Obtained simulation data show the solid-liquid interface changes result in the termination of lamella and enlargement of interlamellar spacing. Another simulation results illustrate a pocket formation in the center of one phase that forestalls nucleation (or intergrowth of the new lamellae of another phase. The data of the solidification study of the transparent material (CBr4 – 8,4% C2Cl6 obtained in the thin layer demonstrate the qualita-tive agreement of the simulation.
Modeling cellular effects of coal pollutants
International Nuclear Information System (INIS)
The goal of this project is to develop and test models for the dose and dose-rate dependence of biological effects of coal pollutants on mammalian cells in tissue culture. Particular attention is given to the interaction of pollutants with the genetic material (deoxyribonucleic acid, or NDA) in the cell. Unlike radiation, which can interact directly with chromatin, chemical pollutants undergo numerous changes before the ultimate carcinogen becomes covalently bound to the DNA. Synthetic vesicles formed from a phospholipid bilayer are being used to investigate chemical transformations that may occur during the transport of pollutants across cellular membranes. The initial damage to DNA is rapidly modified by enzymatic repair systems in most living organisms. A model has been developed for predicting the effects of excision repair on the survival of human cells exposed to chemical carcinogens. In addition to the excision system, normal human cells also have tolerance mechanisms that permit continued growth and division of cells without removal of the damage. We are investigating the biological effect of damage passed to daughter cells by these tolerance mechanisms
Analytical Modeling of Uplink Cellular Networks
Novlan, Thomas D; Andrews, Jeffrey G
2012-01-01
Cellular uplink analysis has typically been undertaken by either a simple approach that lumps all interference into a single deterministic or random parameter in a Wyner-type model, or via complex system level simulations that often do not provide insight into why various trends are observed. This paper proposes a novel middle way that is both accurate and also results in easy-to-evaluate integral expressions based on the Laplace transform of the interference. We assume mobiles and base stations are randomly placed in the network with each mobile pairing up to its closest base station. The model requires two important changes compared to related recent work on the downlink. First, dependence is introduced between the user and base station point processes to make sure each base station serves a single mobile in the given resource block. Second, per-mobile power control is included, which further couples the locations of the mobiles and their receiving base stations. Nevertheless, we succeed in deriving the cov...
Short-Time Dynamics of Random-Bond Potts Ferromagnet with Continuous Self-Dual Quenched Disorders
Institute of Scientific and Technical Information of China (English)
PAN ZhengQuan; YING HePing; CHEN MeL; GU DeWei
2002-01-01
We present our Monte Carlo results of the random-bond Potts ferromagnet with the Olson-Young self-dual distribution of quenched disorders in two dimensions. By exploring the short-time scaling dynamics, we find the universal power-law critical behavior of the magnetization and Binder cumulant at the critical point, and thus obtain estimates of the dynamic exponent z and magnetic exponent η, as well as the exponent θ. Our special attention is paid to the dynamic process for the q = 8 Potts model.
Local Autoencoding for Parameter Estimation in a Hidden Potts-Markov Random Field.
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
Typhoid fever as cellular microbiological model
Andrade Dahir Ramos de; Andrade Júnior Dahir Ramos de
2003-01-01
The knowledge about typhoid fever pathogenesis is growing in the last years, mainly about the cellular and molecular phenomena that are responsible by clinical manifestations of this disease. In this article are discussed several recent discoveries, as follows: a) Bacterial type III protein secretion system; b) The five virulence genes of Salmonella spp. that encoding Sips (Salmonella invasion protein) A, B, C, D and E, which are capable of induce apoptosis in macrophages; c) The function of ...
Typhoid fever as cellular microbiological model
Directory of Open Access Journals (Sweden)
Andrade Dahir Ramos de
2003-01-01
Full Text Available The knowledge about typhoid fever pathogenesis is growing in the last years, mainly about the cellular and molecular phenomena that are responsible by clinical manifestations of this disease. In this article are discussed several recent discoveries, as follows: a Bacterial type III protein secretion system; b The five virulence genes of Salmonella spp. that encoding Sips (Salmonella invasion protein A, B, C, D and E, which are capable of induce apoptosis in macrophages; c The function of Toll R2 and Toll R4 receptors present in the macrophage surface (discovered in the Drosophila. The Toll family receptors are critical in the signalizing mediated by LPS in macrophages in association with LBP and CD14; d The lines of immune defense between intestinal lumen and internal organs; e The fundamental role of the endothelial cells in the inflammatory deviation from bloodstream into infected tissues by bacteria. In addition to above subjects, the authors comment the correlation between the clinical features of typhoid fever and the cellular and molecular phenomena of this disease, as well as the therapeutic consequences of this knowledge.
Typhoid fever as cellular microbiological model.
de Andrade, Dahir Ramos; de Andrade Júnior, Dahir Ramos
2003-01-01
The knowledge about typhoid fever pathogenesis is growing in the last years, mainly about the cellular and molecular phenomena that are responsible by clinical manifestations of this disease. In this article are discussed several recent discoveries, as follows: a) Bacterial type III protein secretion system; b) The five virulence genes of Salmonella spp. that encoding Sips (Salmonella invasion protein) A, B, C, D and E, which are capable of induce apoptosis in macrophages; c) The function of Toll R2 and Toll R4 receptors present in the macrophage surface (discovered in the Drosophila). The Toll family receptors are critical in the signalizing mediated by LPS in macrophages in association with LBP and CD14; d) The lines of immune defense between intestinal lumen and internal organs; e) The fundamental role of the endothelial cells in the inflammatory deviation from bloodstream into infected tissues by bacteria. In addition to above subjects, the authors comment the correlation between the clinical features of typhoid fever and the cellular and molecular phenomena of this disease, as well as the therapeutic consequences of this knowledge. PMID:14502344
Modeling In Vitro Cellular Responses to Silver Nanoparticles
Directory of Open Access Journals (Sweden)
Dwaipayan Mukherjee
2014-01-01
Full Text Available Engineered nanoparticles (NPs have been widely demonstrated to induce toxic effects to various cell types. In vitro cell exposure systems have high potential for reliable, high throughput screening of nanoparticle toxicity, allowing focusing on particular pathways while excluding unwanted effects due to other cells or tissue dosimetry. The work presented here involves a detailed biologically based computational model of cellular interactions with NPs; it utilizes measurements performed in human cell culture systems in vitro, to develop a mechanistic mathematical model that can support analysis and prediction of in vivo effects of NPs. The model considers basic cellular mechanisms including proliferation, apoptosis, and production of cytokines in response to NPs. This new model is implemented for macrophages and parameterized using in vitro measurements of changes in cellular viability and mRNA levels of cytokines: TNF, IL-1b, IL-6, IL-8, and IL-10. The model includes in vitro cellular dosimetry due to nanoparticle transport and transformation. Furthermore, the model developed here optimizes the essential cellular parameters based on in vitro measurements, and provides a “stepping stone” for the development of more advanced in vivo models that will incorporate additional cellular and NP interactions.
TRAFFIC FLOW MODEL BASED ON CELLULAR AUTOMATION WITH ADAPTIVE DECELERATION
Shinkarev, A. A.
2016-01-01
This paper describes continuation of the authors’ work in the field of traffic flow mathematical models based on the cellular automata theory. The refactored representation of the multifactorial traffic flow model based on the cellular automata theory is used for a representation of an adaptive deceleration step implementation. The adaptive deceleration step in the case of a leader deceleration allows slowing down smoothly but not instantly. Concepts of the number of time steps without confli...
Oh, Eung Seok; Heo, Chaejeong; Kim, Ji Seon; Lee, Young Hee; Kim, Jong Min
2013-05-01
Parkinson's disease (PD) is characterized by progressive dopaminergic cell loss in the substantianigra (SN) and elevated iron levels demonstrated by autopsy and with 7-Tesla magnetic resonance imaging. Direct visualization of iron with live imaging techniques has not yet been successful. The aim of this study is to visualize and quantify the distribution of cellular iron using an intrinsic iron hyperspectral fluorescence signal. The 1-methyl-4-phenylpyridinium (MPP+)-induced cellular model of PD was established in SHSY5Y cells. The cells were exposed to iron by treatment with ferric ammonium citrate (FAC, 100 μM) for up to 6 hours. The hyperspectral fluorescence imaging signal of iron was examined usinga high- resolution dark-field optical microscope system with signal absorption for the visible/ near infrared (VNIR) spectral range. The 6-hour group showed heavy cellular iron deposition compared with the small amount of iron accumulation in the 1-hour group. The cellular iron was dispersed in a small, particulate form, whereas extracellular iron was detected in an aggregated form. In addition, iron particles were found to be concentrated on the cell membrane/edge of shrunken cells. The cellular iron accumulation readily occurred in MPP+-induced cells, which is consistent with previous studies demonstrating elevated iron levels in the SN in PD. This direct iron imaging methodology could be applied to analyze the physiological role of iron in PD, and its application might be expanded to various neurological disorders involving other metals, such as copper, manganese or zinc.
Cellular automaton for realistic modelling of landslides
Directory of Open Access Journals (Sweden)
E. Segre
1995-01-01
Full Text Available A numerical model is developed for the simulation of debris flow in landslides over a complex three dimensional topography. The model is then validated by comparing a simulation with reported field data. Our model is in fact a realistic elaboration of simpler "sandpile automata", which have in recent years been studied as supposedly paradigmatic of "self-organized criticality". Statistics and scaling properties of the simulation are examined, and show that the model has an intermittent behaviour.
Body composition analysis: Cellular level modeling of body component ratios
Z. Wang; Heymsfield, S. B.; PI-SUNYER, F.X.; Gallagher, D.; PIERSON, R.N.
2008-01-01
During the past two decades, a major outgrowth of efforts by our research group at St. Luke’s-Roosevelt Hospital is the development of body composition models that include cellular level models, models based on body component ratios, total body potassium models, multi-component models, and resting energy expenditure-body composition models. This review summarizes these models with emphasis on component ratios that we believe are fundamental to understanding human body composition during growt...
Modeling cellular deformations using the level set formalism
Directory of Open Access Journals (Sweden)
Yang Liu
2008-07-01
Full Text Available Abstract Background Many cellular processes involve substantial shape changes. Traditional simulations of these cell shape changes require that grids and boundaries be moved as the cell's shape evolves. Here we demonstrate that accurate cell shape changes can be recreated using level set methods (LSM, in which the cellular shape is defined implicitly, thereby eschewing the need for updating boundaries. Results We obtain a viscoelastic model of Dictyostelium cells using micropipette aspiration and show how this viscoelastic model can be incorporated into LSM simulations to recreate the observed protrusion of cells into the micropipette faithfully. We also demonstrate the use of our techniques by simulating the cell shape changes elicited by the chemotactic response to an external chemoattractant gradient. Conclusion Our results provide a simple but effective means of incorporating cellular deformations into mathematical simulations of cell signaling. Such methods will be useful for simulating important cellular events such as chemotaxis and cytokinesis.
Computational model of cellular metabolic dynamics
DEFF Research Database (Denmark)
Li, Yanjun; Solomon, Thomas; Haus, Jacob M;
2010-01-01
Identifying the mechanisms by which insulin regulates glucose metabolism in skeletal muscle is critical to understanding the etiology of insulin resistance and type 2 diabetes. Our knowledge of these mechanisms is limited by the difficulty of obtaining in vivo intracellular data. To quantitatively...... cytosol and mitochondria. The model simulated skeletal muscle metabolic responses to insulin corresponding to human hyperinsulinemic-euglycemic clamp studies. Insulin-mediated rate of glucose disposal was the primary model input. For model validation, simulations were compared with experimental data...... type 2 diabetes....
Modeling cellular deformations using the level set formalism
Yang Liu; Effler Janet C; Kutscher Brett L; Sullivan Sarah E; Robinson Douglas N; Iglesias Pablo A
2008-01-01
Abstract Background Many cellular processes involve substantial shape changes. Traditional simulations of these cell shape changes require that grids and boundaries be moved as the cell's shape evolves. Here we demonstrate that accurate cell shape changes can be recreated using level set methods (LSM), in which the cellular shape is defined implicitly, thereby eschewing the need for updating boundaries. Results We obtain a viscoelastic model of Dictyostelium cells using micropipette aspiratio...
Cellular automata modeling of cooperative eutectic growth
E. Olejnik; E. Fraś; D. Gurgul; A. Burbelko
2010-01-01
The model and results of the 2D simulation of the cooperative growth of two phases in the lamellar eutectic are presented. The pro-posed model takes into account heat transfer, components diffusion and nonstationary concentration distribution in the liquid and solid phases, non-equlibrium nature of the phase transformation and kinetics of the growth, influence of the surface energy and interface curva-ture on the conditions of the thermodynamic equilibrium. For the determination of the phase ...
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.
The Pott's puffy tumor: a dangerous sign for intracranial complications.
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
Development and validation of computational models of cellular interaction
Smallwood, R H; Holcombe, W.M.L.; Walker, D C
2004-01-01
In this paper we take the view that computational models of biological systems should satisfy two conditions – they should be able to predict function at a systems biology level, and robust techniques of validation against biological models must be available. A modelling paradigm for developing a predictive computational model of cellular interaction is described, and methods of providing robust validation against biological models are explored, followed by a consideration of soft...
Cellular Automaton Model for Immunology of Tumor Growth
Voitikova, M
1998-01-01
The stochastic discrete space-time model of an immune response on tumor spreading in a two-dimensional square lattice has been developed. The immunity-tumor interactions are described at the cellular level and then transferred into the setting of cellular automata (CA). The multistate CA model for system, in which all statesoflattice sites, composing of both immune and tumor cells populations, are the functions of the states of the 12 nearest neighbors. The CA model incorporates the essential featuresof the immunity-tumor system. Three regimes of neoplastic evolution including metastatic tumor growth and screen effect by inactive immune cells surrounding a tumor have been predicted.
A cellular automata evacuation model considering friction and repulsion
Institute of Scientific and Technical Information of China (English)
SONG Weiguo; YU Yanfei; FAN Weicheng; Zhang Heping
2005-01-01
There exist interactions among pedestrians and between pedestrian and environment in evacuation. These interactions include attraction, repulsion and friction that play key roles in human evacuation behaviors, speed and efficiency. Most former evacuation models focus on the attraction force, while repulsion and friction are not well modeled. As a kind of multi-particle self-driven model, the social force model introduced in recent years can represent those three forces but with low simulation efficiency because it is a continuous model with complex rules. Discrete models such as the cellular automata model and the lattice gas model have simple rules and high simulation efficiency, but are not quite suitable for interactions' simulation. In this paper, a new cellular automata model based on traditional models is introduced in which repulsion and friction are modeled quantitatively. It is indicated that the model can simulate some basic behaviors, e.g.arching and the "faster-is-slower" phenomenon, in evacuation as multi-particle self-driven models, but with high efficiency as the normal cellular automata model and the lattice gas model.
Modeling diffusion of innovations with probabilistic cellular automata
Boccara, Nino; Fuks, Henryk
1997-01-01
We present a family of one-dimensional cellular automata modeling the diffusion of an innovation in a population. Starting from simple deterministic rules, we construct models parameterized by the interaction range and exhibiting a second-order phase transition. We show that the number of individuals who eventually keep adopting the innovation strongly depends on connectivity between individuals.
Modeling integrated cellular machinery using hybrid Petri-Boolean networks.
Directory of Open Access Journals (Sweden)
Natalie Berestovsky
Full Text Available The behavior and phenotypic changes of cells are governed by a cellular circuitry that represents a set of biochemical reactions. Based on biological functions, this circuitry is divided into three types of networks, each encoding for a major biological process: signal transduction, transcription regulation, and metabolism. This division has generally enabled taming computational complexity dealing with the entire system, allowed for using modeling techniques that are specific to each of the components, and achieved separation of the different time scales at which reactions in each of the three networks occur. Nonetheless, with this division comes loss of information and power needed to elucidate certain cellular phenomena. Within the cell, these three types of networks work in tandem, and each produces signals and/or substances that are used by the others to process information and operate normally. Therefore, computational techniques for modeling integrated cellular machinery are needed. In this work, we propose an integrated hybrid model (IHM that combines Petri nets and Boolean networks to model integrated cellular networks. Coupled with a stochastic simulation mechanism, the model simulates the dynamics of the integrated network, and can be perturbed to generate testable hypotheses. Our model is qualitative and is mostly built upon knowledge from the literature and requires fine-tuning of very few parameters. We validated our model on two systems: the transcriptional regulation of glucose metabolism in human cells, and cellular osmoregulation in S. cerevisiae. The model produced results that are in very good agreement with experimental data, and produces valid hypotheses. The abstract nature of our model and the ease of its construction makes it a very good candidate for modeling integrated networks from qualitative data. The results it produces can guide the practitioner to zoom into components and interconnections and investigate them
WWW Business Applications Based on the Cellular Model
Institute of Scientific and Technical Information of China (English)
Toshio Kodama; Tosiyasu L. Kunii; Yoichi Seki
2008-01-01
A cellular model based on the Incrementally Modular Abstraction Hierarchy (IMAH) is a novel model that can represent the architecture of and changes in cyberworlds, preserving invariants from a general level to a specific one. We have developed a data processing system called the Cellular Data System (CDS). In the development of business applications, you can prevent combinatorial explosion in the process of business design and testing by using CDS. In this paper, we have first designed and implemented wide-use algebra on the presentation level. Next, we have developed and verified the effectiveness of two general business applications using CDS: 1) a customer information management system, and 2) an estimate system.
Lattice gas cellular automata and lattice Boltzmann models an introduction
Wolf-Gladrow, Dieter A
2000-01-01
Lattice-gas cellular automata (LGCA) and lattice Boltzmann models (LBM) are relatively new and promising methods for the numerical solution of nonlinear partial differential equations. The book provides an introduction for graduate students and researchers. Working knowledge of calculus is required and experience in PDEs and fluid dynamics is recommended. Some peculiarities of cellular automata are outlined in Chapter 2. The properties of various LGCA and special coding techniques are discussed in Chapter 3. Concepts from statistical mechanics (Chapter 4) provide the necessary theoretical background for LGCA and LBM. The properties of lattice Boltzmann models and a method for their construction are presented in Chapter 5.
Modeling evolution and immune system by cellular automata
Energy Technology Data Exchange (ETDEWEB)
Bezzi, M. [Scuola Internazionale Superiore di Studi Avanzati, Trieste (Italy); Istituto Nazionale di Fisica della Materia, Florence (Italy)
2001-07-01
In this review the behavior of two different biological systems is investigated using cellular automata. Starting from this spatially extended approach it is also tried, in some cases, to reduce the complexity of the system introducing mean-field approximation, and solving (or trying to solve) these simplified systems. It is discussed the biological meaning of the results, the comparison with experimental data (if available) and the different features between spatially extended and mean-field versions. The biological systems considered in this review are the following: Darwinian evolution in simple ecosystems and immune system response. In the first section the main features of molecular evolution are introduced, giving a short survey of genetics for physicists and discussing some models for prebiotic systems and simple ecosystems. It is also introduced a cellular automaton model for studying a set of evolving individuals in a general fitness landscape, considering also the effects of co-evolution. In particular the process of species formation (speciation) is described in sect. 5. The second part deals with immune system modeling. The biological features of immune response are discussed, as well as it is introduced the concept of shape space and of idiotypic network. More detailed reviews which deal with immune system models (mainly focused on idiotypic network models) can be found. Other themes here discussed: the applications of CA to immune system modeling, two complex cellular automata for humoral and cellular immune response. Finally, it is discussed the biological data and the general conclusions are drawn in the last section.
Modeling evolution and immune system by cellular automata
International Nuclear Information System (INIS)
In this review the behavior of two different biological systems is investigated using cellular automata. Starting from this spatially extended approach it is also tried, in some cases, to reduce the complexity of the system introducing mean-field approximation, and solving (or trying to solve) these simplified systems. It is discussed the biological meaning of the results, the comparison with experimental data (if available) and the different features between spatially extended and mean-field versions. The biological systems considered in this review are the following: Darwinian evolution in simple ecosystems and immune system response. In the first section the main features of molecular evolution are introduced, giving a short survey of genetics for physicists and discussing some models for prebiotic systems and simple ecosystems. It is also introduced a cellular automaton model for studying a set of evolving individuals in a general fitness landscape, considering also the effects of co-evolution. In particular the process of species formation (speciation) is described in sect. 5. The second part deals with immune system modeling. The biological features of immune response are discussed, as well as it is introduced the concept of shape space and of idiotypic network. More detailed reviews which deal with immune system models (mainly focused on idiotypic network models) can be found. Other themes here discussed: the applications of CA to immune system modeling, two complex cellular automata for humoral and cellular immune response. Finally, it is discussed the biological data and the general conclusions are drawn in the last section
A sub-cellular viscoelastic model for cell population mechanics.
Directory of Open Access Journals (Sweden)
Yousef Jamali
Full Text Available Understanding the biomechanical properties and the effect of biomechanical force on epithelial cells is key to understanding how epithelial cells form uniquely shaped structures in two or three-dimensional space. Nevertheless, with the limitations and challenges posed by biological experiments at this scale, it becomes advantageous to use mathematical and 'in silico' (computational models as an alternate solution. This paper introduces a single-cell-based model representing the cross section of a typical tissue. Each cell in this model is an individual unit containing several sub-cellular elements, such as the elastic plasma membrane, enclosed viscoelastic elements that play the role of cytoskeleton, and the viscoelastic elements of the cell nucleus. The cell membrane is divided into segments where each segment (or point incorporates the cell's interaction and communication with other cells and its environment. The model is capable of simulating how cells cooperate and contribute to the overall structure and function of a particular tissue; it mimics many aspects of cellular behavior such as cell growth, division, apoptosis and polarization. The model allows for investigation of the biomechanical properties of cells, cell-cell interactions, effect of environment on cellular clusters, and how individual cells work together and contribute to the structure and function of a particular tissue. To evaluate the current approach in modeling different topologies of growing tissues in distinct biochemical conditions of the surrounding media, we model several key cellular phenomena, namely monolayer cell culture, effects of adhesion intensity, growth of epithelial cell through interaction with extra-cellular matrix (ECM, effects of a gap in the ECM, tensegrity and tissue morphogenesis and formation of hollow epithelial acini. The proposed computational model enables one to isolate the effects of biomechanical properties of individual cells and the
Station Model for Rail Transit System Using Cellular Automata
Institute of Scientific and Technical Information of China (English)
XUN Jing; NING Bin; LI Ke-Ping
2009-01-01
In this paper, we propose a new cellular automata model to simulate the railway traffic at station.Based on NaSch model, the proposed station model is composed of the main track and the siding track.Two different schemes for trains passing through station are considered.One is the scheme of "pass by the main track, start and stop by the siding track".The other is the scheme of "two tracks play the same role".We simulate the train movement using the proposed model and analyze the traffic flow at station.The simulation results demonstrate that the proposed cellular automata model can be successfully used for the simulations of railway traffic.Some characteristic behaviors of railway traffic flow can be reproduced.Moreover, the simulation values of the minimum headway are close to the theoretical values.This result demonstrates the dependability and availability of the proposed model.
Cellular worlds: a framework for modeling micro - macro dynamics
H Couclelis
1985-01-01
Cellular spaces have recently received a lot of attention in computer science and elsewhere as models capable of bridging the gap between disaggregate and aggregate description. Despite their obvious spatial interpretation, standard cell-space models are too constrained by their background conventions to be useful in realistic geographic applications. In this paper, a generalization of the cell-space principle is presented, based on discrete model theory, and then applied to a hypothetical bu...
A Modified Cellular Automaton Model for Traffic Flow
Institute of Scientific and Technical Information of China (English)
葛红霞; 董力耘; 雷丽; 戴世强
2004-01-01
A modified cellular automaton model for traffic flow was proposed. A novel concept about the changeable security gap was introduced and a parameter related to the variable security gap was determined. The fundamental diagram obtained by simulation shows that the maximum flow more approaches to the observed data than that of the NaSch model, indicating that the presented model is more reasonable and realistic.
The brittleness model of complex system based on cellular automata
Institute of Scientific and Technical Information of China (English)
LIN De-ming; JIN Hong-zhang; LI Qi; WU Hong-mei
2004-01-01
Now the research on the complex system is a hot spot. Brittleness is one of the basic characteristics of a complex system. In a complex system, after one of subsystems is struck to be collapsed, the whole system will collapse. Meanwhile, cellular automata is a discrete dynamic system. When the rule is given, the cellular automata could be defined. Then it can imitate the complex action. Cellular automata is used to simulate the brittleness action in this study. Entropy was used to analyze the action and get the rule. Then,three normal brittleness models were given. The result shows that the brittleness of complex system is existent and in addition some important behavior mode of complex system brittleness has been achieved.
Modeling evolutionary dynamics of epigenetic mutations in hierarchically organized tumors.
Andrea Sottoriva; Louis Vermeulen; Simon Tavaré
2011-01-01
The cancer stem cell (CSC) concept is a highly debated topic in cancer research. While experimental evidence in favor of the cancer stem cell theory is apparently abundant, the results are often criticized as being difficult to interpret. An important reason for this is that most experimental data that support this model rely on transplantation studies. In this study we use a novel cellular Potts model to elucidate the dynamics of established malignancies that are driven by a small subset of ...
Modeling Evolutionary Dynamics of Epigenetic Mutations in Hierarchically Organized Tumors
Sottoriva, A.; Vermeulen, L; Tavare, S
2011-01-01
The cancer stem cell (CSC) concept is a highly debated topic in cancer research. While experimental evidence in favor of the cancer stem cell theory is apparently abundant, the results are often criticized as being difficult to interpret. An important reason for this is that most experimental data that support this model rely on transplantation studies. In this study we use a novel cellular Potts model to elucidate the dynamics of established malignancies that are driven by a small subset of ...
Fire Spread Model for Old Towns Based on Cellular Automaton
Institute of Scientific and Technical Information of China (English)
GAO Nan; WENG Wenguo; MA Wei; NI Shunjiang; HUANG Quanyi; YUAN Hongyong
2008-01-01
Old towns like Lijiang have enormous historic,artistic,and architectural value.The buildings in such old towns are usually made of highly combustible materials,such as wood and grass.If a fire breaks out,it will spread to multiple buildings,so fire spreading and controlling in old towns need to be studied.This paper presents a fire spread model for old towns based on cellular automaton.The cellular automaton rules were set according to historical fire data in empirical formulas.The model also considered the effects of climate.The simulation results were visualized in a geography information system.An example of a fire spread in Lijiang was investigated with the results showing that this model provides a realistic tool for predicting fire spread in old towns.Fire brigades can use this tool to predict when and how a fire spreads to minimize the losses.
An intelligent floor field cellular automata model for pedestrian dynamics
Kirik, Ekaterina; Krouglov, Dmitriy
2009-01-01
A stochastic cellular automata (CA) model for pedestrian dynamics is presented. Our goal is to simulate different types of pedestrian movement, from regular to panic. But here we emphasize regular situations which imply that pedestrians analyze environment and choose their route more carefully. And transition probabilities have to depict such effect. The potentials of floor fields and environment analysis are combined in the model obtained. People patience is included in the model. This makes simulation of pedestrians movement more realistic. Some simulation results are presented and comparison with basic FF-model is made.
A cellular automata model of Ebola virus dynamics
Burkhead, Emily; Hawkins, Jane
2015-11-01
We construct a stochastic cellular automaton (SCA) model for the spread of the Ebola virus (EBOV). We make substantial modifications to an existing SCA model used for HIV, introduced by others and studied by the authors. We give a rigorous analysis of the similarities between models due to the spread of virus and the typical immune response to it, and the differences which reflect the drastically different timing of the course of EBOV. We demonstrate output from the model and compare it with clinical data.
Car Deceleration Considering Its Own Velocity in Cellular Automata Model
Institute of Scientific and Technical Information of China (English)
LI Ke-Ping
2006-01-01
In this paper, we propose a new cellular automaton model, which is based on NaSch traffic model. In our method, when a car has a larger velocity, if the gap between the car and its leading car is not enough large, it will decrease. The aim is that the following car has a buffer space to decrease its velocity at the next time, and then avoid to decelerate too high. The simulation results show that using our model, the car deceleration is realistic, and is closer to thefield measure than that of NaSch model.
Simulations of Living Cell Origins Using a Cellular Automata Model
Ishida, Takeshi
2014-04-01
Understanding the generalized mechanisms of cell self-assembly is fundamental for applications in various fields, such as mass producing molecular machines in nanotechnology. Thus, the details of real cellular reaction networks and the necessary conditions for self-organized cells must be elucidated. We constructed a 2-dimensional cellular automata model to investigate the emergence of biological cell formation, which incorporated a looped membrane and a membrane-bound information system (akin to a genetic code and gene expression system). In particular, with an artificial reaction system coupled with a thermal system, the simultaneous formation of a looped membrane and an inner reaction process resulted in a more stable structure. These double structures inspired the primitive biological cell formation process from chemical evolution stage. With a model to simulate cellular self-organization in a 2-dimensional cellular automata model, 3 phenomena could be realized: (1) an inner reaction system developed as an information carrier precursor (akin to DNA); (2) a cell border emerged (akin to a cell membrane); and (3) these cell structures could divide into 2. This double-structured cell was considered to be a primary biological cell. The outer loop evolved toward a lipid bilayer membrane, and inner polymeric particles evolved toward precursor information carriers (evolved toward DNA). This model did not completely clarify all the necessary and sufficient conditions for biological cell self-organization. Further, our virtual cells remained unstable and fragile. However, the "garbage bag model" of Dyson proposed that the first living cells were deficient; thus, it would be reasonable that the earliest cells were more unstable and fragile than the simplest current unicellular organisms.
Mathematical model for flood routing based on cellular automaton
Directory of Open Access Journals (Sweden)
Xin CAI
2014-04-01
Full Text Available Increasing frequency and severity of flooding have caused tremendous damage in China, requiring more essential countermeasures to alleviate the damage. In this study, the dynamic simulation property of a cellular automaton was used to make further progress in flood routing. In consideration of terrain’s influence on flood routing, we regarded the terrain elevation as an auxiliary attribute of a two-dimensional cellular automaton in path selection for flood routing and developed a mathematical model based on a cellular automaton. A numerical case of propagation of an outburst flood in an area of the lower Yangtze River was analyzed with both the fixed-step and variable-step models. The results show that the flood does not spread simultaneously in all directions, but flows into the lower place first, and that the submerged area grows quickly at the beginning, but slowly later on. The final submerged areas obtained from the two different models are consistent, and the flood volume balance test shows that the flood volume meets the requirement of the total volume balance. The analysis of the case shows that the proposed model can be a valuable tool for flood routing.
Modeling self-organizing traffic lights with elementary cellular automata
Gershenson, Carlos
2009-01-01
There have been several highway traffic models proposed based on cellular automata. The simplest one is elementary cellular automaton rule 184. We extend this model to city traffic with cellular automata coupled at intersections using only rules 184, 252, and 136. The simplicity of the model offers a clear understanding of the main properties of city traffic and its phase transitions. We use the proposed model to compare two methods for coordinating traffic lights: a green-wave method that tries to optimize phases according to expected flows and a self-organizing method that adapts to the current traffic conditions. The self-organizing method delivers considerable improvements over the green-wave method. For low densities, the self-organizing method promotes the formation and coordination of platoons that flow freely in four directions, i.e. with a maximum velocity and no stops. For medium densities, the method allows a constant usage of the intersections, exploiting their maximum flux capacity. For high dens...
A Cellular Model for Screening Neuronal Nitric Oxide Synthase Inhibitors
Fang, Jianguo; Silverman, Richard B.
2009-01-01
Nitric oxide synthase (NOS) inhibitors are potential drug candidates because it has been well demonstrated that excessive production of NO critically contributes to a range of diseases. Most inhibitors have been screened in vitro using recombinant enzymes, leading to the discovery of a variety of potent compounds. To make inhibition studies more physiologically relevant and bridge the gap between the in vitro assay and in vivo studies, we report here a cellular model for screening NOS inhibit...
Cellular-Based Statistical Model for Mobile Dispersion
Abdulla, Mouhamed; Shayan, Yousef R.
2013-01-01
While analyzing mobile systems we often approximate the actual coverage surface and assume an ideal cell shape. In a multi-cellular network, because of its tessellating nature, a hexagon is more preferred than a circular geometry. Despite this reality, perhaps due to the inherent simplicity, only a model for circular based random spreading is available. However, if used, this results an unfair terminal distribution for non-circular contours. Therefore, in this paper we specifically derived an...
Pott's Puffy Tumor Arising from Frontal Sinusitis
Energy Technology Data Exchange (ETDEWEB)
Lim, Ji Yeon; Kang, Hyun Koo [Seoul Veterans Hospital, Seoul (Korea, Republic of)
2010-02-15
Pott's puffy tumor is an extremely rare and potentially life-threatening complication of frontal sinusitis. We report a case of a 64-year-old man who presented at our emergency department with mild tenderness on the glabellar area and diplopia. Computed Tomography (CT) revealed frontal sinusitis and osteomyelitis of the frontal bone. Following sinus trephination and long-term antibiotic therapy, the patient achieved a complete recovery.
Potts ferromagnet: Transformations and critical exponents in planar hierarchical lattices
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.
Potts ferromagnet: transformations and critical exponents in planar hierarchial lattices
International Nuclear Information System (INIS)
We prove that the duality transformation for a Potts ferromagnet on two-rooted planar hierachical lattices (HL) preserves the thermal eigenvalue. This leads to a relation between the correlation lenght critical exponents v 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 v and α. (author)
Modelling of detonation cellular structure in aluminium suspensions
Briand, A.; Veyssiere, B.; Khasainov, B. A.
2010-12-01
Heterogeneous detonations involving aluminium suspensions have been studied for many years for industrial safety policies, and for military and propulsion applications. Owing to their weak detonability and to the lack of available experimental results on the detonation cellular structure, numerical simulations provide a convenient way to improve the knowledge of such detonations. One major difficulty arising in numerical study of heterogeneous detonations involving suspensions of aluminium particles in oxidizing atmospheres is the modelling of aluminium combustion. Our previous two-step model provided results on the effect on the detonation cellular structure of particle diameter and characteristic chemical lengths. In this study, a hybrid model is incorporated in the numerical code EFAE, combining both kinetic and diffusion regimes in parallel. This more realistic model provides good agreement with the previous two-step model and confirms the correlations found between the detonation cell width, and particle diameter and characteristic lengths. Moreover, the linear dependence found between the detonation cell width and the induction length remains valid with the hybrid model.
A cellular automaton model for tumor growth in heterogeneous environment
Jiao, Yang; Torquato, Sal
2011-03-01
Cancer is not a single disease: it exhibits heterogeneity on different spatial and temporal scales and strongly interacts with its host environment. Most mathematical modeling of malignant tumor growth has assumed a homogeneous host environment. We have developed a cellular automaton model for tumor growth that explicitly incorporates the structural heterogeneity of the host environment such as tumor stroma. We show that these structural heterogeneities have non-trivial effects on the tumor growth dynamics and prognosis. Y. J. is supported by PSOC, NCI.
Cellular automata model of magnetospheric-ionospheric coupling
Kozelov, B. V.; Kozelova, T. V.
2003-01-01
We propose a cellular automata model (CAM) to describe the substorm activity of the magnetospheric-ionospheric system. The state of each cell in the model is described by two numbers that correspond to the energy content in a region of the current sheet in the magnetospheric tail and to the conductivity of the ionospheric domain that is magnetically connected with this region. The driving force of the system is supposed to be provided by the solar wind that is convected along the two b...
A Realistic Cellular Automaton Model for Synchronized Traffic Flow
Institute of Scientific and Technical Information of China (English)
ZHAO Bo-Han; HU Mao-Bin; JIANG Rui; WU Qing-Song
2009-01-01
A cellular automaton model is proposed to consider the anticipation effect in drivers' behavior. It is shown that the anticipation effect can be one of the origins of synchronized traffic flow. With anticipation effect, the congested traffic flow simulated by the model exhibits the features of synchronized flow. The spatiotemporal patterns induced by an on-ramp are also consistent with the three-phaee traffic theory. Since the origin of synchronized flow is still controversial, our work can shed some light on the mechanism of synchronized flow.
Cellular automata modelling of phase-change memories
Institute of Scientific and Technical Information of China (English)
Wanhua Yu; David Wright
2008-01-01
A novel approach to modelling phase-transition processes in phase change materials used for optical and electrical data storage applications is presented. The model is based on a cellular automaton (CA) approach to predict crystallization behaviour that is linked to thermal and electrical simulations to enable the study of the data writing and erasing processes. The CA approach is shown to be able to predict the evolution of the microstructure during the rapid heating and cooling cycles pertinent to data storage technology, and maps crystallization behaviour on the nanoscale. A simple example based on possible future nonvolatile phase-change random access solid-state memory is presented.
[Huge dorsolumbar cold abscess associated with Pott's disease].
Rakotoson, J L; Rakotomizao, J R; Andrianarisoa, A C F
2010-12-01
Pott's disease, or tuberculosis of the spine, is the most common osteoarticular tuberculosis. Among them, dorsolumbar impairment is predominant. The authors report the case of a patient with a huge cold lumbar abscess associated with Pott's disease. The patient is a 32-year-old man presenting dorsolumbar tumefaction associated with an alteration in his general condition and fever for three months. Treatment by "traditional healers" did not provide any improvement. He consulted for mild lumbar pain triggered by fatigue appearing one week before and after the failure of the traditional practitioner. The clinical examination found a temperature of 38.5°C, cachexia, mild lumber kyphosis and impressive, soft, painless and non inflammatory dorsolumbar bruised tumefaction, 40 cm high, 15 cm wide and 7 cm deep. He did not present any neurological signs. The dorsolumbar X-ray of the spine revealed a lesion associated with Pott's disease in the first and second lumbar vertebrae with pinching of the disc, punched-out lesions and osteocondensation. The ultrasound examination of the soft tissue revealed the presence of a laterovertebral collection of fluid diffusing in the subcutaneous region. The psoas major and the paravertebral muscles were not affected. A scan or MRI of the spine was not carried out. Examination of the tissue sample and drainage of the abscess confirmed the tubercular origin. Treatment with tuberculostatic drugs for 12 months associated with immobilisation resulted in a cure with sequelae of mild kyphoscoliosis vertebral statics. PMID:21167445
Modeling and simulation for train control system using cellular automata
Institute of Scientific and Technical Information of China (English)
LI; KePing; GAO; ZiYou; YANG; LiXing
2007-01-01
Train control system plays a key role in railway traffic. Its function is to manage and control the train movement on railway networks. In our previous works, based on the cellular automata (CA) model, we proposed several models and algorithms for simulating the train movement under different control system conditions. However, these models are only suitable for some simple traffic conditions. Some basic factors, which are important for train movement, are not considered. In this paper, we extend these models and algorithms and give a unified formula. Using the proposed method, we analyze and discuss the space-time diagram of railway traffic flow and the trajectories of the train movement. The numerical simulation and analytical results demonstrate that the unified CA model is an effective tool for simulating the train control system.
Cellular automaton model considering headway-distance effect
Hu, Shou-Xin; Gao, Kun; Wang, Bing-Hong; Lu, Yu-Feng
2008-05-01
This paper presents a cellular automaton model for single-lane traffic flow. On the basis of the Nagel-Schreckenberg (NS) model, it further considers the effect of headway-distance between two successive cars on the randomization of the latter one. In numerical simulations, this model shows the following characteristics. (1) With a simple structure, this model succeeds in reproducing the hysteresis effect, which is absent in the NS model. (2) Compared with the slow-to-start models, this model exhibits a local fundamental diagram which is more consistent to empirical observations. (3) This model has much higher efficiency in dissolving congestions compared with the so-called NS model with velocity-dependent randomization (VDR model). (4) This model is more robust when facing traffic obstructions. It can resist much longer shock times and has much shorter relaxation times on the other hand. To summarize, compared with the existing models, this model is quite simple in structure, but has good characteristics.
Structural modeling of sandwich structures with lightweight cellular cores
Institute of Scientific and Technical Information of China (English)
T. Liu; Z. C. Deng; T. J. Lu
2007-01-01
An effective single layered finite element (FE) computational model is proposed to predict the structural behavior of lightweight sandwich panels having two dimensional (2D) prismatic or three dimensional (3D) truss cores.Three different types of cellular core topology are considered: pyramidal truss core (3D), Kagome truss core (3D) and corrugated core (2D), representing three kinds of material anisotropy: orthotropic, monoclinic and general anisotropic. A homogenization technique is developed to obtain the homogenized macroscopic stiffness properties of the cellular core. In comparison with the results obtained by using detailed FE model, the single layered computational model cangive acceptable predictions for both the static and dynamic behaviors of orthotropic truss core sandwich panels. However, for non-orthotropic 3D truss cores, the predictions are not so well. For both static and dynamic behaviors of a 2D corrugated core sandwich panel, the predictions derived by the single layered computational model is generally acceptable when the size of the unit cell varies within a certain range, with the predictions for moderately strong or strong corrugated cores more accurate than those for weak cores.
A Fluid Model for Performance Analysis in Cellular Networks
Directory of Open Access Journals (Sweden)
Coupechoux Marceau
2010-01-01
Full Text Available We propose a new framework to study the performance of cellular networks using a fluid model and we derive from this model analytical formulas for interference, outage probability, and spatial outage probability. The key idea of the fluid model is to consider the discrete base station (BS entities as a continuum of transmitters that are spatially distributed in the network. This model allows us to obtain simple analytical expressions to reveal main characteristics of the network. In this paper, we focus on the downlink other-cell interference factor (OCIF, which is defined for a given user as the ratio of its outer cell received power to its inner cell received power. A closed-form formula of the OCIF is provided in this paper. From this formula, we are able to obtain the global outage probability as well as the spatial outage probability, which depends on the location of a mobile station (MS initiating a new call. Our analytical results are compared to Monte Carlo simulations performed in a traditional hexagonal network. Furthermore, we demonstrate an application of the outage probability related to cell breathing and densification of cellular networks.
Integrating cellular metabolism into a multiscale whole-body model.
Directory of Open Access Journals (Sweden)
Markus Krauss
Full Text Available Cellular metabolism continuously processes an enormous range of external compounds into endogenous metabolites and is as such a key element in human physiology. The multifaceted physiological role of the metabolic network fulfilling the catalytic conversions can only be fully understood from a whole-body perspective where the causal interplay of the metabolic states of individual cells, the surrounding tissue and the whole organism are simultaneously considered. We here present an approach relying on dynamic flux balance analysis that allows the integration of metabolic networks at the cellular scale into standardized physiologically-based pharmacokinetic models at the whole-body level. To evaluate our approach we integrated a genome-scale network reconstruction of a human hepatocyte into the liver tissue of a physiologically-based pharmacokinetic model of a human adult. The resulting multiscale model was used to investigate hyperuricemia therapy, ammonia detoxification and paracetamol-induced toxication at a systems level. The specific models simultaneously integrate multiple layers of biological organization and offer mechanistic insights into pathology and medication. The approach presented may in future support a mechanistic understanding in diagnostics and drug development.
Robustness of a Cellular Automata Model for the HIV Infection
Figueirêdo, P H; Santos, R M Zorzenon dos
2008-01-01
An investigation was conducted to study the robustness of the results obtained from the cellular automata model which describes the spread of the HIV infection within lymphoid tissues [R. M. Zorzenon dos Santos and S. Coutinho, Phys. Rev. Lett. 87, 168102 (2001)]. The analysis focussed on the dynamic behavior of the model when defined in lattices with different symmetries and dimensionalities. The results illustrated that the three-phase dynamics of the planar models suffered minor changes in relation to lattice symmetry variations and, while differences were observed regarding dimensionality changes, qualitative behavior was preserved. A further investigation was conducted into primary infection and sensitiveness of the latency period to variations of the model's stochastic parameters over wide ranging values. The variables characterizing primary infection and the latency period exhibited power-law behavior when the stochastic parameters varied over a few orders of magnitude. The power-law exponents were app...
Fluctuation in option pricing using cellular automata based market models
Gao, Yuying; Beni, Gerardo
2005-05-01
A new agent-based Cellular Automaton (CA) computational algorithm for option pricing is proposed. CAs have been extensively used in modeling complex dynamical systems but not in modeling option prices. Compared with traditional tools, which rely on guessing volatilities to calculate option prices, the CA model is directly addressing market mechanisms and simulates price fluctuation from aggregation of actions made by interacting individual market makers in a large population. This paper explores whether CA models can provide reasonable good answers to pricing European options. The Black-Scholes model and the Binomial Tree model are used for comparison. Comparison reveals that CA models perform reasonably well in pricing options, reproducing overall characteristics of random walk based model, while at the same time providing plausible results for the 'fat-tail' phenomenon observed in many markets. We also show that the binomial tree model can be obtained from a CA rule. Thus, CA models are suitable tools to generalize the standard theories of option pricing.
Simulation of root forms using cellular automata model
International Nuclear Information System (INIS)
This research aims to produce a simulation program for root forms using cellular automata model. Stephen Wolfram in his book entitled “A New Kind of Science” discusses the formation rules based on the statistical analysis. In accordance with Stephen Wolfram’s investigation, the research will develop a basic idea of computer program using Delphi 7 programming language. To best of our knowledge, there is no previous research developing a simulation describing root forms using the cellular automata model compared to the natural root form with the presence of stone addition as the disturbance. The result shows that (1) the simulation used four rules comparing results of the program towards the natural photographs and each rule had shown different root forms; (2) the stone disturbances prevent the root growth and the multiplication of root forms had been successfully modeled. Therefore, this research had added some stones, which have size of 120 cells placed randomly in the soil. Like in nature, stones cannot be penetrated by plant roots. The result showed that it is very likely to further develop the program of simulating root forms by 50 variations
Simulation of root forms using cellular automata model
Winarno, Nanang; Prima, Eka Cahya; Afifah, Ratih Mega Ayu
2016-02-01
This research aims to produce a simulation program for root forms using cellular automata model. Stephen Wolfram in his book entitled "A New Kind of Science" discusses the formation rules based on the statistical analysis. In accordance with Stephen Wolfram's investigation, the research will develop a basic idea of computer program using Delphi 7 programming language. To best of our knowledge, there is no previous research developing a simulation describing root forms using the cellular automata model compared to the natural root form with the presence of stone addition as the disturbance. The result shows that (1) the simulation used four rules comparing results of the program towards the natural photographs and each rule had shown different root forms; (2) the stone disturbances prevent the root growth and the multiplication of root forms had been successfully modeled. Therefore, this research had added some stones, which have size of 120 cells placed randomly in the soil. Like in nature, stones cannot be penetrated by plant roots. The result showed that it is very likely to further develop the program of simulating root forms by 50 variations.
Simulation of root forms using cellular automata model
Energy Technology Data Exchange (ETDEWEB)
Winarno, Nanang, E-mail: nanang-winarno@upi.edu; Prima, Eka Cahya [International Program on Science Education, Universitas Pendidikan Indonesia, Jl. Dr. Setiabudi no 229, Bandung40154 (Indonesia); Afifah, Ratih Mega Ayu [Department of Physics Education, Post Graduate School, Universitas Pendidikan Indonesia, Jl. Dr. Setiabudi no 229, Bandung40154 (Indonesia)
2016-02-08
This research aims to produce a simulation program for root forms using cellular automata model. Stephen Wolfram in his book entitled “A New Kind of Science” discusses the formation rules based on the statistical analysis. In accordance with Stephen Wolfram’s investigation, the research will develop a basic idea of computer program using Delphi 7 programming language. To best of our knowledge, there is no previous research developing a simulation describing root forms using the cellular automata model compared to the natural root form with the presence of stone addition as the disturbance. The result shows that (1) the simulation used four rules comparing results of the program towards the natural photographs and each rule had shown different root forms; (2) the stone disturbances prevent the root growth and the multiplication of root forms had been successfully modeled. Therefore, this research had added some stones, which have size of 120 cells placed randomly in the soil. Like in nature, stones cannot be penetrated by plant roots. The result showed that it is very likely to further develop the program of simulating root forms by 50 variations.
National Oceanic and Atmospheric Administration, Department of Commerce — The purpose of this project is to adapt cellular in vitro assay systems of the rainbow trout pituitary, liver and ovary for high-throughput screening (HTS) of...
Cellular automaton model of cell response to targeted radiation
International Nuclear Information System (INIS)
It has been shown that the response of cells to low doses of radiation is not linear and cannot be accurately extrapolated from the high dose response. To investigate possible mechanisms involved in the behaviour of cells under very low doses of radiation, a cellular automaton (CA) model was created. The diffusion and consumption of glucose in the culture dish were computed in parallel to the growth of cells. A new model for calculating survival probability was introduced; the communication between targeted and non-targeted cells was also included. Early results on the response of non-confluent cells to targeted irradiation showed the capability of the model to take account for the non-linear response in the low-dose domain
Cellular automaton model of coupled mass transport and chemical reactions
International Nuclear Information System (INIS)
Mass transport, coupled with chemical reactions, is modelled as a cellular automaton in which solute molecules perform a random walk on a lattice and react according to a local probabilistic rule. Assuming molecular chaos and a smooth density function, we obtain the standard reaction-transport equations in the continuum limit. The model is applied to the reactions a + b ↔c and a + b →c, where we observe interesting macroscopic effects resulting from microscopic fluctuations and spatial correlations between molecules. We also simulate autocatalytic reaction schemes displaying spontaneous formation of spatial concentration patterns. Finally, we propose and discuss the limitations of a simple model for mineral-solute interaction. (author) 5 figs., 20 refs
Global Network Model based on Earth Grid and Cellular
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Dongqi Lu
2014-06-01
Full Text Available We aim to understand the current health state of the Earth and find how human activities influence it. Based on the theory of Earth’s Grid and Cellular Automata, we define and test a global network model, analyze the mutual interactions and feedbacks of ecosystem, hydrologic circle and atmosphere. In addition, we consult a lot of data to find a benchmark for the “Earth Health Map”, with the ecosystem distribution on it, which can be helpful for making a strategic decision for policy makers and prediction. Our model can be extended to other similar fields. In the end, we discuss the sensitivity of parameters selection, and the superiorities and weaknesses of our model.
A cellular automata-based mathematical model for thymocyte development.
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Hallan Souza-e-Silva
Full Text Available Intrathymic T cell development is an important process necessary for the normal formation of cell-mediated immune responses. Importantly, such a process depends on interactions of developing thymocytes with cellular and extracellular elements of the thymic microenvironment. Additionally, it includes a series of oriented and tunely regulated migration events, ultimately allowing mature cells to cross endothelial barriers and leave the organ. Herein we built a cellular automata-based mathematical model for thymocyte migration and development. The rules comprised in this model take into account the main stages of thymocyte development, two-dimensional sections of the normal thymic microenvironmental network, as well as the chemokines involved in intrathymic cell migration. Parameters of our computer simulations with further adjusted to results derived from previous experimental data using sub-lethally irradiated mice, in which thymus recovery can be evaluated. The model fitted with the increasing numbers of each CD4/CD8-defined thymocyte subset. It was further validated since it fitted with the times of permanence experimentally ascertained in each CD4/CD8-defined differentiation stage. Importantly, correlations using the whole mean volume of young normal adult mice revealed that the numbers of cells generated in silico with the mathematical model fall within the range of total thymocyte numbers seen in these animals. Furthermore, simulations made with a human thymic epithelial network using the same mathematical model generated similar profiles for temporal evolution of thymocyte developmental stages. Lastly, we provided in silico evidence that the thymus architecture is important in the thymocyte development, since changes in the epithelial network result in different theoretical profiles for T cell development/migration. This model likely can be used to predict thymocyte evolution following therapeutic strategies designed for recovery of the
Motor Schema-Based Cellular Automaton Model for Pedestrian Dynamics
Weng, Wenguo; Hasemi, Yuji; Fan, Weicheng
A new cellular automaton model for pedestrian dynamics based on motor schema is presented. Each pedestrian is treated as an intelligent mobile robot, and motor schemas including move-to-goal, avoid-away and avoid-around drive pedestrians to interact with their environment. We investigate the phenomenon of many pedestrians with different move velocities escaping from a room. The results show that the pedestrian with high velocity have predominance in competitive evacuation, if we only consider repulsion from or avoiding around other pedestrians, and interaction with each other leads to disordered evacuation, i.e., decreased evacuation efficiency. Extensions of the model using learning algorithms for controlling pedestrians, i.e., reinforcement learning, neural network and genetic algorithms, etc. are noted.
Critical Behavior in a Cellular Automata Animal Disease Transmission Model
Morley, P D; Chang, Julius
2003-01-01
Using a cellular automata model, we simulate the British Government Policy (BGP) in the 2001 foot and mouth epidemic in Great Britain. When clinical symptoms of the disease appeared on a farm, there is mandatory slaughter (culling) of all livestock on an infected premise (IP). Those farms that neighbor an IP (contiguous premise, CP), are also culled, aka nearest neighbor interaction. Farms where the disease may be prevalent from animal, human, vehicle or airborne transmission (dangerous contact, DC), are additionally culled, aka next-to-nearest neighbor iteractions and lightning factor. The resulting mathematical model possesses a phase transition, whereupon if the physical disease transmission kernel exceeds a critical value, catastrophic loss of animals ensues. The non-local disease transport probability can be as low as .01% per day and the disease can still be in the high mortality phase. We show that the fundamental equation for sustainable disease transport is the criticality equation for neutron fissio...
Computer Modeling of the Earliest Cellular Structures and Functions
Pohorille, Andrew
2000-03-01
In the absence of extinct or extant record of protocells (the earliest ancestors of contemporary cells), the most direct way to test ourunderstanding of the origin of cellular life is to construct laboratory models of protocells. Such efforts are currently underway in the NASA Astrobiology Program. They are accompanied by computational studies aimed at explaining self-organization of simple molecules into ordered structures and developing designs for molecules that perform protocellular functions. Many of these functions, such as import of nutrients, capture and storage of energy, and response to changes in the environment are carried out by proteins bound to membranes. We will discuss a series of large-scale, molecular-level computer simulations which demonstrate (a) how small proteins (peptides)organize themselves into ordered structures at water-membrane interfaces and insert into membranes, (b) how these peptides aggregate to form membrane-spanning structures (e.g. channels), and (c) by what mechanisms such aggregates perform essential protocellular functions, such as proton transport of protons across cell walls, a key step in cellular bioenergetics. The simulations were performed using the molecular dynamics method, in which Newton's equations of motion for each atom in the system are solved iteratively. The problems of interest required simulations on multi-nanosecond time scales, which corresponded to 10^6-10^8 time steps.
Pott's Disease in a Pediatric Patient. A Case Report
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Lourdes Marimón Amador
2014-08-01
Full Text Available The case of a four-year old boy with Pott's disease diagnosed by clinical, radiological and laboratory study at the Guido Valladares National Hospital in East Timor is presented. Inquiries about the etiopathogenesis of the disease in relation to the family and personal history were conducted. This is a very complex and clinically important case since a rare and serious complication was observed in the child. It is concluded that early diagnosis of this condition is essential due to its poor prognosis once developed.
Credit Default Swaps and Insurance: Against the Potts Opinion
Juurikkala, Oskari
2011-01-01
Little attention has been given to the possibility that CDS transactions might be construed as insurance contracts in English law. This article challenges the widespread âPotts opinionâ, which states that CDSs are not insurance, because they do not require the protection buyer to sustain a loss or to have an insurable interest in the subject matter. CDSs often do provide protection against loss that the buyer is exposed to; loss indemnity is not a necessary characterisation of an insuranc...
Load-Aware Modeling and Analysis of Heterogeneous Cellular Networks
Dhillon, Harpreet S; Andrews, Jeffrey G
2012-01-01
Random spatial models are attractive for modeling heterogeneous cellular networks (HCNs) due to their realism, tractability, and scalability. A major limitation of such models to date in the context of HCNs is the neglect of network traffic and load: all base stations (BSs) have typically been assumed to always be transmitting. Small cells in particular will have a lighter load than macrocells, and so their contribution to the network interference may be significantly overstated in a fully loaded model. This paper incorporates a flexible notion of BS load by introducing a new idea of conditionally thinning the interference field. For a $K$-tier HCN where BSs across tiers differ in terms of transmit power, supported data rate, deployment density, and now load, we derive the coverage probability for a typical mobile, which connects to the strongest BS signal. Conditioned on this connection, the interfering BSs of the $i^{th}$ tier are assumed to transmit independently with probability $p_i$, which models the lo...
A Computational Model of Cellular Response to Modulated Radiation Fields
International Nuclear Information System (INIS)
Purpose: To develop a model to describe the response of cell populations to spatially modulated radiation exposures of relevance to advanced radiotherapies. Materials and Methods: A Monte Carlo model of cellular radiation response was developed. This model incorporated damage from both direct radiation and intercellular communication including bystander signaling. The predictions of this model were compared to previously measured survival curves for a normal human fibroblast line (AGO1522) and prostate tumor cells (DU145) exposed to spatially modulated fields. Results: The model was found to be able to accurately reproduce cell survival both in populations which were directly exposed to radiation and those which were outside the primary treatment field. The model predicts that the bystander effect makes a significant contribution to cell killing even in uniformly irradiated cells. The bystander effect contribution varies strongly with dose, falling from a high of 80% at low doses to 25% and 50% at 4 Gy for AGO1522 and DU145 cells, respectively. This was verified using the inducible nitric oxide synthase inhibitor aminoguanidine to inhibit the bystander effect in cells exposed to different doses, which showed significantly larger reductions in cell killing at lower doses. Conclusions: The model presented in this work accurately reproduces cell survival following modulated radiation exposures, both in and out of the primary treatment field, by incorporating a bystander component. In addition, the model suggests that the bystander effect is responsible for a significant portion of cell killing in uniformly irradiated cells, 50% and 70% at doses of 2 Gy in AGO1522 and DU145 cells, respectively. This description is a significant departure from accepted radiobiological models and may have a significant impact on optimization of treatment planning approaches if proven to be applicable in vivo.
A cellular automaton model for neurogenesis in Drosophila
Luthi, Pascal O.; Chopard, Bastien; Preiss, Anette; Ramsden, Jeremy J.
1998-07-01
A cellular automaton (CA) is constructed for the formation of the central nervous system of the Drosophila embryo. This is an experimentally well-studied system in which complex interactions between neighbouring cells appear to drive their differentiation into different types. It appears that all the cells initially have the potential to become neuroblasts, and all strive to this end, but those which differentiate first block their as yet undifferentiated neighbours from doing so. The CA makes use of observational evidence for a lateral inhibition mechanism involving signalling products S of the ‘proneural’ or neuralizing genes. The key concept of the model is that cells are continuously producing S, but the production rate is lowered by inhibitory signals received from neighbouring cells which have advanced further along the developmental pathway. Comparison with experimental data shows that it well accounts for the observed proportion of neuroectodermal cells delaminating as neuroblasts.
Cellular automaton model of mass transport with chemical reactions
International Nuclear Information System (INIS)
The transport and chemical reactions of solutes are modelled as a cellular automaton in which molecules of different species perform a random walk on a regular lattice and react according to a local probabilistic rule. The model describes advection and diffusion in a simple way, and as no restriction is placed on the number of particles at a lattice site, it is also able to describe a wide variety of chemical reactions. Assuming molecular chaos and a smooth density function, we obtain the standard reaction-transport equations in the continuum limit. Simulations on one-and two-dimensional lattices show that the discrete model can be used to approximate the solutions of the continuum equations. We discuss discrepancies which arise from correlations between molecules and how these discrepancies disappear as the continuum limit is approached. Of particular interest are simulations displaying long-time behaviour which depends on long-wavelength statistical fluctuations not accounted for by the standard equations. The model is applied to the reactions a + b ↔ c and a + b → c with homogeneous and inhomogeneous initial conditions as well as to systems subject to autocatalytic reactions and displaying spontaneous formation of spatial concentration patterns. (author) 9 figs., 34 refs
COMPARATIVE ANALYSIS OF CONGESTION CONTROL MODELS FOR CELLULAR WIRELESS NETWORK
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Falade A. J
2015-08-01
Full Text Available Cellular wireless systems like GSM suffer from congestion resulting in overall system degradation and poor service delivery. When the traffic demand in a geographical area is high, the input traffic rate will exceed thecapacity of the output lines. This work focused on homogenous wireless network (the network traffic and resource dimensioning that are statistically identical such that the network performance evaluation can be reduced to a system with single cell and a single traffic type. Such system can employa queuing model to evaluate the performance metric of a cell in terms of blocking probability. Five congestion control models were compared in the work to ascertain their peculiarities, they are Erlang B, Erlang C, Engset (cleared, Engset (buffered, and Bernoulli. To analyze the system, an aggregate onedimensional Markov chain wasderived, such that it describes a call arrival process under the assumption that it is Poisson distributed. The models were simulated and their results show varying performances, however the Bernoulli model (Pb5 tends to show a situation that allows more users access to the system and the congestion level remain unaffected despite increase in the number of users and the offered traffic into the system.
Cellular automaton model of crowd evacuation inspired by slime mould
Kalogeiton, V. S.; Papadopoulos, D. P.; Georgilas, I. P.; Sirakoulis, G. Ch.; Adamatzky, A. I.
2015-04-01
In all the living organisms, the self-preservation behaviour is almost universal. Even the most simple of living organisms, like slime mould, is typically under intense selective pressure to evolve a response to ensure their evolution and safety in the best possible way. On the other hand, evacuation of a place can be easily characterized as one of the most stressful situations for the individuals taking part on it. Taking inspiration from the slime mould behaviour, we are introducing a computational bio-inspired model crowd evacuation model. Cellular Automata (CA) were selected as a fully parallel advanced computation tool able to mimic the Physarum's behaviour. In particular, the proposed CA model takes into account while mimicking the Physarum foraging process, the food diffusion, the organism's growth, the creation of tubes for each organism, the selection of optimum tube for each human in correspondence to the crowd evacuation under study and finally, the movement of all humans at each time step towards near exit. To test the model's efficiency and robustness, several simulation scenarios were proposed both in virtual and real-life indoor environments (namely, the first floor of office building B of the Department of Electrical and Computer Engineering of Democritus University of Thrace). The proposed model is further evaluated in a purely quantitative way by comparing the simulation results with the corresponding ones from the bibliography taken by real data. The examined fundamental diagrams of velocity-density and flow-density are found in full agreement with many of the already published corresponding results proving the adequacy, the fitness and the resulting dynamics of the model. Finally, several real Physarum experiments were conducted in an archetype of the aforementioned real-life environment proving at last that the proposed model succeeded in reproducing sufficiently the Physarum's recorded behaviour derived from observation of the aforementioned
Some properties of the floor field cellular automata evacuation model
Gwizdałła, Tomasz M.
2015-02-01
We study the process of evacuation of pedestrians from the room with the given arrangement of doors and obstacles by using the cellular automata technique. The technique which became quite popular is characterized by the discretization of time as well as space. For such a discretized space we use so-called floor field model which generally corresponds to the description of every cell by some monotonic function of distance between this cell and the closest exit. We study several types of effects. We start from some general features of model like the kind of a neighborhood or the factors disrupting the motion. Then we analyze the influence of asymmetry and size on the evacuation time. Finally we show characteristics concerning different arrangements of exits and include a particular approach to the proxemics effects. The scaling analyses help us to distinguish these cases which just reflect the geometry of the system and those which depend also on the simulation properties. All calculations are performed for a wide range of initial densities corresponding to different occupation rates as described by the typical crowd counting techniques.
From equilibrium spin models to probabilistic cellular automata
International Nuclear Information System (INIS)
The general equivalence between D-dimensional probabilistic cellular automata (PCA) and (D + 1)-dimensional equilibrium spin models satisfying a disorder condition is first described in a pedagogical way and then used to analyze the phase diagrams, the critical behavior, and the universality classes of some automato. Diagrammatic representations of time-dependent correlation functions PCA are introduced. Two important classes of PCA are singled out for which these correlation functions simplify: (1) Quasi-Hamiltonian automata, which have a current-carrying steady state, and for which some correlation functions are those of a D-dimensional static model PCA satisfying the detailed balance condition appear as a particular case of these rules for which the current vanishes. (2) Linear (and more generally affine) PCA for which the diagrammatics reduces to a random walk problem closely related to (D + 1)-dimensional directed SAWs: both problems display a critical behavior with mean-field exponents in any dimension. The correlation length and effective velocity of propagation of excitations can be calculated for affine PCA, as is shown on an explicit D = 1 example. The authors conclude with some remarks on nonlinear PCA, for which the diagrammatics is related to reaction-diffusion processes, and which belong in some cases to the universality class of Reggeon field theory
Modeling chemical systems using cellular automata a textbook and laboratory manual
Kier, Lemont B; Cheng, Chao-Kun
2006-01-01
Provides a practical introduction to an exciting modeling paradigm for complex systems. This book discusses the nature of scientific inquiry using models and simulations, and describes the nature of cellular automata models. It gives descriptions of how cellular automata models can be used in the study of a variety of phenomena.
Relationship between cellular response models and biochemical mechanisms
International Nuclear Information System (INIS)
In most cellular response experiments, survival reflects the kinetics of a variety of damage and repair processes. Unfortunately, biochemical studies of molecular repair deal with mechanisms which cannot be readily correlated with these kinetic observations. The difference in these approaches sometimes leads to confusion over terms such as potentially-lethal and sublethal damage. These terms were introduced with operation definitions, derived from kinetic studies of cell survival, but some researchers have since attempted to associate them with specific biochemical mechanisms. Consequently, the terms are often used in totally different ways be different investigators. The use of carefully constructed models originating either out of assumptions based on mechanisms, or on kinetics, can be used to design experiments to eliminate some alternative kinetic schemes. In turn, some mechanisms may also be eliminated, resulting in a reduction in the number of mechanisms which must be investigated biochemically. One must take advantage of a wide range of specialized radiation procedures in order to accomplish this. Examples of the use of such specialized experimental designs, which have led to a more detailed understanding of the kinetics of both algal and mammalian cell responses, are discussed
Modeling and Performance Analyses of Hybrid Cellular and Broadcasting Networks
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Peter Unger
2009-01-01
Full Text Available Mobile communication services are getting more and more important and, in particular, multimedia services have attracted the interest of the users. Mobile TV is one of the most demanded candidates. Powerful and efficient communication systems are needed, which provide high capacities, especially at the downlink. Furthermore, interactivity is essential for supporting the user needs and to extend the service offering. As one possible solution to meet the mentioned requirements, we consider the combination of the cellular network UMTS and the mobile broadcast network DVB-H, which form a hybrid network. We investigate the performance of hybrid networks and develop a system model, which describes the hybrid network and the load switching between both networks. One of the contributions is the definition of the switching bound concept, which represents an efficient tool to assess the necessity and the feasibility of hybrid networks and the amount of load switching. The performance indicators cell load and grade of service are analyzed by using theoretical and realistic scenarios.
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Chang-Hua Zou
2009-01-01
Full Text Available Problem statement: Cardiovascular Diseases (CVD continued to be the leading cause of death. Failure or abnormal cardiac cellular or sub-cellular vibrations (oscillations could lead failure or abnormal heart beats that could cause CVD. Understanding the mechanisms of the vibrations (oscillations could help to prevent or to treat the diseases. Scientists have studied the mechanisms for more than 100 years. To our knowledge, the mechanisms are still unclear today. In this investigation, based on published data or results, conservation laws of the momentum as well as the energy, in views of biology, biochemistry, informatics and physics (BioChemInfoPhysics, we proposed our models of cardiac cellular and sub-cellular vibrations (oscillations of biological components, such as free ions in Biological Fluids (BF, Biological Membranes (BM, Ca++H+ (Ca++ and Na+K+ ATPases, Na+Ca++ exchangers (NCX, Ca++ carriers and myosin heads. Approach: Our models were described with 4-D (x, y, z, t or r, ?, z, t momentum transfer equations in mathematical physics. Results: The momentum transfer equations were solved with free and forced, damped, un-damped and over-damped, vibrations (oscillations. The biological components could be modeled as resonators or vibrators (oscillators, such as liquid plasmas, membranes, active springs, passive springs and active swings. Conclusion: We systematically provided new insights of automation (ignition and maintain, transportation, propagation and orientation of the cardiac cellular and sub-cellular vibrations (oscillations and resonances, with our BioChemInfoPhysics models of 4-D momentum transfer equations. Our modeling results implied: Auto-rhythmic cells (Sinoatrial Node Cells (SANC, Atrioventricular Node Cells (AVNC, Purkinje fibers, non-Auto-rhythmic ventricular myocytes and their Sarcoplasmic Reticulums (SR work as Biological Liquid Plasma Resonators (BLPR. The resonators were
Cellular automata model of magnetospheric-ionospheric coupling
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B. V. Kozelov
Full Text Available We propose a cellular automata model (CAM to describe the substorm activity of the magnetospheric-ionospheric system. The state of each cell in the model is described by two numbers that correspond to the energy content in a region of the current sheet in the magnetospheric tail and to the conductivity of the ionospheric domain that is magnetically connected with this region. The driving force of the system is supposed to be provided by the solar wind that is convected along the two boundaries of the system. The energy flux inside is ensured by the penetration of the energy from the solar wind into the array of cells (magnetospheric tail with a finite velocity. The third boundary (near to the Earth is closed and the fourth boundary is opened, thereby modeling the flux far away from the tail. The energy dissipation in the system is quite similar to other CAM models, when the energy in a particular cell exceeds some pre-defined threshold, and the part of the energy excess is redistributed between the neighbouring cells. The second number attributed to each cell mimics ionospheric conductivity that can allow for a part of the energy to be shed on field-aligned currents. The feedback between "ionosphere" and "magnetospheric tail" is provided by the change in a part of the energy, which is redistributed in the tail when the threshold is surpassed. The control parameter of the model is the z-component of the interplanetary magnetic field (Bz IMF, "frozen" into the solar wind. To study the internal dynamics of the system at the beginning, this control parameter is taken to be constant. The dynamics of the system undergoes several bifurcations, when the constant varies from - 0.6 to - 6.0. The Bz IMF input results in the periodic transients (activation regions and the inter-transient period decreases with the decrease of Bz. At the same time the onset of activations in the array shifts towards the "Earth". When the modulus of the Bz IMF exceeds some
Millimeter Wave Channel Modeling and Cellular Capacity Evaluation
Akdeniz, Mustafa Riza; Liu, Yuanpeng; Samimi, Mathew K.; Sun, Shu; Rangan, Sundeep; Rappaport, Theodore S.; Erkip, Elza
2013-01-01
With the severe spectrum shortage in conventional cellular bands, millimeter wave (mmW) frequencies between 30 and 300 GHz have been attracting growing attention as a possible candidate for next-generation micro- and picocellular wireless networks. The mmW bands offer orders of magnitude greater spectrum than current cellular allocations and enable very high-dimensional antenna arrays for further gains via beamforming and spatial multiplexing. This paper uses recent real-world measurements at...
A Cellular Automata Model for the Study of Landslides
Liucci, Luisa; Suteanu, Cristian; Melelli, Laura
2016-04-01
Power-law scaling has been observed in the frequency distribution of landslide sizes in many regions of the world, for landslides triggered by different factors, and in both multi-temporal and post-event datasets, thus indicating the universal character of this property of landslides and suggesting that the same mechanisms drive the dynamics of mass wasting processes. The reasons for the scaling behavior of landslide sizes are widely debated, since their understanding would improve our knowledge of the spatial and temporal evolution of this phenomenon. Self-Organized Critical (SOC) dynamics and the key role of topography have been suggested as possible explanations. The scaling exponent of the landslide size-frequency distribution defines the probability of landslide magnitudes and it thus represents an important parameter for hazard assessment. Therefore, another - still unanswered - important question concerns the factors on which its value depends. This paper investigates these issues using a Cellular Automata (CA) model. The CA uses a real topographic surface acquired from a Digital Elevation Model to represent the initial state of the system, where the states of cells are defined in terms of altitude. The stability criterion is based on the slope gradient. The system is driven to instability through a temporal decrease of the stability condition of cells, which may be thought of as representing the temporal weakening of soil caused by factors like rainfall. A transition rule defines the way in which instabilities lead to discharge from unstable cells to the neighboring cells, deciding upon the landslide direction and the quantity of mass involved. Both the direction and the transferred mass depend on the local topographic features. The scaling properties of the area-frequency distributions of the resulting landslide series are investigated for several rates of weakening and for different time windows, in order to explore the response of the system to model
Anisotropic square lattice Potts ferromagnet: renormalization group treatment
International Nuclear Information System (INIS)
The choice of a convenient self-dual cell within a real space renormalization group framework enables a satisfactory treatment of the anisotropic square lattice q-state Potts ferromagnet criticality. The exact critical frontier and dimensionality crossover exponent PHI as well as the expected universality behaviour (renormalization flow sense) are recovered for any linear scaling factor b and all values of q(q -< 4). The b = 2 and b = 3 approximate correlation lenght critical exponent ν is calculated for all values of q and compared with den Nijs conjecture. The same calculation is performed, for all values of b, for the exponent ν(d=1) associated to the one-dimensional limit and the exact result ν (d=1) = 1 is recovered in the limit b → infinite. (Author)
Cellular Automata Models Applied to the Study of Landslide Dynamics
Liucci, Luisa; Melelli, Laura; Suteanu, Cristian
2015-04-01
Landslides are caused by complex processes controlled by the interaction of numerous factors. Increasing efforts are being made to understand the spatial and temporal evolution of this phenomenon, and the use of remote sensing data is making significant contributions in improving forecast. This paper studies landslides seen as complex dynamic systems, in order to investigate their potential Self Organized Critical (SOC) behavior, and in particular, scale-invariant aspects of processes governing the spatial development of landslides and their temporal evolution, as well as the mechanisms involved in driving the system and keeping it in a critical state. For this purpose, we build Cellular Automata Models, which have been shown to be capable of reproducing the complexity of real world features using a small number of variables and simple rules, thus allowing for the reduction of the number of input parameters commonly used in the study of processes governing landslide evolution, such as those linked to the geomechanical properties of soils. This type of models has already been successfully applied in studying the dynamics of other natural hazards, such as earthquakes and forest fires. The basic structure of the model is composed of three modules: (i) An initialization module, which defines the topographic surface at time zero as a grid of square cells, each described by an altitude value; the surface is acquired from real Digital Elevation Models (DEMs). (ii) A transition function, which defines the rules used by the model to update the state of the system at each iteration. The rules use a stability criterion based on the slope angle and introduce a variable describing the weakening of the material over time, caused for example by rainfall. The weakening brings some sites of the system out of equilibrium thus causing the triggering of landslides, which propagate within the system through local interactions between neighboring cells. By using different rates of
Genetic Algorithm Calibration of Probabilistic Cellular Automata for Modeling Mining Permit Activity
Louis, S.J.; Raines, G.L.
2003-01-01
We use a genetic algorithm to calibrate a spatially and temporally resolved cellular automata to model mining activity on public land in Idaho and western Montana. The genetic algorithm searches through a space of transition rule parameters of a two dimensional cellular automata model to find rule parameters that fit observed mining activity data. Previous work by one of the authors in calibrating the cellular automaton took weeks - the genetic algorithm takes a day and produces rules leading to about the same (or better) fit to observed data. These preliminary results indicate that genetic algorithms are a viable tool in calibrating cellular automata for this application. Experience gained during the calibration of this cellular automata suggests that mineral resource information is a critical factor in the quality of the results. With automated calibration, further refinements of how the mineral-resource information is provided to the cellular automaton will probably improve our model.
The similia principle: results obtained in a cellular model system.
Wiegant, Fred; Van Wijk, Roeland
2010-01-01
This paper describes the results of a research program focused on the beneficial effect of low dose stress conditions that were applied according to the similia principle to cells previously disturbed by more severe stress conditions. In first instance, we discuss criteria for research on the similia principle at the cellular level. Then, the homologous ('isopathic') approach is reviewed, in which the initial (high dose) stress used to disturb cellular physiology and the subsequent (low dose) stress are identical. Beneficial effects of low dose stress are described in terms of increased cellular survival capacity and at the molecular level as an increase in the synthesis of heat shock proteins (hsps). Both phenomena reflect a stimulation of the endogenous cellular self-recovery capacity. Low dose stress conditions applied in a homologous approach stimulate the synthesis of hsps and enhance survival in comparison with stressed cells that were incubated in the absence of low dose stress conditions. Thirdly, the specificity of the low dose stress condition is described where the initial (high dose) stress is different in nature from the subsequently applied (low dose) stress; the heterologous or 'heteropathic' approach. The results support the similia principle at the cellular level and add to understanding of how low dose stress conditions influence the regulatory processes underlying self-recovery. In addition, the phenomenon of 'symptom aggravation' which is also observed at the cellular level, is discussed in the context of self-recovery. Finally, the difference in efficiency between the homologous and the heterologous approach is discussed; a perspective is indicated for further research; and the relationship between studies on the similia principle and the recently introduced concept of 'postconditioning hormesis' is emphasized. PMID:20129172
Cellular-automata model of the dwarf shrubs populations and communities dynamics
A. S. Komarov; E. V. Zubkova; P. V. Frolov
2015-01-01
The probabilistic cellular-automata model of development and long-time dynamics of dwarf shrub populations and communities is developed. It is based on the concept of discrete description of the plant ontogenesis and joint model approaches in terms of probabilistic cellular automata and L-systems by Lindenmayer. Short representation of the basic model allows evaluation of the approach and software implementation. The main variables of the model are a number of partial bushes in clones or area...
Stochastic Models of Vesicular Sorting in Cellular Organelles
Vagne, Quentin
2016-01-01
The proper sorting of membrane components by regulated exchange between cellular organelles is crucial to intra-cellular organization. This process relies on the budding and fusion of transport vesicles, and should be strongly influenced by stochastic fluctuations considering the relatively small size of many organelles. We identify the perfect sorting of two membrane components initially mixed in a single compartment as a first passage process, and we show that the mean sorting time exhibits two distinct regimes as a function of the ratio of vesicle fusion to budding rates. Low ratio values leads to fast sorting, but results in a broad size distribution of sorted compartments dominated by small entities. High ratio values result in two well defined sorted compartments but is exponentially slow. Our results suggests an optimal balance between vesicle budding and fusion for the rapid and efficient sorting of membrane components, and highlight the importance of stochastic effects for the steady-state organizati...
Mathematical models and multiscale simulations of cellular secretion processes
González-Vélez, Virginia
2011-01-01
Exocytosis is the cellular process whereby a product such as a hormone or a neurotransmitter is released as a response to stimulation. There are a lot of exocytotic cells in mammals, and each cell type has their specific subcellular mechanisms, needed to achieve the final substance release. Therefore, unveiling the role of subcellular mechanisms in secretion processes is highly relevant to understand disease evolution and possible therapies. The efficiency of the coupling between stimulus...
A Large Deformation Model for the Elastic Moduli of Two-dimensional Cellular Materials
Institute of Scientific and Technical Information of China (English)
HU Guoming; WAN Hui; ZHANG Youlin; BAO Wujun
2006-01-01
We developed a large deformation model for predicting the elastic moduli of two-dimensional cellular materials. This large deformation model was based on the large deflection of the inclined members of the cells of cellular materials. The deflection of the inclined member, the strain of the representative structure and the elastic moduli of two-dimensional cellular materials were expressed using incomplete elliptic integrals. The experimental results show that these elastic moduli are no longer constant at large deformation, but vary significantly with the strain. A comparison was made between this large deformation model and the small deformation model proposed by Gibson and Ashby.
Simulating tissue mechanics with agent-based models: concepts, perspectives and some novel results
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.
A mathematical model of amphibian skin epithelium with two types of transporting cellular units
DEFF Research Database (Denmark)
Larsen, Erik Hviid; Rasmussen, B E
1985-01-01
A computer model of ion transport across amphibian skin epithelium containing two types of cellular units, their relative number and sizes, and a paracellular pathway has been developed. The two cellular units are, a large Na+ transporting compartment representing the major epithelium from stratum...
Predictive model to describe water migration in cellular solid foods during storage
Voogt, J.A.; Hirte, A.; Meinders, M.B.J.
2011-01-01
BACKGROUND: Water migration in cellular solid foods during storage causes loss of crispness. To improve crispness retention, physical understanding of this process is needed. Mathematical models are suitable tools to gain this physical knowledge. RESULTS: Water migration in cellular solid foods invo
Excellent approach to modeling urban expansion by fuzzy cellular automata: agent base model
Khajavigodellou, Yousef; Alesheikh, Ali A.; Mohammed, Abdulrazak A. S.; Chapi, Kamran
2014-09-01
Recently, the interaction between humans and their environment is the one of important challenges in the world. Landuse/ cover change (LUCC) is a complex process that includes actors and factors at different social and spatial levels. The complexity and dynamics of urban systems make the applicable practice of urban modeling very difficult. With the increased computational power and the greater availability of spatial data, micro-simulation such as the agent based and cellular automata simulation methods, has been developed by geographers, planners, and scholars, and it has shown great potential for representing and simulating the complexity of the dynamic processes involved in urban growth and land use change. This paper presents Fuzzy Cellular Automata in Geospatial Information System and remote Sensing to simulated and predicted urban expansion pattern. These FCA-based dynamic spatial urban models provide an improved ability to forecast and assess future urban growth and to create planning scenarios, allowing us to explore the potential impacts of simulations that correspond to urban planning and management policies. A fuzzy inference guided cellular automata approach. Semantic or linguistic knowledge on Land use change is expressed as fuzzy rules, based on which fuzzy inference is applied to determine the urban development potential for each pixel. The model integrates an ABM (agent-based model) and FCA (Fuzzy Cellular Automata) to investigate a complex decision-making process and future urban dynamic processes. Based on this model rapid development and green land protection under the influences of the behaviors and decision modes of regional authority agents, real estate developer agents, resident agents and non- resident agents and their interactions have been applied to predict the future development patterns of the Erbil metropolitan region.
Dynamic modeling of cellular response to DNA damage based on p53 stress response networks
Institute of Scientific and Technical Information of China (English)
Jinpeng Qi; Yongsheng Ding; Shihuang Shao
2009-01-01
Under acute perturbations from the outside, cells can trigger self-defensive mechanisms to fight against genome stress. To investigate the cellular response to continuous ion radiation (IR), a dynamic model for p53 stress response networks at the cellular level is proposed. The model can successfully be used to simulate the dynamic processes of double-strand breaks (DSBs) generation and their repair, switch-like ataxia telangiectasia mutated (ATM) activation, oscillations occurring in the p53-MDM2 feedback loop, as well as toxins elimination triggered by p53 stress response networks. Especially, the model can predict the plausible outcomes of cellular response under different IR dose regimes.
Modeling and Analysis of Cellular Networks using Stochastic Geometry: A Tutorial
ElSawy, Hesham
2016-03-22
This paper presents a tutorial on stochastic geometry (SG) based analysis for cellular networks. This tutorial is distinguished by its depth with respect to wireless communication details and its focus on cellular networks. The paper starts by modeling and analyzing the baseband interference in a basic cellular network model. Then, it characterizes signal-tointerference- plus-noise-ratio (SINR) and its related performance metrics. In particular, a unified approach to conduct error probability, outage probability, and rate analysis is presented. Although the main focus of the paper is on cellular networks, the presented unified approach applies for other types of wireless networks that impose interference protection around receivers. The paper then extends the baseline unified approach to capture cellular network characteristics (e.g., frequency reuse, multiple antenna, power control, etc.). It also presents numerical examples associated with demonstrations and discussions. Finally, we point out future research directions.
Cellular Automation Model of Traffic Flow Based on the Car-Following Model
Institute of Scientific and Technical Information of China (English)
LI Ke-Ping; GAO Zi-You
2004-01-01
@@ We propose a new cellular automation (CA) traffic model that is based on the car-following model. A class of driving strategies is used in the car-following model instead of the acceleration in the NaSch traffic model. In our model, some realistic driver behaviour and detailed vehicle characteristics have been taken into account, such as distance-headway and safe distance, etc. The simulation results show that our model can exhibit some traffic flow states that have been observed in the real traffic, and both of the maximum flux and the critical density are very close to the real measurement. Moreover, it is easy to extend our method to multi-lane traffic.
Kapitanov, Georgi I.; Wang, Xiayi; Ayati, Bruce P; Brouillette, Marc J.; Martin, James A.
2016-01-01
A severe application of stress on articular cartilage can initiate a cascade of biochemical reactions that can lead to the development of osteoarthritis. We constructed a multiscale mathematical model of the process with three components: cellular, chemical, and mechanical. The cellular component describes the different chondrocyte states according to the chemicals these cells release. The chemical component models the change in concentrations of those chemicals. The mechanical component cont...
Excitation spectrum and correlation functions of the Z3 chiral Potts quantum spin chain
International Nuclear Information System (INIS)
We study the excitation spectrum and the correlation functions of the Z3 chiral Potts model in the massive high-temperature phase using perturbation expansions and numerical diagonalization. We are mainly interested in results for general chiral angles but we consider also the superintegrable case. For the parameter values considered, we find that the band structure of the low-lying part of the excitation spectrum has the form expected from a quasiparticle picture with two fundamental particles. Studying the chain-size dependence of the spectrum, we find a remarkable stability of the second fundamental particle in a limited range of the momentum, even when its energy becomes so high that it lies very high up among the multiparticle scattering states. This is not a phenomenon restricted to the superintegrable line. Calculating a non-translationally invariant correlation function, we give evidence that it is oscillating. Within our numerical accuracy we find a relation between the oscillation length and the dip position of the momentum dispersion of the lightest particle which seems to be quite independent of the chiral angles. ((orig.))
Simulation Modeling by Classification of Problems: A Case of Cellular Manufacturing
Afiqah, K. N.; Mahayuddin, Z. R.
2016-02-01
Cellular manufacturing provides good solution approach to manufacturing area by applying Group Technology concept. The evolution of cellular manufacturing can enhance performance of the cell and to increase the quality of the product manufactured but it triggers other problem. Generally, this paper highlights factors and problems which emerge commonly in cellular manufacturing. The aim of the research is to develop a thorough understanding of common problems in cellular manufacturing. A part from that, in order to find a solution to the problems exist using simulation technique, this classification framework is very useful to be adapted during model building. Biology evolution tool was used in the research in order to classify the problems emerge. The result reveals 22 problems and 25 factors using cladistic technique. In this research, the expected result is the cladogram established based on the problems in cellular manufacturing gathered.
Cellular cardiac electrophysiology modeling with Chaste and CellML
Cooper, Jonathan; Spiteri, Raymond J.; Mirams, Gary R
2014-01-01
Chaste is an open-source C++ library for computational biology that has well-developed cardiac electrophysiology tissue simulation support. In this paper, we introduce the features available for performing cardiac electrophysiology action potential simulations using a wide range of models from the Physiome repository. The mathematics of the models are described in CellML, with units for all quantities. The primary idea is that the model is defined in one place (the CellML file), and all model...
Modelling lava flows by Cellular Nonlinear Networks (CNN: preliminary results
Directory of Open Access Journals (Sweden)
C. Del Negro
2005-01-01
Full Text Available The forecasting of lava flow paths is a complex problem in which temperature, rheology and flux-rate all vary with space and time. The problem is more difficult to solve when lava runs down a real topography, considering that the relations between characteristic parameters of flow are typically nonlinear. An alternative approach to this problem that does not use standard differential equation methods is Cellular Nonlinear Networks (CNNs. The CNN paradigm is a natural and flexible framework for describing locally interconnected, simple, dynamic systems that have a lattice-like structure. They consist of arrays of essentially simple, nonlinearly coupled dynamic circuits containing linear and non-linear elements able to process large amounts of information in real time. Two different approaches have been implemented in simulating some lava flows. Firstly, a typical technique of the CNNs to analyze spatio-temporal phenomena (as Autowaves in 2-D and in 3-D has been utilized. Secondly, the CNNs have been used as solvers of partial differential equations of the Navier-Stokes treatment of Newtonian flow.
Study of phase separation using liquid-gas model of lattice-gas cellular automata
International Nuclear Information System (INIS)
This report describes the study of phase separation by the liquid gas model of lattice gas cellular automata. The lattice gas cellular automaton is one model for simulating fluid phenomena which was proposed by Frisch, Hasslacher and Pomeau in 1986. In 1990, Appert and Zaleski added a new long-range interaction to lattice gas cellular automata to construct a model, the liquid-gas model, which could simulate phase separation using lattice-gas cellular automata. Gerits et al formulated the liquid-gas model mathematically using the theory of statistical dynamics in 1993 and explained the mechanism of phase separation in the liquid-gas model using the equation of state. At first this report explains the FHP model of lattice gas cellular automata and derives fluid dynamics equations such as the equation of continuity and the Navier-Stokes equation. Then the equation of state for the liquid-gas model which was derived by Gerits et al is modified by adding the interactions which were proposed by Appert but not considered by Gerits et al. The modified equation of state is verified by the computer simulation using the liquid gas model. The relation between phase separation and the equation of state is discussed. (author)
Institute of Scientific and Technical Information of China (English)
ZHU Ming-fang; CAO Wei-sheng; CHEN Shuang-lin; XIE Fan-you; HONG Chunpyo; CHANG Y. Austin
2006-01-01
A modified cellular automaton (MCA) model has been extended to the ternary alloy system by coupling thermodynamic and phase equilibrium calculation engine PanEngine. In the present model the dendrite growth is driven by the difference between the local equilibrium liquidus temperature and local actual temperature, incorporating the effect of curvature. The local equilibrium liquidus temperature is calculated with PanEngine according to the local liquid concentrations of two solutes, which are determined by numerically solving the species transport equation in the domain. Model validation was carried out through the comparison of the simulated values to the prediction of the Scheil model for solute profiles in the primary dendrites. The simulated data with zero solid diffusivity and limited liquid diffusivity were increasingly close to the Scheil profiles as the solidification rate decreased. The simulated microstructure and microsegregation in an Al-Cu-Mg ternary alloy were compared with those obtained experimentally.
Jeans type instability for a chemotactic model of cellular aggregation
Chavanis, Pierre-Henri
2008-01-01
We consider an inertial model of chemotactic aggregation generalizing the Keller-Segel model and we study the linear dynamical stability of an infinite and homogeneous distribution of cells (bacteria, amoebae, endothelial cells,...) when inertial effects are accounted for. These inertial terms model cells directional persistance. We determine the condition of instability and the growth rate of the perturbation as a function of the cell density and the wavelength of the perturbation. We discuss the differences between overdamped (Keller-Segel) and inertial models. Finally, we show the analogy between the instability criterion for biological populations and the Jeans instability criterion in astrophysics.
From cellular to tissue scales by asymptotic limits of thermostatted kinetic models
Bianca, Carlo; Dogbe, Christian; Lemarchand, Annie
2016-02-01
Tumor growth strictly depends on the interactions occurring at the cellular scale. In order to obtain the linking between the dynamics described at tissue and cellular scales, asymptotic methods have been employed, consisting in deriving tissue equations by suitable limits of mesoscopic models. In this paper, the evolution at the cellular scale is described by thermostatted kinetic theory that include conservative, nonconservative (proliferation, destruction and mutations), stochastic terms, and the role of external agents. The dynamics at the tissue scale (cell-density evolution) is obtained by performing a low-field scaling and considering the related convergence of the rescaled framework when the scaling parameter goes to zero.
Cellular cardiac electrophysiology modeling with Chaste and CellML.
Cooper, Jonathan; Spiteri, Raymond J; Mirams, Gary R
2014-01-01
Chaste is an open-source C++ library for computational biology that has well-developed cardiac electrophysiology tissue simulation support. In this paper, we introduce the features available for performing cardiac electrophysiology action potential simulations using a wide range of models from the Physiome repository. The mathematics of the models are described in CellML, with units for all quantities. The primary idea is that the model is defined in one place (the CellML file), and all model code is auto-generated at compile or run time; it never has to be manually edited. We use ontological annotation to identify model variables describing certain biological quantities (membrane voltage, capacitance, etc.) to allow us to import any relevant CellML models into the Chaste framework in consistent units and to interact with them via consistent interfaces. This approach provides a great deal of flexibility for analysing different models of the same system. Chaste provides a wide choice of numerical methods for solving the ordinary differential equations that describe the models. Fixed-timestep explicit and implicit solvers are provided, as discussed in previous work. Here we introduce the Rush-Larsen and Generalized Rush-Larsen integration techniques, made available via symbolic manipulation of the model equations, which are automatically rearranged into the forms required by these approaches. We have also integrated the CVODE solvers, a 'gold standard' for stiff systems, and we have developed support for symbolic computation of the Jacobian matrix, yielding further increases in the performance and accuracy of CVODE. We discuss some of the technical details of this work and compare the performance of the available numerical methods. Finally, we discuss how this is generalized in our functional curation framework, which uses a domain-specific language for defining complex experiments as a basis for comparison of model behavior. PMID:25610400
A study of a main-road cellular automata traffic flow model
Institute of Scientific and Technical Information of China (English)
黄乒花; 孔令江; 刘慕仁
2002-01-01
A main-road cellular automata traffic flow model on two dimensions is presented based on the Biham-Middleton-Levine traffic model. Its evolution equations are given and the self-organization and organization cooperation phenomenain this model are also studied by using computer simulation.
Propagation Path Loss Models for 5G Urban Micro- and Macro-Cellular Scenarios
DEFF Research Database (Denmark)
Sun, Shu; Rappaport, Theodore S.; Rangan, Sundeep;
2016-01-01
This paper presents and compares two candidate large-scale propagation path loss models, the alpha-beta-gamma (ABG) model and the close-in (CI) free space reference distance model, for the design of fifth generation (5G) wireless communication systems in urban micro- and macro-cellular scenarios...
Jokar Arsanjani, J.; Helbich, M.; Kainz, W.; Boloorani, A.
2013-01-01
This research analyses the suburban expansion in the metropolitan area of Tehran, Iran. A hybrid model consisting of logistic regression model, Markov chain (MC), and cellular automata (CA) was designed to improve the performance of the standard logistic regression model. Environmental and socio-eco
On Modeling Coverage and Rate of Random Cellular Networks under Generic Channel Fading
Al-Hourani, Akram; Kandeepan, Sithamparanathan
2016-01-01
In this paper we provide an analytic framework for computing the expected downlink coverage probability, and the associated data rate of cellular networks, where base stations are distributed in a random manner. The provided expressions are in computable integral forms that accommodate generic channel fading conditions. We develop these expressions by modelling the cellular interference using stochastic geometry analysis, then we employ them for comparing the coverage resulting from various c...
A cellular network model with Ginibre configured base stations
Miyoshi, Naoto; Shirai, Tomoyuki
2014-01-01
Stochastic geometry models for wireless communication networks have recently attracted much attention. This is because the performance of such networks critically depends on the spatial configuration of wireless nodes and the irregularity of the node configuration in a real network can be captured by a spatial point process. However, most analysis of such stochastic geometry models for wireless networks assumes, owing to its tractability, that the wireless nodes are deployed...
A cellular automata model for simulating fed-batch penicillin fermentation process
Institute of Scientific and Technical Information of China (English)
Yu Naigong; Ruan Xiaogang
2006-01-01
A cellular automata model to simulate penicillin fed-batch fermentation process(CAPFM)was established in this study,based on a morphologically structured dynamic penicillin production model,that is in turn based on the growth mechanism of penicillin producing microorganisms and the characteristics of penicillin fed-batch fermentation.CAPFM uses the three-dimensional cellular automata as a growth space,and a Moore-type neighborhood as the cellular neighborhood.The transition roles of CAPFM are designed based on mechanical and structural kinetic models of penicillin batch-fed fermentation processes.Every cell of CAPFM represents a single or specific number of penicillin producing microorganisms,and has various state.The simulation experimental results show that CAPFM replicates the evolutionary behavior of penicillin batch-fed fermentation processes described by the structured penicillin production kinetic model accordingly.
Mathematical Modeling Predicts How Proteins Affect Cellular Communication
Lee Ethan; Salic Adrian; Krüger Roland; Heinrich Reinhart; Kirschner Marc W
2003-01-01
Wnt signaling plays an important role in both oncogenesis and development. Activation of the Wnt pathway results in stabilization of the transcriptional coactivator beta-catenin. Recent studies have demonstrated that axin, which coordinates beta-catenin degradation, is itself degraded. Although the key molecules required for transducing a Wnt signal have been identified, a quantitative understanding of this pathway has been lacking. We have developed a mathematical model for the canonical Wnt...
Cellular automata cell structure for modeling heterogeneous traffic
Pal, Dibyendu; C.Mallikarjuna
2010-01-01
Gap maintaining behavior significantly affects the traffic flow modeling under heterogeneous traffic conditions. The clearance between two adjacent moving vehicles varies depending on several traffic conditions. From the data collected on the gap maintaining behavior it has been observed that vehicles maintain different gaps when travelling under different traffic conditions and this is also influenced by lateral position of the vehicle. Mallikarjuna (2007) has found that this variable gap ma...
Cellular models and therapies for age-related macular degeneration
Directory of Open Access Journals (Sweden)
David L. Forest
2015-05-01
Full Text Available Age-related macular degeneration (AMD is a complex neurodegenerative visual disorder that causes profound physical and psychosocial effects. Visual impairment in AMD is caused by the loss of retinal pigmented epithelium (RPE cells and the light-sensitive photoreceptor cells that they support. There is currently no effective treatment for the most common form of this disease (dry AMD. A new approach to treating AMD involves the transplantation of RPE cells derived from either human embryonic or induced pluripotent stem cells. Multiple clinical trials are being initiated using a variety of cell therapies. Although many animal models are available for AMD research, most do not recapitulate all aspects of the disease, hampering progress. However, the use of cultured RPE cells in AMD research is well established and, indeed, some of the more recently described RPE-based models show promise for investigating the molecular mechanisms of AMD and for screening drug candidates. Here, we discuss innovative cell-culture models of AMD and emerging stem-cell-based therapies for the treatment of this vision-robbing disease.
Equal Distribution Model of Epidemic Drugs Based on a Cellular Automata Model
Directory of Open Access Journals (Sweden)
Huang Xinyi
2015-01-01
Full Text Available The epidemic spreading of infectious disease is a process of evolution over time. Based on the cellular automata model[1], this paper analyzes the epidemic spreading rules, and establishes an efficient equal distribution model of drugs in a broad sense. For multiple regions, in case of demand of drugs exceeding supply, the drugs shall be distributed according to the proportion of a total number of people in each region, the number of patients, the number of the isolated, and the number of deaths. It is necessary to simulate based on these four schemes to obtain simulation results. The results show that, when the drugs are distributed by the proportion of the number of deaths, it is optimal for controlling over epidemic situations.
Stochastic Model of Maturation and Vesicular Exchange in Cellular Organelles
Vagne, Quentin
2016-01-01
The dynamical organization of membrane-bound organelles along intracellular transport pathways relies on vesicular exchange between organelles and on biochemical maturation of the organelle content by specific enzymes. The relative importance of each mechanism in controlling organelle dynamics remains controversial, in particular for transport through the Golgi apparatus. Using a stochastic model, we show that full maturation of membrane-bound compartments can be seen as the stochastic escape from a steady-state in which export is dominated by vesicular exchange. We show that full maturation can contribute a significant fraction of the total out-flux for small organelles such as endosomes and Golgi cisternae.
Designing and implementing a regional urban modeling system using the SLEUTH cellular urban model
Jantz, C.A.; Goetz, S.J.; Donato, D.; Claggett, P.
2010-01-01
This paper presents a fine-scale (30 meter resolution) regional land cover modeling system, based on the SLEUTH cellular automata model, that was developed for a 257000 km2 area comprising the Chesapeake Bay drainage basin in the eastern United States. As part of this effort, we developed a new version of the SLEUTH model (SLEUTH-3r), which introduces new functionality and fit metrics that substantially increase the performance and applicability of the model. In addition, we developed methods that expand the capability of SLEUTH to incorporate economic, cultural and policy information, opening up new avenues for the integration of SLEUTH with other land-change models. SLEUTH-3r is also more computationally efficient (by a factor of 5) and uses less memory (reduced 65%) than the original software. With the new version of SLEUTH, we were able to achieve high accuracies at both the aggregate level of 15 sub-regional modeling units and at finer scales. We present forecasts to 2030 of urban development under a current trends scenario across the entire Chesapeake Bay drainage basin, and three alternative scenarios for a sub-region within the Chesapeake Bay watershed to illustrate the new ability of SLEUTH-3r to generate forecasts across a broad range of conditions. ?? 2009 Elsevier Ltd.
Modelling Cellular Processes using Membrane Systems with Peripheral and Integral Proteins
Cavaliere, Matteo; Sedwards, Sean
2006-01-01
Membrane systems were introduced as models of computation inspired by the structure and functioning of biological cells. Recently, membrane systems have also been shown to be suitable to model cellular processes. We introduce a new model called Membrane Systems with Peripheral and Integral Proteins. The model has compartments enclosed by membranes, floating objects, objects associated to the internal and external surfaces of the membranes and also objects integral to the membranes. The floati...
Evaluation of BACE1 Silencing in Cellular Models
Directory of Open Access Journals (Sweden)
Barbara Nawrot
2009-01-01
Full Text Available Beta-secretase (BACE1 is the major enzyme participating in generation of toxic amyloid-beta (Aβ peptides, identified in amyloid plaques of Alzheimer's disease (AD brains. Its downregulation results in decreasing secretion of Aβ. Thus, BACE1 silencing by RNAi represents possible strategy for antiamyloid therapy in the treatment of AD. In this study, a series of newly designed sequences of synthetic and vector-encoded siRNAs (pSilencer, pcPURhU6, and lentivirus were tested against overexpressed and endogenous BACE1 in several cell lines and in adult neural progenitor cells, derived from rat hippocampus. SiRNAs active in human, mouse, and rat cell models were shown to diminish the level of BACE1. In HCN A94 cells, two BACE1-specific siRNAs did not alter the expression of genes of BACE2 and several selected genes involved in neurogenesis (Synapsin I, βIII-Tubulin, Calbidin, NeuroD1, GluR2, CREB, MeCP2, PKR, however, remarkable lowering of SCG10 mRNA, coding protein of stathmin family, important in the development of nervous system, was observed.
Tools and Models for Integrating Multiple Cellular Networks
Energy Technology Data Exchange (ETDEWEB)
Gerstein, Mark [Yale Univ., New Haven, CT (United States). Gerstein Lab.
2015-11-06
CRIT for correlation analysis in systems biology [5]. For Aim 3, we have further investigated the scaling relationship that the number of Transcription Factors (TFs) in a genome is proportional to the square of the total number of genes. We have extended the analysis from transcription factors to various classes of functional categories, and from individual categories to joint distribution [6]. By introducing a new analytical framework, we have generalized the original toolbox model to take into account of metabolic network with arbitrary network topology [7].
Directory of Open Access Journals (Sweden)
Mondry Adrian
2004-08-01
Full Text Available Abstract Background Many arrhythmias are triggered by abnormal electrical activity at the ionic channel and cell level, and then evolve spatio-temporally within the heart. To understand arrhythmias better and to diagnose them more precisely by their ECG waveforms, a whole-heart model is required to explore the association between the massively parallel activities at the channel/cell level and the integrative electrophysiological phenomena at organ level. Methods We have developed a method to build large-scale electrophysiological models by using extended cellular automata, and to run such models on a cluster of shared memory machines. We describe here the method, including the extension of a language-based cellular automaton to implement quantitative computing, the building of a whole-heart model with Visible Human Project data, the parallelization of the model on a cluster of shared memory computers with OpenMP and MPI hybrid programming, and a simulation algorithm that links cellular activity with the ECG. Results We demonstrate that electrical activities at channel, cell, and organ levels can be traced and captured conveniently in our extended cellular automaton system. Examples of some ECG waveforms simulated with a 2-D slice are given to support the ECG simulation algorithm. A performance evaluation of the 3-D model on a four-node cluster is also given. Conclusions Quantitative multicellular modeling with extended cellular automata is a highly efficient and widely applicable method to weave experimental data at different levels into computational models. This process can be used to investigate complex and collective biological activities that can be described neither by their governing differentiation equations nor by discrete parallel computation. Transparent cluster computing is a convenient and effective method to make time-consuming simulation feasible. Arrhythmias, as a typical case, can be effectively simulated with the methods
Directory of Open Access Journals (Sweden)
Wimol San-Um
2015-12-01
Full Text Available This paper presents a robust cellular associative memory for pattern recognitions using composite trigonometric chaotic neuron models. Robust chaotic neurons are designed through a scan of positive Lyapunov Exponent (LE bifurcation structures, which indicate the quantitative measure of chaoticity for one-dimensional discrete-time dynamical systems. The proposed chaotic neuron model is a composite of sine and cosine chaotic maps, which are independent from the output activation function. Dynamics behaviors are demonstrated through bifurcation diagrams and LE-based bifurcation structures. An application to associative memories of binary patterns in Cellular Neural Networks (CNN topology is demonstrated using a signum output activation function. Examples of English alphabets are stored using symmetric auto-associative matrix of n-binary patterns. Simulation results have demonstrated that the cellular neural network can quickly and effectively restore the distorted pattern to expected information.
Platinum nanozymes recover cellular ROS homeostasis in an oxidative stress-mediated disease model
Moglianetti, Mauro; de Luca, Elisa; Pedone, Deborah; Marotta, Roberto; Catelani, Tiziano; Sartori, Barbara; Amenitsch, Heinz; Retta, Saverio Francesco; Pompa, Pier Paolo
2016-02-01
In recent years, the use of nanomaterials as biomimetic enzymes has attracted great interest. In this work, we show the potential of biocompatible platinum nanoparticles (Pt NPs) as antioxidant nanozymes, which combine abundant cellular internalization and efficient scavenging activity of cellular reactive oxygen species (ROS), thus simultaneously integrating the functions of nanocarriers and antioxidant drugs. Careful toxicity assessment and intracellular tracking of Pt NPs proved their cytocompatibility and high cellular uptake, with compartmentalization within the endo/lysosomal vesicles. We have demonstrated that Pt NPs possess strong and broad antioxidant properties, acting as superoxide dismutase, catalase, and peroxidase enzymes, with similar or even superior performance than natural enzymes, along with higher adaptability to the changes in environmental conditions. We then exploited their potent activity as radical scavenging materials in a cellular model of an oxidative stress-related disorder, namely human Cerebral Cavernous Malformation (CCM) disease, which is associated with a significant increase in intracellular ROS levels. Noteworthily, we found that Pt nanozymes can efficiently reduce ROS levels, completely restoring the cellular physiological homeostasis.In recent years, the use of nanomaterials as biomimetic enzymes has attracted great interest. In this work, we show the potential of biocompatible platinum nanoparticles (Pt NPs) as antioxidant nanozymes, which combine abundant cellular internalization and efficient scavenging activity of cellular reactive oxygen species (ROS), thus simultaneously integrating the functions of nanocarriers and antioxidant drugs. Careful toxicity assessment and intracellular tracking of Pt NPs proved their cytocompatibility and high cellular uptake, with compartmentalization within the endo/lysosomal vesicles. We have demonstrated that Pt NPs possess strong and broad antioxidant properties, acting as superoxide
Kirchner, Ansgar; Schadschneider, Andreas
2002-01-01
We present simulations of evacuation processes using a recently introduced cellular automaton model for pedestrian dynamics. This model applies a bionics approach to describe the interaction between the pedestrians using ideas from chemotaxis. Here we study a rather simple situation, namely the evacuation from a large room with one or two doors. It is shown that the variation of the model parameters allows to describe different types of behaviour, from regular to panic. We find a non-monotoni...
Color Graphs: An Efficient Model For Two-Dimensional Cellular Automata Linear Rules
Nayak, Birendra Kumar; Rout, Sushant Kumar
2008-01-01
Two-dimensional nine neighbor hood rectangular Cellular Automata rules can be modeled using many different techniques like Rule matrices, State Transition Diagrams, Boolean functions, Algebraic Normal Form etc. In this paper, a new model is introduced using color graphs to model all the 512 linear rules. The graph theoretic properties therefore studied in this paper simplifies the analysis of all linear rules in comparison with other ways of its study.
A Modified Cellular Automaton Approach for Mixed Bicycle Traffic Flow Modeling
Xiaonian Shan; Zhibin Li; Xiaohong Chen; Jianhong Ye
2015-01-01
Several previous studies have used the Cellular Automaton (CA) for the modeling of bicycle traffic flow. However, previous CA models have several limitations, resulting in differences between the simulated and the observed traffic flow features. The primary objective of this study is to propose a modified CA model for simulating the characteristics of mixed bicycle traffic flow. Field data were collected on physically separated bicycle path in Shanghai, China, and were used to calibrate the C...
Lattice gas cellular automata model for rippling and aggregation in myxobacteria
Alber, Mark S.; Jiang, Yi; Kiskowski, Maria A.
2004-01-01
A lattice-gas cellular automaton (LGCA) model is used to simulate rippling and aggregation in myxobacteria. An efficient way of representing cells of different cell size, shape and orientation is presented that may be easily extended to model later stages of fruiting body formation. This LGCA model is designed to investigate whether a refractory period, a minimum response time, a maximum oscillation period and non-linear dependence of reversals of cells on C-factor are necessary assumptions f...
Özen, Şükrü; Köylü, Halis
2010-01-01
ABSTRACTThere is a necessity of tissue equivalent (phantom) models in research of electromagnetic (EM) effects in biologic tissues. Recently, many kinds of tissue models depend on the different aim were proposed. So many studies were carried on the interaction of human-head and cellular phone. The most of them are related to numerical models. Owing to difficulty of study on human body, simulation of human tissues is required. In this study two different, for 900MHz and for 1800MHz, brain equi...
Embryonic stem cells as an ectodermal cellular model of human p63-related dysplasia syndromes.
Rostagno, P.; Wolchinsky, Z.; Vigano, A.M.; Shivtiel, S.; Zhou, H.; Bokhoven, J.H.L.M. van; Ferone, G.; Missero, C.; Mantovani, R.; Aberdam, D.; Virolle, T.
2010-01-01
Heterozygous mutations in the TP63 transcription factor underlie the molecular basis of several similar autosomal dominant ectodermal dysplasia (ED) syndromes. Here we provide a novel cellular model derived from embryonic stem (ES) cells that recapitulates in vitro the main steps of embryonic skin d
An agent-based model of cellular dynamics and circadian variability in human endotoxemia.
Directory of Open Access Journals (Sweden)
Tung T Nguyen
Full Text Available As cellular variability and circadian rhythmicity play critical roles in immune and inflammatory responses, we present in this study an agent-based model of human endotoxemia to examine the interplay between circadian controls, cellular variability and stochastic dynamics of inflammatory cytokines. The model is qualitatively validated by its ability to reproduce circadian dynamics of inflammatory mediators and critical inflammatory responses after endotoxin administration in vivo. Novel computational concepts are proposed to characterize the cellular variability and synchronization of inflammatory cytokines in a population of heterogeneous leukocytes. Our results suggest that there is a decrease in cell-to-cell variability of inflammatory cytokines while their synchronization is increased after endotoxin challenge. Model parameters that are responsible for IκB production stimulated by NFκB activation and for the production of anti-inflammatory cytokines have large impacts on system behaviors. Additionally, examining time-dependent systemic responses revealed that the system is least vulnerable to endotoxin in the early morning and most vulnerable around midnight. Although much remains to be explored, proposed computational concepts and the model we have pioneered will provide important insights for future investigations and extensions, especially for single-cell studies to discover how cellular variability contributes to clinical implications.
DEFF Research Database (Denmark)
Guedes, J.M.; Rodrigues, H.C.; Bendsøe, Martin P.
2003-01-01
This paper describes a computational model, based on inverse homogenization and topology design, for approximating energy bounds for two-phase composites under multiple load cases. The approach allows for the identification of possible single-scale cellular materials that give rise to the optimal...
Model Perubahan Penggunaan Lahan Menggunakan Cellular Automata-Markov Chain di Kawasan Mamminasata
Vera Damayanti Peruge, Tiur
2012-01-01
Telah dilakukan penelitian tentang perubahan penggunaan lahan di kawasan Mamminasata menggunakan model Cellular Automata-Markov Chain. Tujuan dari penelitian ini adalah menganalisis perubahan penggunaan lahan melalui peta penggunaan lahan kawasan Mamminasata tahun 2004 dan 2009 untuk memperoleh penggunaan lahan tahun 2012 berbasis Markov Chain dengan analisis probabilitas transisi Markov. Hasil analisis yang diperoleh dilakukan validasi dengan validasi Kappa m...
Hannan, Shabab B; Dräger, Nina M; Rasse, Tobias M; Voigt, Aaron; Jahn, Thomas R
2016-04-01
Abnormal tau accumulations were observed and documented in post-mortem brains of patients affected by Alzheimer's disease (AD) long before the identification of mutations in the Microtubule-associated protein tau (MAPT) gene, encoding the tau protein, in a different neurodegenerative disease called Frontotemporal dementia and Parkinsonism linked to chromosome 17 (FTDP-17). The discovery of mutations in the MAPT gene associated with FTDP-17 highlighted that dysfunctions in tau alone are sufficient to cause neurodegeneration. Invertebrate models have been diligently utilized in investigating tauopathies, contributing to the understanding of cellular and molecular pathways involved in disease etiology. An important discovery came with the demonstration that over-expression of human tau in Drosophila leads to premature mortality and neuronal dysfunction including neurodegeneration, recapitulating some key neuropathological features of the human disease. The simplicity of handling invertebrate models combined with the availability of a diverse range of experimental resources make these models, in particular Drosophila a powerful invertebrate screening tool. Consequently, several large-scale screens have been performed using Drosophila, to identify modifiers of tau toxicity. The screens have revealed not only common cellular and molecular pathways, but in some instances the same modifier has been independently identified in two or more screens suggesting a possible role for these modifiers in regulating tau toxicity. The purpose of this review is to discuss the genetic modifier screens on tauopathies performed in Drosophila and C. elegans models, and to highlight the common cellular and molecular pathways that have emerged from these studies. Here, we summarize results of tau toxicity screens providing mechanistic insights into pathological alterations in tauopathies. Key pathways or modifiers that have been identified are associated with a broad range of processes
Directory of Open Access Journals (Sweden)
J. P. M. Whitty
2014-01-01
Full Text Available A novel computational technique is presented for embedding mass-loss due to burning into the ANSYS finite element modelling code. The approaches employ a range of computational modelling methods in order to provide more complete theoretical treatment of thermoelasticity absent from the literature for over six decades. Techniques are employed to evaluate structural integrity (namely, elastic moduli, Poisson’s ratios, and compressive brittle strength of honeycomb systems known to approximate three-dimensional cellular chars. That is, reducing the mass of diagonal ribs and both diagonal-plus-vertical ribs simultaneously show rapid decreases in the structural integrity of both conventional and reentrant (auxetic, i.e., possessing a negative Poisson’s ratio honeycombs. On the other hand, reducing only the vertical ribs shows initially modest reductions in such properties, followed by catastrophic failure of the material system. Calculations of thermal stress distributions indicate that in all cases the total stress is reduced in reentrant (auxetic cellular solids. This indicates that conventional cellular solids are expected to fail before their auxetic counterparts. Furthermore, both analytical and FE modelling predictions of the brittle crush strength of both auxteic and conventional cellular solids show a relationship with structural stiffness.
Modeling of solidification grain structure for Ti-45%Al alloy ingot by cellular automaton
Institute of Scientific and Technical Information of China (English)
WU Shi-ping; LIU Dong-rong; GUO Jing-jie; FU Heng-zhi
2005-01-01
A cellular automaton model for simulating grain structure formation during solidification processes of Ti45%Al(mole fraction) alloy ingot was developed, based on finite differential method for macroscopic modeling of heat transfer and a cellular automaton technique for microscopic modeling of nucleation, growth, solute redistribution and solute diffusion. The relation between the growth velocity of a dendrite tip and the local undercooling,which consists of constitutional, thermal, curvature and attachment kinetics undercooling is calculated according to the Kurz-Giovanola-Trivedi model. The effect of solidification contraction is taken into consideration. The influence of process variables upon the resultant grain structures was investigated. Special moving allocation technique was designed to minimize the computation time and memory size associated with a large number of cells. The predicted grain structures are in good agreement with the experimental results.
Parallel Genetic Algorithms for calibrating Cellular Automata models: Application to lava flows
International Nuclear Information System (INIS)
Cellular Automata are highly nonlinear dynamical systems which are suitable far simulating natural phenomena whose behaviour may be specified in terms of local interactions. The Cellular Automata model SCIARA, developed far the simulation of lava flows, demonstrated to be able to reproduce the behaviour of Etnean events. However, in order to apply the model far the prediction of future scenarios, a thorough calibrating phase is required. This work presents the application of Genetic Algorithms, general-purpose search algorithms inspired to natural selection and genetics, far the parameters optimisation of the model SCIARA. Difficulties due to the elevated computational time suggested the adoption a Master-Slave Parallel Genetic Algorithm far the calibration of the model with respect to the 2001 Mt. Etna eruption. Results demonstrated the usefulness of the approach, both in terms of computing time and quality of performed simulations
Tamaddon AM.; Hosseini-Shirazi F.; Moghimi HR
2007-01-01
Cationic liposomes are used for cellular delivery of antisense oligodeoxynucleotide (AsODN), where release of encapsulated AsODN is mainly controlled by endocytosis and fusion mechanisms. In this investigation, it was tried to model such a release process that is difficult to evaluate in cell culture. For this purpose, an AsODN model (against protein kinase C-α) was encapsulated in a DODAP-containing cationic liposome and evaluated for size, zeta-potential, encapsulation and ODN stab...
Modeling of aluminum-silicon irregular eutectic growth by cellular automaton model
Directory of Open Access Journals (Sweden)
Rui Chen
2016-03-01
Full Text Available Due to the extensive application of Al-Si alloys in the automotive and aerospace industries as structural components, an understanding of their microstructural formation, such as dendrite and (Al+Si eutectic, is of great importance to control the desirable microstructure, so as to modify the performance of castings. Since previous major themes of microstructural simulation are dendrite and regular eutectic growth, few efforts have been paid to simulate the irregular eutectic growth. Therefore, a multiphase cellular automaton (CA model is developed and applied to simulate the time-dependent Al-Si irregular eutectic growth. Prior to model establishment, related experiments were carried out to investigate the influence of cooling rate and Sr modification on the growth of eutectic Si. This CA model incorporates several aspects, including growth algorithms and nucleation criterion, to achieve the competitive and cooperative growth mechanism for nonfaceted-faceted Al-Si irregular eutectic. The growth kinetics considers thermal undercooling, constitutional undercooling, and curvature undercooling, as well as the anisotropic characteristic of eutectic Si growth. The capturing rule takes into account the effects of modification on the silicon growth behaviors. The simulated results indicate that for unmodified alloy, the higher eutectic undercooling results in the higher eutectic growth velocity, and a more refined eutectic microstructure as well as narrower eutectic lamellar spacing. For modified alloy, the eutectic silicon tends to be obvious fibrous morphology and the morphology of eutectic Si is determined by both chemical modifier and cooling rate. The predicted microstructure of Al-7Si alloy under different solidification conditions shows that this proposed model can successfully reproduce both dendrite and eutectic microstructures.
Energy Technology Data Exchange (ETDEWEB)
Schmidt, Brian; Ebrahim, Ali; Metz, Thomas O.; Adkins, Joshua N.; Palsson, Bernard O.; Hyduke, Daniel R.
2013-11-15
Motivation: Genome-scale metabolic models have been used extensively to investigate alterations in cellular metabolism. The accuracy of these models to represent cellular metabolism in specific conditions has been improved by constraining the model with omics data sources. However, few practical methods for integrating metabolomics data with other omics data sources into genome-scale models of metabolism have been reported. Results: GIMMME (Gene Inactivation Moderated by Metabolism, Metabolomics, and Expression) is an algorithm that enables the development of condition-specific models based on an objective function, transcriptomics, and intracellular metabolomics data. GIMMME establishes metabolite utilization requirements with metabolomics data, uses model-paired transcriptomics data to find experimentally supported solutions, and also provides calculations of the turnover (production / consumption) flux of metabolites. GIMMME was employed to investigate the effects of integrating additional omics datasets to create increasingly constrained solution spaces of Salmonella Typhimurium metabolism during growth in both rich and virulence media. This integration proved to be informative and resulted in a requirement of additional active reactions (12 in each case) or metabolites (26 or 29, respectively). The addition of constraints from transcriptomics also impacted the allowed solution space, and the cellular metabolites with turnover fluxes that were necessarily altered by the change in conditions increased from 118 to 271 of 1397. Availability: GIMMME has been implemented in Python and requires a COBRApy 0.2.x. The algorithm and sample data described here are freely available at: http://opencobra.sourceforge.net/
Magneto-optical cellular chip model for intracellular orientational-dynamic-activity detection
Miyashita, Y.; Iwasaka, M.; Kurita, S.; Owada, N.
2012-04-01
In the present study, a magneto-optical cellular chip model (MoCCM) was developed to detect intracellular dynamics in macromolecules by using magneto-optical effects. For the purpose of cell-measurement under strong static magnetic fields of up to 10 T, we constructed a cellular chip model, which was a thin glass plate with a well for a cell culture. A cell line of osteoblast MC3T3-E1 was incubated in the glass well, and the well, 0.3 mm in depth, was sealed by a cover glass when the MoCCM was set in a fiber optic system. An initial intensity change of the polarized light transmission, which dispersed perpendicular to the cell's attaching surface, was collected for 10 to 60 min, and then magnetic fields were applied parallel and perpendicular to the surface and light direction, respectively. The magnetic birefringence signals that originated from the magnetic orientation of intracellular molecules such as cytoskeletons apparently appeared when the magnetic fields were constant at 10 T. A statistical analysis with 15 experiments confirmed that the cellular components under 10 T magnetic fields caused a stronger alignment, which was transferred into polarizing light intensity that increased more than the case before exposure. Cellular conditions such as generation and cell density affected the magnetic birefringence signals.
Modeling of time-dose-LET effects in the cellular response to radiation
International Nuclear Information System (INIS)
This work is dedicated to the elucidation of time-dose- and if applicable linear energy transfer (LET) effects in the cellular response to ion or photon radiation. In particular, the common concept of the Local Effect Model (LEM) and the Giant Loop Binary Lesion (GLOBLE) model, which explains cell survival probabilities on the hand of clustering of double-strand breaks (DSB) in micrometer-sized sub-structural units of the DNA, was investigated with regard to temporal aspects. In previous studies with the LEM and GLOBLE model, it has been demonstrated that the definition of two lesion classes, characterized by single or multiple DSB in a DNA giant loop, with two repair fidelities is adequate to comprehensively describe the dose dependence of the cellular response to instantaneous photon irradiation or ion irradiation with varying LET. Furthermore, with the GLOBLE model for photon radiation, it has been shown that the assignment of two repair time scales to the two lesion classes allows to adequately reproduce time-dose effects after photon irradiation with an arbitrary constant dose-rate. In this work, the results of four projects that strengthen the mechanistic consistency and the practical applicability of the LEM and GLOBLE model will be presented. First, it was found that the GLOBLE model is applicable to describe time-dose effects in the cellular response to two split photon doses and in the occurrence of deterministic radiation effects. Second, in a comparison of ten models for the temporal course of DSB rejoining, it was revealed that a bi-exponential approach, as suggested by the LEM and GLOBLE model, finds a relatively large support by 61 experimental data sets. Third, in a comparison of four kinetic photon cell survival models that was based on fits to 13 dose-rate experiments, it was shown that the GLOBLE model performs well with respect to e.g. accuracy, parsimony, reliability and other factors that characterize a good approach. Last but not least, the
Modeling of time-dose-LET effects in the cellular response to radiation
Energy Technology Data Exchange (ETDEWEB)
Herr, Lisa Antje
2015-07-20
This work is dedicated to the elucidation of time-dose- and if applicable linear energy transfer (LET) effects in the cellular response to ion or photon radiation. In particular, the common concept of the Local Effect Model (LEM) and the Giant Loop Binary Lesion (GLOBLE) model, which explains cell survival probabilities on the hand of clustering of double-strand breaks (DSB) in micrometer-sized sub-structural units of the DNA, was investigated with regard to temporal aspects. In previous studies with the LEM and GLOBLE model, it has been demonstrated that the definition of two lesion classes, characterized by single or multiple DSB in a DNA giant loop, with two repair fidelities is adequate to comprehensively describe the dose dependence of the cellular response to instantaneous photon irradiation or ion irradiation with varying LET. Furthermore, with the GLOBLE model for photon radiation, it has been shown that the assignment of two repair time scales to the two lesion classes allows to adequately reproduce time-dose effects after photon irradiation with an arbitrary constant dose-rate. In this work, the results of four projects that strengthen the mechanistic consistency and the practical applicability of the LEM and GLOBLE model will be presented. First, it was found that the GLOBLE model is applicable to describe time-dose effects in the cellular response to two split photon doses and in the occurrence of deterministic radiation effects. Second, in a comparison of ten models for the temporal course of DSB rejoining, it was revealed that a bi-exponential approach, as suggested by the LEM and GLOBLE model, finds a relatively large support by 61 experimental data sets. Third, in a comparison of four kinetic photon cell survival models that was based on fits to 13 dose-rate experiments, it was shown that the GLOBLE model performs well with respect to e.g. accuracy, parsimony, reliability and other factors that characterize a good approach. Last but not least, the
A Cellular Automaton Model for Tumor Dormancy: Emergence of a Proliferative Switch
Chen, Duyu; Torquato, Salvatore
2014-01-01
Malignant cancers that lead to fatal outcomes for patients may remain dormant for very long periods of time. Although individual mechanisms such as cellular dormancy, angiogenic dormancy and immunosurveillance have been proposed, a comprehensive understanding of cancer dormancy and the "switch" from a dormant to a proliferative state still needs to be strengthened from both a basic and clinical point of view. Computational modeling enables one to explore a variety of scenarios for possible but realistic microscopic dormancy mechanisms and their predicted outcomes. The aim of this paper is to devise such a predictive computational model of dormancy with an emergent "switch" behavior. Specifically, we generalize a previous cellular automaton (CA) model for proliferative growth of solid tumor that now incorporates a variety of cell-level tumor-host interactions and different mechanisms for tumor dormancy, for example the effects of the immune system. Our new CA rules induce a natural "competition" between the tu...
Li, Qi-Lang; Wong, S. C.; Min, Jie; Tian, Shuo; Wang, Bing-Hong
2016-08-01
This study examines the cellular automata traffic flow model, which considers the heterogeneity of vehicle acceleration and the delay probability of vehicles. Computer simulations are used to identify three typical phases in the model: free-flow, synchronized flow, and wide moving traffic jam. In the synchronized flow region of the fundamental diagram, the low and high velocity vehicles compete with each other and play an important role in the evolution of the system. The analysis shows that there are two types of bistable phases. However, in the original Nagel and Schreckenberg cellular automata traffic model, there are only two kinds of traffic conditions, namely, free-flow and traffic jams. The synchronized flow phase and bistable phase have not been found.
Criticality of the Potts ferromagnet in Midgal-Kadanoff - like hierarchical lattices
International Nuclear Information System (INIS)
Within the real space renormalisation group framework, we discuss the critical point and exponent υ of the Potts ferromagnet in b-sized Migdal-Kadanoff-like hierarchical lattices. Both b → ∞ and b → 1 limits are exhibited. The important discrepancies that might exist between the exact results for d-dimensional hierarchical lattices and d-dimensional Bravais lattices are illustrated. (Author)
An Extended Cellular Automaton Model for Train Traffic Flow on the Dedicated Passenger Lines
Directory of Open Access Journals (Sweden)
Wenbo Zhao
2014-01-01
Full Text Available As one of the key components for the railway transportation system, the Train Operation Diagram can be greatly influenced by many extrinsic and intrinsic factors. Therefore, the railway train flow has shown the strong nonlinear characteristics, which makes it quite difficult to take further relative studies. Fortunately, the cellular automaton model has its own advantages in solving nonlinear problems and traffic flow simulation. Considering the mixed features of multispeed running trains on the passenger dedicated lines, this paper presents a new train model under the moving block system with different types of trains running with the cellular automaton idea. By analyzing such key factors as the maintenance skylight, the proportion of the multispeed running trains, and the distance between adjacent stations and departure intervals, the corresponding running rules for the cellular automaton model are reestablished herewith. By means of this CA model, the program of train running system is designed to analyze the potential impact on railway carrying capacity by various factors; the model can also be implemented to simulate the actual train running process and to draw the train operation diagram by computers. Basically the theory can be applied to organize the train operation on the dedicated passenger lines.
A generalized cellular automata approach to modeling first order enzyme kinetics
Indian Academy of Sciences (India)
Abhishek Dutta; Saurajyoti Kar; Advait Apte; Ingmar Nopens; Denis Constales
2015-04-01
Biochemical processes occur through intermediate steps which are associated with the formation of reaction complexes. These enzyme-catalyzed biochemical reactions are inhibited in a number of ways such as inhibitors competing for the binding site directly, inhibitors deforming the allosteric site or inhibitors changing the structure of active substrate. Using an in silico approach, the concentration of various reaction agents can be monitored at every single time step, which are otherwise difficult to analyze experimentally. Cell-based models with discrete state variables, such as Cellular Automata (CA) provide an understanding of the organizational principles of interacting cellular systems to link the individual cell (microscopic) dynamics wit a particular collective (macroscopic) phenomenon. In this study, a CA model representing a first order enzyme kinetics with inhibitor activity is formulated. The framework of enzyme reaction rules described in this study is probabilistic. An extended von Neumann neighborhood with periodic boundary condition is implemented on a two-dimensional (2D) lattice framework. The effect of lattice-size variation is studied followed by a sensitivity analysis of the model output to the probabilistic parameters which represent various kinetic reaction constants in the enzyme kinetic model. This provides a deeper insight into the sensitivity of the CA model to these parameters. It is observed that cellular automata can capture the essential features of a discrete real system, consisting of space, time and state, structured with simple local rules without making complex implementations but resulting in complex but explainable patterns.
In Silico Modeling of the Immune System: Cellular and Molecular Scale Approaches
Directory of Open Access Journals (Sweden)
Mariagrazia Belfiore
2014-01-01
Full Text Available The revolutions in biotechnology and information technology have produced clinical data, which complement biological data. These data enable detailed descriptions of various healthy and diseased states and responses to therapies. For the investigation of the physiology and pathology of the immune responses, computer and mathematical models have been used in the last decades, enabling the representation of biological processes. In this modeling effort, a major issue is represented by the communication between models that work at cellular and molecular level, that is, multiscale representation. Here we sketch some attempts to model immune system dynamics at both levels.
A Stochastic Cellular Automaton Model of Non-linear Diffusion and Diffusion with Reaction
Brieger, Leesa M.; Bonomi, Ernesto
1991-06-01
This article presents a stochastic cellular automaton model of diffusion and diffusion with reaction. The master equations for the model are examined, and we assess the difference between the implementation in which a single particle at a time moves (asynchronous dynamics) and one implementation in which all particles move simultaneously (synchronous dynamics). Biasing locally each particle's random walk, we alter the diffusion coefficients of the system. By appropriately choosing the biasing function, we can impose a desired non-linear diffusive behaviour in the model. We present an application of this model, adapted to include two diffusing species, two static species, and a chemical reaction in a prototypical simulation of carbonation in concrete.
Efficient Analysis of Systems Biology Markup Language Models of Cellular Populations Using Arrays.
Watanabe, Leandro; Myers, Chris J
2016-08-19
The Systems Biology Markup Language (SBML) has been widely used for modeling biological systems. Although SBML has been successful in representing a wide variety of biochemical models, the core standard lacks the structure for representing large complex regular systems in a standard way, such as whole-cell and cellular population models. These models require a large number of variables to represent certain aspects of these types of models, such as the chromosome in the whole-cell model and the many identical cell models in a cellular population. While SBML core is not designed to handle these types of models efficiently, the proposed SBML arrays package can represent such regular structures more easily. However, in order to take full advantage of the package, analysis needs to be aware of the arrays structure. When expanding the array constructs within a model, some of the advantages of using arrays are lost. This paper describes a more efficient way to simulate arrayed models. To illustrate the proposed method, this paper uses a population of repressilator and genetic toggle switch circuits as examples. Results show that there are memory benefits using this approach with a modest cost in runtime. PMID:26912276
Continuous macroscopic limit of a discrete stochastic model for interaction of living cells
Alber, M; Lushnikov, P M; Newman, S A; Alber, Mark; Chen, Nan; Lushnikov, Pavel M.; Newman, Stuart A.
2007-01-01
In the development of multiscale biological models it is crucial to establish a connection between discrete microscopic or mesoscopic stochastic models and macroscopic continuous descriptions based on cellular density. In this paper a continuous limit of a two-dimensional Cellular Potts Model (CPM) with excluded volume is derived, describing cells moving in a medium and reacting to each other through both direct contact and long range chemotaxis. The continuous macroscopic model is obtained as a Fokker-Planck equation describing evolution of the cell probability density function. All coefficients of the general macroscopic model are derived from parameters of the CPM and a very good agreement is demonstrated between CPM Monte Carlo simulations and numerical solution of the macroscopic model. It is also shown that in the absence of contact cell-cell interactions, the obtained model reduces to the classical macroscopic Keller-Segel model. General multiscale approach is demonstrated by simulating spongy bone for...
Directory of Open Access Journals (Sweden)
Konstantinos B. Baltzis
2008-10-01
Full Text Available A common assumption in cellular communications is the circular-cell approximation. In this paper, an alternative analysis based on the hexagonal shape of the cells is presented. A geometrical-based stochastic model is proposed to describe the angle of arrival of the interfering signals in the reverse link of a cellular system. Explicit closed form expressions are derived, and simulations performed exhibit the characteristics and validate the accuracy of the proposed model. Applications in the capacity estimation of WCDMA cellular networks are presented. Dependence of system capacity of the sectorization of the cells and the base station antenna radiation pattern is explored. Comparisons with data in literature validate the accuracy of the proposed model. The degree of error of the hexagonal and the circular-cell approaches has been investigated indicating the validity of the proposed model. Results have also shown that, in many cases, the two approaches give similar results when the radius of the circle equals to the hexagon inradius. A brief discussion on how the proposed technique may be applied to broadband access networks is finally made.
Directory of Open Access Journals (Sweden)
Hui Guo
2016-07-01
Full Text Available Evodiamine (EVO and rutaecarpine (RUT are promising anti-tumor drug candidates. The evaluation of the anti-proliferative activity and cellular uptake of EVO and RUT in 3D multicellular spheroids of cancer cells would better recapitulate the native situation and thus better reflect an in vivo response to the treatment. Herein, we employed the 3D culture of MCF-7 and SMMC-7721 cells based on hanging drop method and evaluated the anti-proliferative activity and cellular uptake of EVO and RUT in 3D multicellular spheroids, and compared the results with those obtained from 2D monolayers. The drugs’ IC50 values were significantly increased from the range of 6.4–44.1 μM in 2D monolayers to 21.8–138.0 μM in 3D multicellular spheroids, which may be due to enhanced mass barrier and reduced drug penetration in 3D models. The fluorescence of EVO and RUT was measured via fluorescence spectroscopy and the cellular uptake of both drugs was characterized in 2D tumor models. The results showed that the cellular uptake concentrations of RUT increased with increasing drug concentrations. However, the EVO concentrations uptaken by the cells showed only a small change with increasing drug concentrations, which may be due to the different solubility of EVO and Rut in solvents. Overall, this study provided a new vision of the anti-tumor activity of EVO and RUT via 3D multicellular spheroids and cellular uptake through the fluorescence of compounds.
Analysis on Traffic Conflicts of Two-lane Highway Based on Improved Cellular Automation Model
Directory of Open Access Journals (Sweden)
Xiru Tang
2013-06-01
Full Text Available Based on microscopic traffic characteristics of two-lane highway and different driving characteristics for drivers, the characteristics of drivers and vehicle structure are introduced into Cellular Automation model for establishing new Cellular Automation model of two-lane highway. Through computer simulation, the paper analyzes the effect of the promotion of different vehicles, drivers and arrival rates on traffic conflicts of two-lane highway, which gets the relationship between the parameters such as road traffic and velocity variance and collision. The results indicate that the frequency of traffic conflicts has close relationship with the product of traffic flow and velocity variation. When the traffic flow and velocity variation are great, the frequency of the conflict is the greatest, and when the traffic flow and velocity variation are little, the frequency of the conflict is the least.
Bit-Vectorized GPU Implementation of a Stochastic Cellular Automaton Model for Surface Growth
Kelling, Jeffrey; Gemming, Sibylle
2016-01-01
Stochastic surface growth models aid in studying properties of universality classes like the Kardar--Paris--Zhang class. High precision results obtained from large scale computational studies can be transferred to many physical systems. Many properties, such as roughening and some two-time functions can be studied using stochastic cellular automaton (SCA) variants of stochastic models. Here we present a highly efficient SCA implementation of a surface growth model capable of simulating billions of lattice sites on a single GPU. We also provide insight into cases requiring arbitrary random probabilities which are not accessible through bit-vectorization.
Transfer-matrix DMRG for stochastic models: The Domany-Kinzel cellular automaton
Kemper, A.; Schadschneider, A.; Zittartz, J.
2001-01-01
We apply the transfer-matrix DMRG (TMRG) to a stochastic model, the Domany-Kinzel cellular automaton, which exhibits a non-equilibrium phase transition in the directed percolation universality class. Estimates for the stochastic time evolution, phase boundaries and critical exponents can be obtained with high precision. This is possible using only modest numerical effort since the thermodynamic limit can be taken analytically in our approach. We also point out further advantages of the TMRG o...
An Exact Path-Loss Density Model for Mobiles in a Cellular System
Abdulla, Mouhamed; Shayan, Yousef R.
2013-01-01
In trying to emulate the spatial position of wireless nodes for purpose of analysis, we rely on stochastic simulation. And, it is customary, for mobile systems, to consider a base-station radiation coverage by an ideal cell shape. For cellular analysis, a hexagon contour is always preferred mainly because of its tessellating nature. Despite this fact, largely due to its intrinsic simplicity, in literature only random dispersion model for a circular shape is known. However, if considered, this...
Tóth, Attila; Brózik, Anna; Szakács, Gergely; Sarkadi, Balázs; Hegedüs, Tamás
2015-01-01
Cells cope with the threat of xenobiotic stress by activating a complex molecular network that recognizes and eliminates chemically diverse toxic compounds. This “chemoimmune system” consists of cellular Phase I and Phase II metabolic enzymes, Phase 0 and Phase III ATP Binding Cassette (ABC) membrane transporters, and nuclear receptors regulating these components. In order to provide a systems biology characterization of the chemoimmune network, we designed a reaction kinetic model based on d...
Van De Wiel, Marco J.; Coulthard, Tom J.; Macklin, Mark G.; Lewin, John
2007-10-01
We introduce a new computational model designed to simulate and investigate reach-scale alluvial dynamics within a landscape evolution model. The model is based on the cellular automaton concept, whereby the continued iteration of a series of local process 'rules' governs the behaviour of the entire system. The model is a modified version of the CAESAR landscape evolution model, which applies a suite of physically based rules to simulate the entrainment, transport and deposition of sediments. The CAESAR model has been altered to improve the representation of hydraulic and geomorphic processes in an alluvial environment. In-channel and overbank flow, sediment entrainment and deposition, suspended load and bed load transport, lateral erosion and bank failure have all been represented as local cellular automaton rules. Although these rules are relatively simple and straightforward, their combined and repeatedly iterated effect is such that complex, non-linear geomorphological response can be simulated within the model. Examples of such larger-scale, emergent responses include channel incision and aggradation, terrace formation, channel migration and river meandering, formation of meander cutoffs, and transitions between braided and single-thread channel patterns. In the current study, the model is illustrated on a reach of the River Teifi, near Lampeter, Wales, UK.
Institute of Scientific and Technical Information of China (English)
HE; Chunyang; SHI; Peijun; CHEN; Jin; Li; Xiaobing; PAN; Ya
2005-01-01
Modeling land use scenario changes and its potential impacts on the structure and function of the ecosystem in the typical regions are helpful to understanding the interactive mechanism between land use system and ecological system. A Land Use Scenario Dynamics (LUSD) model by the integration of System Dynamics (SD) model and Cellular Automata (CA) model is developed with land use scenario changes in northern China in the next 20 years simulated in this paper. The basic idea of LUSD model is to simulate the land use scenario demands by using SD model at first, then allocate the land use scenario patterns at the local scale with the considerations of land use suitability, inheritance ability and neighborhood effect by using CA model to satisfy the balance between land use scenario demands and supply. The application of LUSD model in northern China suggests that the model has the ability to reflect the complex behavior of land use system at different scales to some extent and is a useful tool for assessing the potential impacts of land use system on ecological system. In addition, the simulated results also indicate that obvious land use changes will take place in the farming-pastoral zone of northern China in the next 20 years with cultivated land and urban land being the most active land use types.
Ozcan, H. Kurtulus; Bilgili, Erdem; Sahin, Ulku; Ucan, O. Nuri; Bayat, Cuma
2007-09-01
Tropospheric ozone concentrations, which are an important air pollutant, are modeled by the use of an artificial intelligence structure. Data obtained from air pollution measurement stations in the city of Istanbul are utilized in constituting the model. A supervised algorithm for the evaluation of ozone concentration using a genetically trained multi-level cellular neural network (ML-CNN) is introduced, developed, and applied to real data. A genetic algorithm is used in the optimization of CNN templates. The model results and the actual measurement results are compared and statistically evaluated. It is observed that seasonal changes in ozone concentrations are reflected effectively by the concentrations estimated by the multilevel-CNN model structure, with a correlation value of 0.57 ascertained between actual and model results. It is shown that the multilevel-CNN modeling technique is as satisfactory as other modeling techniques in associating the data in a complex medium in air pollution applications.
Institute of Scientific and Technical Information of China (English)
H. Kurtulus OZCAN; Erdem BILGILI; Ulku SAHIN; O. Nuri UCAN; Cuma BAYAT
2007-01-01
Tropospheric ozone concentrations, which are an important air pollutant, are modeled by the use of an artificial intelligence structure. Data obtained from air pollution measurement stations in the city of Istanbul are utilized in constituting the model. A supervised algorithm for the evaluation of ozone concentration using a genetically trained multi-level cellular neural network (ML-CNN) is introduced, developed, and applied to real data. A genetic algorithm is used in the optimization of CNN templates. The model results and the actual measurement results are compared and statistically evaluated. It is observed that seasonal changes in ozone concentrations are reflected effectively by the concentrations estimated by the multilevel-CNN model structure, with a correlation value of 0.57 ascertained between actual and model results. It is shown that the multilevel-CNN modeling technique is as satisfactory as other modeling techniques in associating the data in a complex medium in air pollution applications.
An improved multi-value cellular automata model for heterogeneous bicycle traffic flow
International Nuclear Information System (INIS)
This letter develops an improved multi-value cellular automata model for heterogeneous bicycle traffic flow taking the higher maximum speed of electric bicycles into consideration. The update rules of both regular and electric bicycles are improved, with maximum speeds of two and three cells per second respectively. Numerical simulation results for deterministic and stochastic cases are obtained. The fundamental diagrams and multiple states effects under different model parameters are analyzed and discussed. Field observations were made to calibrate the slowdown probabilities. The results imply that the improved extended Burgers cellular automata (IEBCA) model is more consistent with the field observations than previous models and greatly enhances the realism of the bicycle traffic model. - Highlights: • We proposed an improved multi-value CA model with higher maximum speed. • Update rules are introduced for heterogeneous bicycle traffic with maximum speed 2 and 3 cells/s. • Simulation results of the proposed model are consistent with field bicycle data. • Slowdown probabilities of both regular and electric bicycles are calibrated
An improved multi-value cellular automata model for heterogeneous bicycle traffic flow
Energy Technology Data Exchange (ETDEWEB)
Jin, Sheng [College of Civil Engineering and Architecture, Zhejiang University, Hangzhou, 310058 China (China); Qu, Xiaobo [Griffith School of Engineering, Griffith University, Gold Coast, 4222 Australia (Australia); Xu, Cheng [Department of Transportation Management Engineering, Zhejiang Police College, Hangzhou, 310053 China (China); College of Transportation, Jilin University, Changchun, 130022 China (China); Ma, Dongfang, E-mail: mdf2004@zju.edu.cn [Ocean College, Zhejiang University, Hangzhou, 310058 China (China); Wang, Dianhai [College of Civil Engineering and Architecture, Zhejiang University, Hangzhou, 310058 China (China)
2015-10-16
This letter develops an improved multi-value cellular automata model for heterogeneous bicycle traffic flow taking the higher maximum speed of electric bicycles into consideration. The update rules of both regular and electric bicycles are improved, with maximum speeds of two and three cells per second respectively. Numerical simulation results for deterministic and stochastic cases are obtained. The fundamental diagrams and multiple states effects under different model parameters are analyzed and discussed. Field observations were made to calibrate the slowdown probabilities. The results imply that the improved extended Burgers cellular automata (IEBCA) model is more consistent with the field observations than previous models and greatly enhances the realism of the bicycle traffic model. - Highlights: • We proposed an improved multi-value CA model with higher maximum speed. • Update rules are introduced for heterogeneous bicycle traffic with maximum speed 2 and 3 cells/s. • Simulation results of the proposed model are consistent with field bicycle data. • Slowdown probabilities of both regular and electric bicycles are calibrated.
Modelling land-use effects of future urbanization using cellular automata
DEFF Research Database (Denmark)
Fuglsang, Morten; Münier, B.; Hansen, H.S.
2013-01-01
The modelling of land use change is a way to analyse future scenarios by modelling different pathways. Application of spatial data of different scales coupled with socio-economic data makes it possible to explore and test the understanding of land use change relations. In the EU-FP7 research...... project PASHMINA (Paradigm Shift modelling and innovative approaches), three storylines of future transportation paradigm shifts towards 2040 are created. These storylines are translated into spatial planning strategies and modelled using the cellular automata model LUCIA. For the modelling, an Eastern...... Danish case area was selected, comprising of the Copenhagen metropolitan area and its hinterland. The different scenarios are described using a range of different descriptive GIS datasets. These include mapping of accessibility based on public and private transportation, urban density and structure, and...
Guided Inquiry and Consensus-Building Used to Construct Cellular Models
Directory of Open Access Journals (Sweden)
Joel I. Cohen
2015-02-01
Full Text Available Using models helps students learn from a “whole systems” perspective when studying the cell. This paper describes a model that employs guided inquiry and requires consensus building among students for its completion. The model is interactive, meaning that it expands upon a static model which, once completed, cannot be altered and additionally relates various levels of biological organization (molecular, organelle, and cellular to define cell and organelle function and interaction. Learning goals are assessed using data summed from final grades and from images of the student’s final cell model (plant, bacteria, and yeast taken from diverse seventh grade classes. Instructional figures showing consensus-building pathways and seating arrangements are discussed. Results suggest that the model leads to a high rate of participation, facilitates guided inquiry, and fosters group and individual exploration by challenging student understanding of the living cell.
Institute of Scientific and Technical Information of China (English)
W.H. Yu; E.J. Palmiere; S.P. Banks; J.T. Han
2005-01-01
A novel 2D cellular automata (CA) model has been developed for description of normal grain coarsening and abnormal grain coarsening process. The program reflects the grain coarsening quite well even through the average grain size becomes very large. Follow results have been obtained: (a) The model reflect the normal grain growth kinetics gradually increase with probability and grain growth speed can be controlled. Based on this result, temperature can be coupled in the model. (b) Abnormal grain growth is modelled successfully. (c) Methodology has been put forward to find the relationship between the experiment results and modelling results. The experimental work on the grain coarsening has been carried out. Graphical output matched the realistic microstructure in every detail. Because many physical parameters can be taken into account in the CA programme, this CA model could not only qualitatively demonstrate the grain growth process, but also quantitatively predict and analyse the grain coarsening process.
Random walk theory of jamming in a cellular automaton model for traffic flow
Barlovic, Robert; Schadschneider, Andreas; Schreckenberg, Michael
2001-05-01
The jamming behavior of a single lane traffic model based on a cellular automaton approach is studied. Our investigations concentrate on the so-called VDR model which is a simple generalization of the well-known Nagel-Schreckenberg model. In the VDR model one finds a separation between a free flow phase and jammed vehicles. This phase separation allows to use random walk like arguments to predict the resolving probabilities and lifetimes of jam clusters or disturbances. These predictions are in good agreement with the results of computer simulations and even become exact for a special case of the model. Our findings allow a deeper insight into the dynamics of wide jams occuring in the model.
McCune, Matthew; Shafiee, Ashkan; Forgacs, Gabor; Kosztin, Ioan
2014-03-01
Cellular Particle Dynamics (CPD) is an effective computational method for describing and predicting the time evolution of biomechanical relaxation processes of multicellular systems. A typical example is the fusion of spheroidal bioink particles during post bioprinting structure formation. In CPD cells are modeled as an ensemble of cellular particles (CPs) that interact via short-range contact interactions, characterized by an attractive (adhesive interaction) and a repulsive (excluded volume interaction) component. The time evolution of the spatial conformation of the multicellular system is determined by following the trajectories of all CPs through integration of their equations of motion. CPD was successfully applied to describe and predict the fusion of 3D tissue construct involving identical spherical aggregates. Here, we demonstrate that CPD can also predict tissue formation involving uneven spherical aggregates whose volumes decrease during the fusion process. Work supported by NSF [PHY-0957914]. Computer time provided by the University of Missouri Bioinformatics Consortium.
A Cellular Automaton Model for Heterogeneous and Incosistent Driver Behavior in Urban Traffic
Liu, Ming-Zhe; Zhao, Shi-Bo; Wang, Rui-Li
2012-11-01
In this paper a cellular automaton model is proposed to describe driver behavior at a single-lane urban roundabout. Driver behavior has been considered as heterogeneous and inconsistent. Most traffic papers in the literature just discussed heterogeneous driver behavior, to our best knowledge. Two truncated Gaussian distributions are used to model heterogeneous and inconsistent driver behavior, respectively. The physical meanings of two truncated distributions are indicated. This method may help enhance a better understanding of driver behavior at roundabout traffic, and even possibly provide references for roundabout design and management.
Institute of Scientific and Technical Information of China (English)
ZHANG Lin; ZHANG Cai-bei
2006-01-01
Two-dimensional cellular automaton(CA) simulations of phase transformations of binary alloys during solidification were reported. The modelling incorporates local concentration and heat changes into a nucleation or growth function, which is utilized by the automaton in a probabilistic fashion. These simulations may provide an efficient method of discovering how the physical processes involved in solidification processes dynamically progress and how they interact with each other during solidification. The simulated results show that the final morphology during solidification is related with the cooling conditions. The established model can be used to evaluate the phase transformation of binary alloys during solidification.
A Cellular Automaton Model for Heterogeneous and Incosistent Driver Behavior in Urban Traffic
Institute of Scientific and Technical Information of China (English)
LIUMing-Zhe; ZHAO Shi-Bo; WANG Rui-Li
2012-01-01
In this paper a cellular automaton model is proposed to describe driver behavior at a single-lane urban roundabout. Driver behavior has been considered as heterogeneous and inconsistent. Most traffic papers in the literature just discussed heterogeneous driver behavior, to our best knowledge. Two truncated Caussian distributions are used to model heterogeneous and inconsistent driver behavior, respectively. The physical meanings of two truncated distributions are indicated. This method may help enhance a better understanding of driver behavior at roundabout traffic, and even possibly provide references for roundabout design and management.
Modeling Mixed Bicycle Traffic Flow: A Comparative Study on the Cellular Automata Approach
Directory of Open Access Journals (Sweden)
Dan Zhou
2015-01-01
Full Text Available Simulation, as a powerful tool for evaluating transportation systems, has been widely used in transportation planning, management, and operations. Most of the simulation models are focused on motorized vehicles, and the modeling of nonmotorized vehicles is ignored. The cellular automata (CA model is a very important simulation approach and is widely used for motorized vehicle traffic. The Nagel-Schreckenberg (NS CA model and the multivalue CA (M-CA model are two categories of CA model that have been used in previous studies on bicycle traffic flow. This paper improves on these two CA models and also compares their characteristics. It introduces a two-lane NS CA model and M-CA model for both regular bicycles (RBs and electric bicycles (EBs. In the research for this paper, many cases, featuring different values for the slowing down probability, lane-changing probability, and proportion of EBs, were simulated, while the fundamental diagrams and capacities of the proposed models were analyzed and compared between the two models. Field data were collected for the evaluation of the two models. The results show that the M-CA model exhibits more stable performance than the two-lane NS model and provides results that are closer to real bicycle traffic.
2D cellular automaton model for the evolution of active region coronal plasmas
Fuentes, Marcelo López
2016-01-01
We study a 2D cellular automaton (CA) model for the evolution of coronal loop plasmas. The model is based on the idea that coronal loops are made of elementary magnetic strands that are tangled and stressed by the displacement of their footpoints by photospheric motions. The magnetic stress accumulated between neighbor strands is released in sudden reconnection events or nanoflares that heat the plasma. We combine the CA model with the Enthalpy Based Thermal Evolution of Loops (EBTEL) model to compute the response of the plasma to the heating events. Using the known response of the XRT telescope on board Hinode we also obtain synthetic data. The model obeys easy to understand scaling laws relating the output (nanoflare energy, temperature, density, intensity) to the input parameters (field strength, strand length, critical misalignment angle). The nanoflares have a power-law distribution with a universal slope of -2.5, independent of the input parameters. The repetition frequency of nanoflares, expressed in t...
Numerical study on photoresist etching processes based on a cellular automata model
Institute of Scientific and Technical Information of China (English)
2007-01-01
For the three-dimensional (3-D) numerical study of photoresist etching processes, the 2-D dynamic cellular automata (CA) model has been successfully extended to a 3-D dynamic CA model. Only the boundary cells will be processed in the 3-D dy-namic CA model and the structure of “if-else” description in the simulation pro-gram is avoided to speed up the simulation. The 3-D dynamic CA model has found to be stable, fast and accurate for the numerical study of photoresist etching processes. The exposure simulation, post-exposure bake (PEB) simulation and etching simulation are integrated together to further investigate the performances of the CA model. Simulation results have been compared with the available ex-perimental results and the simulations show good agreement with the available experiments.
Numerical study on photoresist etching processes based on a cellular automata model
Institute of Scientific and Technical Information of China (English)
ZHOU ZaiFa; HUANG QingAn; LI WeiHua; LU Wei
2007-01-01
For the three-dimensional (3-D) numerical study of photoresist etching processes, the 2-D dynamic cellular automata (CA) model has been successfully extended to a 3-D dynamic CA model. Only the boundary cells will be processed in the 3-D dynamic CA model and the structure of "if-else" description in the simulation program is avoided to speed up the simulation. The 3-D dynamic CA model has found to be stable, fast and accurate for the numerical study of photoresist etching processes. The exposure simulation, post-exposure bake (PEB) simulation and etching simulation are integrated together to further investigate the performances of the CA model. Simulation results have been compared with the available experimental results and the simulations show good agreement with the available experiments.
A traffic flow cellular automaton model to considering drivers' learning and forgetting behaviour
Institute of Scientific and Technical Information of China (English)
Ding Jian-Xun; Huang Hai-Jun; Tian Qiong
2011-01-01
It is known that the commonly used NaSch cellular automaton (CA) model and its modifications can help explain the internal causes of the macro phenomena of traffic flow. However, the randomization probability of vehicle velocity used in these models is assumed to be an exogenous constant or a conditional constant, which cannot reflect the learning and forgetting behaviour of drivers with historical experiences. This paper further modifies the NaSch model by enabling the randomization probability to be adjusted on the bases of drivers' memory. The Markov properties of this modified model are discussed. Analytical and simulation results show that the traffic fundamental diagrams can be indeed improved when considering drivers' intelligent behaviour. Some new features of traffic are revealed by differently combining the model parameters representing learning and forgetting behaviour.
Directory of Open Access Journals (Sweden)
Attila Tóth
Full Text Available Cells cope with the threat of xenobiotic stress by activating a complex molecular network that recognizes and eliminates chemically diverse toxic compounds. This "chemoimmune system" consists of cellular Phase I and Phase II metabolic enzymes, Phase 0 and Phase III ATP Binding Cassette (ABC membrane transporters, and nuclear receptors regulating these components. In order to provide a systems biology characterization of the chemoimmune network, we designed a reaction kinetic model based on differential equations describing Phase 0-III participants and regulatory elements, and characterized cellular fitness to evaluate toxicity. In spite of the simplifications, the model recapitulates changes associated with acquired drug resistance and allows toxicity predictions under variable protein expression and xenobiotic exposure conditions. Our simulations suggest that multidrug ABC transporters at Phase 0 significantly facilitate the defense function of successive network members by lowering intracellular drug concentrations. The model was extended with a novel toxicity framework which opened the possibility of performing in silico cytotoxicity assays. The alterations of the in silico cytotoxicity curves show good agreement with in vitro cell killing experiments. The behavior of the simplified kinetic model suggests that it can serve as a basis for more complex models to efficiently predict xenobiotic and drug metabolism for human medical applications.
Calibrating Cellular Automata of Land Use/cover Change Models Using a Genetic Algorithm
Mas, J. F.; Soares-Filho, B.; Rodrigues, H.
2015-08-01
Spatially explicit land use / land cover (LUCC) models aim at simulating the patterns of change on the landscape. In order to simulate landscape structure, the simulation procedures of most computational LUCC models use a cellular automata to replicate the land use / cover patches. Generally, model evaluation is based on assessing the location of the simulated changes in comparison to the true locations but landscapes metrics can also be used to assess landscape structure. As model complexity increases, the need to improve calibration and assessment techniques also increases. In this study, we applied a genetic algorithm tool to optimize cellular automata's parameters to simulate deforestation in a region of the Brazilian Amazon. We found that the genetic algorithm was able to calibrate the model to simulate more realistic landscape in term of connectivity. Results show also that more realistic simulated landscapes are often obtained at the expense of the location coincidence. However, when considering processes such as the fragmentation impacts on biodiversity, the simulation of more realistic landscape structure should be preferred to spatial coincidence performance.
Solari, Cristian A; Kessler, John O; Goldstein, Raymond E
2013-03-01
The transition from unicellular, to colonial, to larger multicellular organisms has benefits, costs, and requirements. Here we present a model inspired by the volvocine green algae that explains the dynamics involved in the unicellular-multicellular transition using life-history theory and allometry. We model the two fitness components (fecundity and viability) and compare the fitness of hypothetical colonies of different sizes with varying degrees of cellular differentiation to understand the general principles that underlie the evolution of multicellularity. We argue that germ-soma separation may have evolved to counteract the increasing costs and requirements of larger multicellular colonies. The model shows that the cost of investing in soma decreases with size. For lineages such as the Volvocales, as reproduction costs increase with size for undifferentiated colonies, soma specialization benefits the colony indirectly by decreasing such costs and directly by helping reproductive cells acquire resources for their metabolic needs. Germ specialization is favored once soma evolves and takes care of vegetative functions. To illustrate the model, we use some allometric relationships measured in Volvocales. Our analysis shows that the cost of reproducing an increasingly larger group has likely played an important role in the transition to multicellularity and cellular differentiation. PMID:23448886
Simulation of emotional contagion using modified SIR model: A cellular automaton approach
Fu, Libi; Song, Weiguo; Lv, Wei; Lo, Siuming
2014-07-01
Emotion plays an important role in the decision-making of individuals in some emergency situations. The contagion of emotion may induce either normal or abnormal consolidated crowd behavior. This paper aims to simulate the dynamics of emotional contagion among crowds by modifying the epidemiological SIR model to a cellular automaton approach. This new cellular automaton model, entitled the “CA-SIRS model”, captures the dynamic process ‘susceptible-infected-recovered-susceptible', which is based on SIRS contagion in epidemiological theory. Moreover, in this new model, the process is integrated with individual movement. The simulation results of this model show that multiple waves and dynamical stability around a mean value will appear during emotion spreading. It was found that the proportion of initial infected individuals had little influence on the final stable proportion of infected population in a given system, and that infection frequency increased with an increase in the average crowd density. Our results further suggest that individual movement accelerates the spread speed of emotion and increases the stable proportion of infected population. Furthermore, decreasing the duration of an infection and the probability of reinfection can markedly reduce the number of infected individuals. It is hoped that this study will be helpful in crowd management and evacuation organization.
Non-linearity and spatial resolution in a cellular automaton model of a small upland basin
Directory of Open Access Journals (Sweden)
T. J. Coulthard
1998-01-01
Full Text Available The continuing development of computational fluid dynamics is allowing the high resolution study of hydraulic and sediment transport processes but, due to computational complexities, these are rarely applied to areas larger than a reach. Existing approaches, based upon linked cross sections, can give a quasi two-dimensional view, effectively simulating sediment transport for a single river reach. However, a basin represents a whole discrete dynamic system within which channel, floodplain and slope processes operate over a wide range of space and time scales. Here, a cellular automaton (CA approach has been used to overcome some of these difficulties, in which the landscape is represented as a series of fixed size cells. For every model iteration, each cell acts only in relation to the influence of its immediate neighbours in accordance with appropriate rules. The model presented here takes approximations of existing flow and sediment transport equations, and integrates them, together with slope and floodplain approximations, within a cellular automaton framework. This method has been applied to the basin of Cam Gill Beck (4.2 km2 above Starbotton, upper Wharfedale, a tributary of the River Wharfe, North Yorkshire, UK. This approach provides, for the first time, a workable model of the whole basin at a 1 m resolution. Preliminary results show the evolution of bars, braids, terraces and alluvial fans which are similar to those observed in the field, and examples of large and small scale non-linear behaviour which may have considerable implications for future models.
Advanced spatial metrics analysis in cellular automata land use and cover change modeling
International Nuclear Information System (INIS)
This paper proposes an approach for a more effective definition of cellular automata transition rules for landscape change modeling using an advanced spatial metrics analysis. This approach considers a four-stage methodology based on: (i) the search for the appropriate spatial metrics with minimal correlations; (ii) the selection of the appropriate neighborhood size; (iii) the selection of the appropriate technique for spatial metrics application; and (iv) the analysis of the contribution level of each spatial metric for joint use. The case study uses an initial set of 7 spatial metrics of which 4 are selected for modeling. Results show a better model performance when compared to modeling without any spatial metrics or with the initial set of 7 metrics.
Empirical results for pedestrian dynamics and their implications for cellular automata models
Schadschneider, Andreas
2010-01-01
A large number of models for pedestrian dynamics have been developed over the years. However, so far not much attention has been paid to their quantitative validation. Usually the focus is on the reproduction of empirically observed collective phenomena, as lane formation in counterflow. This can give an indication for the realism of the model, but practical applications, e.g. in safety analysis, require quantitative predictions. We discuss the current experimental situation, especially for the fundamental diagram which is the most important quantity needed for calibration. In addition we consider the implications for the modelling based on cellular automata. As specific example the floor field model is introduced. Apart from the properties of its fundamental diagram we discuss the implications of an egress experiment for the relevance of conflicts and friction effects.
A new three-step cellular automaton model considering a realistic driving decision
International Nuclear Information System (INIS)
Most cellular automaton (CA) traffic flow models include four steps and take the velocity as the driver’s main concern. To better understand traffic behaviors, a new three-step CA model is studied, in which a realistic driving decision is divided into three stages: decision-making, action and result. The new model is novel in using the acceleration as a decision variable. It considers the deceleration limitation and proposes the maximum deceleration to be 2 cells per time step, based on real experimental data. Simulation results show that the model can reproduce the synchronized flow effectively and describe the phase transition well. Moreover, it can exhibit metastability and hysteresis if the slow-to-start effect is involved. Finally, a realistic application to systematic flow optimization is analyzed and an interesting result is obtained that a restriction of the inflow can lead to an improvement of the total flow through a bottleneck. (paper)
Directory of Open Access Journals (Sweden)
M. Górny
2012-12-01
Full Text Available The mathematical model of the globular eutectic solidification in 2D was designed. Proposed model is based on the Cellular AutomatonFinite Differences (CA-FD calculation method. Model has been used for studies of the primary austenite and of globular eutectic grainsgrowth during the ductile iron solidification in the thin wall casting. Model takes into account, among other things, non-uniformtemperature distribution in the casting wall cross-section, kinetics of the austenite and graphite grains nucleation, and non-equilibriumnature of the interphase boundary migration. Calculation of eutectic saturation influence (Sc = 0.9 - 1.1 on microstructure (austenite and graphite fraction, density of austenite and graphite grains and temperature curves in 2 mm wall ductile iron casting has been done.
Directory of Open Access Journals (Sweden)
Luciano Farage
2002-03-01
Full Text Available Relatamos caso de tratamento cirúrgico com instrumentação anterior em espondilite tuberculosa (mal de Pott, em mulher de 71 anos, que se encontrava em tratamento para tuberculose na forma pulmonar e evoluiu com dor lombar, dificuldade progressiva para deambular, cifose e disfunção vesical. A ressonância magnética revelou lesão nos corpos vertebrais de T12 e L1 com abcesso paravertebral. A paciente foi tratada cirurgicamente por acesso tóraco-abdominal lateral. Os corpos vertebrais foram ressecados, foi instalado uma gaiola vertical (mesh cage e a coluna foi estabilizada com placa lateral (Z plate e parafusos fixados em T11 e L2. Essa técnica permite boa artrodese dos corpos vertebrais remanescentes e boa estabilidade da coluna, sem comprometer a eficácia dos tuberculostáticos. A paciente foi avaliada um ano após a operação e não apresentava déficit motor, dor residual e a cifose foi desfeita.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 deformit 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.
Cellular-automata model of the dwarf shrubs populations and communities dynamics
Directory of Open Access Journals (Sweden)
A. S. Komarov
2015-06-01
Full Text Available The probabilistic cellular-automata model of development and long-time dynamics of dwarf shrub populations and communities is developed. It is based on the concept of discrete description of the plant ontogenesis and joint model approaches in terms of probabilistic cellular automata and L-systems by Lindenmayer. Short representation of the basic model allows evaluation of the approach and software implementation. The main variables of the model are a number of partial bushes in clones or area projective cover. The model allows us to investigate the conditions of self-maintenance and sustainability population under different environmental conditions (inaccessibility of the territory for settlement, mosaic moisture conditions of soil and wealth. The model provides a forecast of the total biomass dynamics shrubs and their fractions (stems, leaves, roots, fine roots, fruits on the basis of the data obtained in the discrete description of ontogenesis and further information on the productivity of the plant fractions. The inclusion of the joint dynamics of biomass of shrubs and soil in EFIMOD models cycle of carbon and nitrogen to evaluate the role of shrubs in these circulations, especially at high impact, such as forest fires and clear cutting, allow forecasting of the dynamics of populations and ecosystem functions of shrubs (regulation of biogeochemical cycles maintaining biodiversity, participation in the creation of non-wood products with changing climatic conditions and strong damaging effects (logging, fires; and application of the models developed to investigate the stability and productivity of shrubs and their participation in the cycle of carbon and nitrogen in different climatic and edaphic conditions.
Cellular automata model based on GIS and urban sprawl dynamics simulation
Mu, Fengyun; Zhang, Zengxiang
2005-10-01
The simulation of land use change process needs the support of Geographical Information System (GIS) and other relative technologies. While the present commercial GIS lack capabilities of distribution, prediction, and simulation of spatial-temporal data. Cellular automata (CA) provide dynamically modeling "from bottom-to-top" framework and posses the capability of modeling spatial-temporal evolvement process of a complicated geographical system, which is composed of a fourfold: cells, states, neighbors and rules. The simplicity and flexibility make CA have the ability to simulate a variety of behaviors of complex systems. One of the most potentially useful applications of cellular automata from the point of view of spatial planning is their use in simulations of urban sprawl at local and regional level. The paper firstly introduces the principles and characters of the cellular automata, and then discusses three methods of the integration of CA and GIS. The paper analyses from a practical point of view the factors that effect urban activities in the science of spatial decision-making. The status of using CA to dynamic simulates of urban expansion at home and abroad is analyzed. Finally, the problems and tendencies that exist in the application of CA model are detailed discussed, such as the quality of the data that the CA needs, the self-organization of the CA roots in the mutual function among the elements of the system, the partition of the space scale, the time calibration of the CA and the integration of the CA with other modular such as artificial nerve net modular and population modular etc.
Khan, Muhammad Sadiq Ali; Yousuf, Sidrah
2016-03-01
Cardiac Electrical Activity is commonly distributed into three dimensions of Cardiac Tissue (Myocardium) and evolves with duration of time. The indicator of heart diseases can occur randomly at any time of a day. Heart rate, conduction and each electrical activity during cardiac cycle should be monitor non-invasively for the assessment of "Action Potential" (regular) and "Arrhythmia" (irregular) rhythms. Many heart diseases can easily be examined through Automata model like Cellular Automata concepts. This paper deals with the different states of cardiac rhythms using cellular automata with the comparison of neural network also provides fast and highly effective stimulation for the contraction of cardiac muscles on the Atria in the result of genesis of electrical spark or wave. The specific formulated model named as "States of automaton Proposed Model for CEA (Cardiac Electrical Activity)" by using Cellular Automata Methodology is commonly shows the three states of cardiac tissues conduction phenomena (i) Resting (Relax and Excitable state), (ii) ARP (Excited but Absolutely refractory Phase i.e. Excited but not able to excite neighboring cells) (iii) RRP (Excited but Relatively Refractory Phase i.e. Excited and able to excite neighboring cells). The result indicates most efficient modeling with few burden of computation and it is Action Potential during the pumping of blood in cardiac cycle. PMID:27087101
In situ sensing and modeling of molecular events at the cellular level
Yang, Ruiguo
We developed the Atomic Force Microscopy (AFM) based nanorobot in combination with other nanomechanical sensors for the investigation of cell signaling pathways. The AFM nanorobotics hinge on the superior spatial resolution of AFM in imaging and extends it into the measurement of biological processes and manipulation of biological matters. A multiple input single output control system was designed and implemented to solve the issues of nanomanipulation of biological materials, feedback, response frequency and nonlinearity. The AFM nanorobotic system therefore provide the human-directed position, velocity and force control with high frequency feedback, and more importantly it can feed the operator with the real-time imaging of manipulation result from the fast-imaging based local scanning. The use of the system has taken the study of cellular process at the molecular scale into a new level. The cellular response to the physiological conditions can be significantly manifested in cellular mechanics. Dynamic mechanical property has been regarded as biomarkers, sometimes even regulators of the signaling and physiological processes, thus the name mechanobiology. We sought to characterize the relationship between the structural dynamics and the molecular dynamics and the role of them in the regulation of cell behavior. We used the AFM nanorobotics to investigate the mechanical properties in real-time of cells that are stimulated by different chemical species. These reagents could result in similar ion channel responses but distinctive mechanical behaviors. We applied these measurement results to establish a model that describes the cellular stimulation and the mechanical property change, a "two-hit" model that comprises the loss of cell adhesion and the initiation of cell apoptosis. The first hit was verified by functional experiments: depletion of Calcium and nanosurgery to disrupt the cellular adhesion. The second hit was tested by a labeling of apoptotic markers that
Bagnoli, Franco
1998-01-01
An introduction to cellular automata (both deterministic and probabilistic) with examples. Definition of deterministic automata, dynamical properties, damage spreading and Lyapunov exponents; probabilistic automata and Markov processes, nonequilibrium phase transitions, directed percolation, diffusion; simulation techniques, mean field. Investigation themes: life, epidemics, forest fires, percolation, modeling of ecosystems and speciation. They represent my notes for the school "Dynamical Mod...
A novel model for studies of blood-mediated long-term responses to cellular transplants
Hårdstedt, Maria; Lindblom, Susanne; Hong, Jaan; Nilsson, Bo; Korsgren, Olle; Ronquist, Gunnar
2015-01-01
Aims Interaction between blood and bio-surfaces is important in many medical fields. With the aim of studying blood-mediated reactions to cellular transplants, we developed a whole-blood model for incubation of small volumes for up to 48 h. Methods Heparinized polyvinyl chloride tubing was cut in suitable lengths and sealed to create small bags. Multiple bags, with fresh venous blood, were incubated attached to a rotating wheel at 37°C. Physiological variables in blood were monitored: glucose...
Case Study of Phase Transition in Cellular Models of Pedestrian Flow
Czech Academy of Sciences Publication Activity Database
Bukáček, M.; Hrabák, Pavel
Cham : Springer, 2014 - (Was, J.; Sirakoulis, G.; Bandini, S.), s. 508-517 ISBN 978-3-319-11519-1. ISSN 0302-9743. - (Lecture Notes in Computer Science. 8751). [ACRI 2014. International Conference on Cellular Automata for Research and Industry /11./. Krakov (PL), 22.09.2014-25.09.2014] R&D Projects: GA ČR GA13-13502S Institutional support: RVO:67985556 Keywords : Floor field model * phase transition * travel time * bounds principle * asynchronous update Subject RIV: IN - Informatics, Computer Science http://library.utia.cas.cz/separaty/2014/AS/hrabak-0432244.pdf
Metabolically active portion of fat-free mass: a cellular body composition level modeling analysis
Wang, ZiMian; Heshka, Stanley; Wang, Jack; Gallagher, Dympna; Deurenberg, Paul; Chen, Zhao; Heymsfield, Steven B
2006-01-01
The proportion of fat-free mass (FFM) as body cell mass (BCM) is highly related to whole body resting energy expenditure. However, the magnitude of BCM/FFM may have been underestimated in previous studies. This is because Moore’s equation [BCM (kg) =0.00833 × total body potassium (in mmol)], which was used to predict BCM, underestimates BCM by ~ %. The aims of the present study were to develop a theoretical BCM/FFM model at the cellular level and to explore the influences of sex, age, and adi...
Driver’s Awareness and Lane Changing Maneuver in Traffic Flow based on Cellular Automaton Model
Kohei Arai; Steven Ray Sentinuwo
2015-01-01
Effect of driver’s awareness (e.g., to estimate the speed and arrival time of another vehicle) on the lane changing maneuver is discussed. “Scope awareness” is defined as the visibility which is required for the driver to make a visual perception about road condition and the speed of vehicle that appears in the target lane for lane changing in the road. Cellular automaton based simulation model is created and applied to simulation studies for driver awareness behavior. This study clarifies re...
Enayatifar, Rasul; Sadaei, Hossein Javedani; Abdullah, Abdul Hanan; Lee, Malrey; Isnin, Ismail Fauzi
2015-08-01
Currently, there are many studies have conducted on developing security of the digital image in order to protect such data while they are sending on the internet. This work aims to propose a new approach based on a hybrid model of the Tinkerbell chaotic map, deoxyribonucleic acid (DNA) and cellular automata (CA). DNA rules, DNA sequence XOR operator and CA rules are used simultaneously to encrypt the plain-image pixels. To determine rule number in DNA sequence and also CA, a 2-dimension Tinkerbell chaotic map is employed. Experimental results and computer simulations, both confirm that the proposed scheme not only demonstrates outstanding encryption, but also resists various typical attacks.
Transition between immune and disease states in a cellular automaton model of clonal immune response
Bezzi, M; Ruffo, S; Seiden, P E; Bezzi, Michele; Celada, Franco; Ruffo, Stefano; Seiden, Philip E.
1997-01-01
In this paper we extend the Celada-Seiden (CS) model of the humoral immune response to include infectious virus and cytotoxic T lymphocytes (cellular response). The response of the system to virus involves a competition between the ability of the virus to kill the host cells and the host's ability to eliminate the virus. We find two basins of attraction in the dynamics of this system, one is identified with disease and the other with the immune state. There is also an oscillating state that exists on the border of these two stable states. Fluctuations in the population of virus or antibody can end the oscillation and drive the system into one of the stable states. The introduction of mechanisms of cross-regulation between the two responses can bias the system towards one of them. We also study a mean field model, based on coupled maps, to investigate virus-like infections. This simple model reproduces the attractors for average populations observed in the cellular automaton. All the dynamical behavior connect...
An implementation of cellular automaton model for single-line train working diagram
Institute of Scientific and Technical Information of China (English)
Hua Wei; Liu Jun
2006-01-01
According to the railway transportation system's characteristics,a new cellular automaton model for the singleline railway system is presented in this paper.Based on this model,several simulations were done to imitate the train operation under three working diagrams.From a different angle the results show how the organization of train operation impacts on the railway carrying capacity.By using the non-parallel train working diagram the influence of fast-train on slow-train is found to be the strongest.Many slow-trains have to wait in-between neighbouring stations to let the fast-train(s) pass through first.So the slow-train will advance like a wave propagating from the departure station to the arrival station.This also resembles the situation of a highway jammed traffic flow.Furthermore,the nonuniformity of travel times between the sections also greatly limits the railway carrying capacity.After converting the nonuniform sections into the sections with uniform travel times while the total travel time is kept unchanged,all three carrying capacities are improved greatly as shown by simulation.It also shows that the cellular automaton model is an effective and feasible way to investigate the railway transDortation system.
Mal de Pott em Crianças de 15 Meses
de Miguel, Cristina; Ferreira, Gabriel; Miranda, Francisco; Oliveira, António; Geraldes, Amadeu; Seabra, Jorge; de Oliveira, Gonçalves
2014-01-01
A tuberculose da coluna vertebral descrita pela primeira vez por Percival Pott e desde então associada ao seu nome, é uma doença de desenvolvimento lento, caracterizada por dor, deformidade vertebral e por vezes paralisia.Um alto índice de suspeição, assim como um tratamento precoce e adequado são necessários na abordagem da tuberculose vertebral.Os autores apresentam um caso clínico de uma criança com 15 meses de idade com tuberculose vertebral, apresentando cifose e paraparesia no momento d...
Modeling of the competition life cycle using the software complex of cellular automata PyCAlab
Berg, D. B.; Beklemishev, K. A.; Medvedev, A. N.; Medvedeva, M. A.
2015-11-01
The aim of the work is to develop a numerical model of the life cycle of competition on the basis of software complex cellular automata PyCAlab. The model is based on the general patterns of growth of various systems in resource-limited settings. At examples it is shown that the period of transition from an unlimited growth of the market agents to the stage of competitive growth takes quite a long time and may be characterized as monotonic. During this period two main strategies of competitive selection coexist: 1) capture of maximum market space with any reasonable costs; 2) saving by reducing costs. The obtained results allow concluding that the competitive strategies of companies must combine two mentioned types of behavior, and this issue needs to be given adequate attention in the academic literature on management. The created numerical model may be used for market research when developing of the strategies for promotion of new goods and services.
A Two-Lane Cellular Automata Model with Influence of Next-Nearest Neighbor Vehicle
International Nuclear Information System (INIS)
In this paper, we propose a new two-lane cellular automata model in which the influence of the next-nearest neighbor vehicle is considered. The attributes of the traffic system composed of fast-lane and slow-lane are investigated by the new traffic model. The simulation results show that the proposed two-lane traffic model can reproduce some traffic phenomena observed in real traffic, and that maximum flux and critical density are close to the field measurements. Moreover, the initial density distribution of the fast-lane and slow-lane has much influence on the traffic flow states. With the ratio between the densities of slow lane and fast lane increasing the lane changing frequency increases, but maximum flux decreases. Finally, the influence of the sensitivity coefficients is discussed.
Aalaei, Amin; Davoudpour, Hamid
2012-11-01
This article presents designing a new mathematical model for integrating dynamic cellular manufacturing into supply chain system with an extensive coverage of important manufacturing features consideration of multiple plants location, multi-markets allocation, multi-period planning horizons with demand and part mix variation, machine capacity, and the main constraints are demand of markets satisfaction in each period, machine availability, machine time-capacity, worker assignment, available time of worker, production volume for each plant and the amounts allocated to each market. The aim of the proposed model is to minimize holding and outsourcing costs, inter-cell material handling cost, external transportation cost, procurement & maintenance and overhead cost of machines, setup cost, reconfiguration cost of machines installation and removal, hiring, firing and salary worker costs. Aimed to prove the potential benefits of such a design, presented an example is shown using a proposed model.
Ren, Gang; Jiang, Hang; Chen, Jingxu; Huang, Zhengfeng; Lu, Lili
2016-06-01
This paper presents a cellular automata (CA) model to elucidate the straight-through movements of the heterogeneous bicycle traffic at signalized intersection. The CA model, via simulation, particularly exposits the dispersion phenomenon existing in the straight-through bicycle traffic. The nonlane-based cycling behavior and diverse bicycle properties are also incorporated in the CA model. A series of simulations are conducted to reveal the travel process, bicycles interaction and influence of the dispersion phenomenon. The simulation results show that the dispersion phenomenon significantly results in more bicycles interactions in terms of spilling maneuvers and overtaking maneuvers during the straight-through movements. Meanwhile, the dispersion phenomenon could contribute to the efficiency of the bicycle traffic, and straight-through bicycles need less time to depart the intersection under the circumstance of dispersion phenomenon. The simulation results are able to provide specific guideline for reasonably utilizing the dispersion phenomenon to improve the operational efficiency of straight-through bicycle traffic.
Directory of Open Access Journals (Sweden)
Kamran Forghani
2012-10-01
Full Text Available In this paper, a new mathematical model in cellular manufacturing systems (CMSs has been presented. In order to increase the performance of manufacturing system, the production quantity of parts has been considered as a decision variable, i.e. each part can be produced and outsourced, simultaneously. This extension would be minimized the unused capacity of machines. The exceptional elements (EEs are taken into account and would be totally outsourced to the external supplier in order to remove intercellular material handling cost. The problem has been formulated as a mixed-integer programming to minimize the sum of manufacturing variable costs under budget, machines capacity and demand constraints. Also, to evaluate advantages of the model, several illustrative numerical examples have been provided to compare the performance of the proposed model with the available classical approaches in the literature.
Steady state speed distribution analysis for a combined cellular automaton traffic model
Institute of Scientific and Technical Information of China (English)
Wang Jun-Feng; Chen Gui-Sheng; Liu Jin
2008-01-01
Cellular Automaton (CA) baaed traffic flow models have been extensively studied due to their effectiveness and simplicity in recent years. This paper develops a discrete time Markov chain (DTMC) analytical framework for a Nagel-Schreckenberg and Fukui-Ishibashi combined CA model (W2H traffic flow model) from microscopic point of view to capture the macroscopic steady state speed distributions. The inter-vehicle spacing Markov chain and the steady state speed Markov chain are proved to be irreducible and ergodie. The theoretical speed probability distributions depending on the traffic density and stochastic delay probability are in good accordance with numerical simulations. The derived fundamental diagram of the average speed from theoretical speed distributions is equivalent to the results in the previous work.
International Nuclear Information System (INIS)
The problem of quantitative mathematical models in cellular radiation biology is discussed in a general way. It is emphasized that there are a number of stages, starting from the spatial pattern of energy deposition and ending with repair/misrepair processes which all need to be incorporated. Since different types of radiation commonly yield very similar dose-response curves a model which is only valid for one special case cannot claim general applicability. Interaction experiments with ultraviolet and ionizing radiation are discussed in this context. Also the role of different experimental systems (microorganisms versus mammalian cells) has to be taken into account. A number of current model approaches are discussed within this context, and it is shown that most of them do not satisfy the criterion of universal applicability and can therefore not claim to give a 'true' picture of biological reality. Shouldered survival curves are taken as an example to illustrate these points in a more specific way
A computable cellular stress network model for non-diseased pulmonary and cardiovascular tissue
Directory of Open Access Journals (Sweden)
Drubin David
2011-10-01
Full Text Available Abstract Background Humans and other organisms are equipped with a set of responses that can prevent damage from exposure to a multitude of endogenous and environmental stressors. If these stress responses are overwhelmed, this can result in pathogenesis of diseases, which is reflected by an increased development of, e.g., pulmonary and cardiac diseases in humans exposed to chronic levels of environmental stress, including inhaled cigarette smoke (CS. Systems biology data sets (e.g., transcriptomics, phosphoproteomics, metabolomics could enable comprehensive investigation of the biological impact of these stressors. However, detailed mechanistic networks are needed to determine which specific pathways are activated in response to different stressors and to drive the qualitative and eventually quantitative assessment of these data. A current limiting step in this process is the availability of detailed mechanistic networks that can be used as an analytical substrate. Results We have built a detailed network model that captures the biology underlying the physiological cellular response to endogenous and exogenous stressors in non-diseased mammalian pulmonary and cardiovascular cells. The contents of the network model reflect several diverse areas of signaling, including oxidative stress, hypoxia, shear stress, endoplasmic reticulum stress, and xenobiotic stress, that are elicited in response to common pulmonary and cardiovascular stressors. We then tested the ability of the network model to identify the mechanisms that are activated in response to CS, a broad inducer of cellular stress. Using transcriptomic data from the lungs of mice exposed to CS, the network model identified a robust increase in the oxidative stress response, largely mediated by the anti-oxidant NRF2 pathways, consistent with previous reports on the impact of CS exposure in the mammalian lung. Conclusions The results presented here describe the construction of a cellular stress
Energy Technology Data Exchange (ETDEWEB)
Zhao, Yuchao; Conolly, Rory B; Andersen, Melvin E.
2006-11-21
This report describes the development of a computational systems biology approach to evaluate the hypotheses of molecular and cellular mechanisms of adaptive response to low dose ionizing radiation. Our concept is that computational models of signaling pathways can be developed and linked to biologically based dose response models to evaluate the underlying molecular mechanisms which lead to adaptive response. For development of quantitatively accurate, predictive models, it will be necessary to describe tissues consisting of multiple cell types where the different types each contribute in their own way to the overall function of the tissue. Such a model will probably need to incorporate not only cell type-specific data but also spatial information on the architecture of the tissue and on intercellular signaling. The scope of the current model was more limited. Data obtained in a number of different biological systems were synthesized to describe a chimeric, “average” population cell. Biochemical signaling pathways involved in sensing of DNA damage and in the activation of cell cycle checkpoint controls and the apoptotic path were also included. As with any computational modeling effort, it was necessary to develop these simplified initial descriptions (models) that can be iteratively refined. This preliminary model is a starting point which, with time, can evolve to a level of refinement where large amounts of detailed biological information are synthesized and a capability for robust predictions of dose- and time-response behaviors is obtained.
A Vector-based Cellular Automata Model for Simulating Urban Land Use Change
Institute of Scientific and Technical Information of China (English)
LU Yi; CAO Min; ZHANG Lei
2015-01-01
Cellular Automata (CA) is widely used for the simulation of land use changes.This study applied a vector-based CA model to simulate land use change in order to minimize or eliminate the scale sensitivity in traditional raster-based CA model.The cells of vector-based CA model are presented according to the shapes and attributes of geographic entities,and the transition rules of vector-based CA model are improved by taking spatial variables of the study area into consideration.The vector-based CA model is applied to simulate land use changes in downtown of Qidong City,Jiangsu Province,China and its validation is confirmed by the methods of visual assessment and spatial accuracy.The simulation result of vector-based CA model reveals that nearly 75％ of newly increased urban cells are located in the northwest and southwest parts of the study area from 2002 to 2007,which is in consistent with real land use map.In addition,the simulation results of the vector-based and raster-based CA models are compared to real land use data and their spatial accuracies are found to be 84.0％ and 81.9％,respectively.In conclusion,results from this study indicate that the vector-based CA model is a practical and applicable method for the simulation of urbanization processes.
Geographic Spatiotemporal Dynamic Model using Cellular Automata and Data Mining Techniques
Directory of Open Access Journals (Sweden)
Ahmad Zuhdi
2011-05-01
Full Text Available Geospatial data and information availability has been increasing rapidly and has provided users with knowledge on entities change and movement in a system. Cellular Geography model applies Cellular Automata on Geographic data by defining transition rules to the data grid. This paper presents the techniques for extracting transition rule(s from time series data grids, using multiple linear regression analysis. Clustering technique is applied to minimize the number of transition rules, which can be offered and chosen to change a new unknown grid. Each centroid of a cluster is associated with a transition rule and a grid of data. The chosen transition rule is associated with grid that has a minimum distance to the new data grid to be simulated. Validation of the model can be provided either quantitatively through an error measurement or qualitatively by visualizing the result of the simulation process. The visualization can also be more informative by adding the error information. Increasing number of cluster may give possibility to improve the simulation accuracy.
The mechanics of cellular compartmentalization as a model for tumor spreading
Fritsch, Anatol; Pawlizak, Steve; Zink, Mareike; Kaes, Josef A.
2012-02-01
Based on a recently developed surgical method of Michael H"ockel, which makes use of cellular confinement to compartments in the human body, we study the mechanics of the process of cell segregation. Compartmentalization is a fundamental process of cellular organization and occurs during embryonic development. A simple model system can demonstrate the process of compartmentalization: When two populations of suspended cells are mixed, this mixture will eventually segregate into two phases, whereas mixtures of the same cell type will not. In the 1960s, Malcolm S. Steinberg formulated the so-called differential adhesion hypothesis which explains the segregation in the model system and the process of compartmentalization by differences in surface tension and adhesiveness of the interacting cells. We are interested in to which extend the same physical principles affect tumor growth and spreading between compartments. For our studies, we use healthy and cancerous breast cell lines of different malignancy as well as primary cells from human cervix carcinoma. We apply a set of techniques to study their mechanical properties and interactions. The Optical Stretcher is used for whole cell rheology, while Cell-cell-adhesion forces are directly measured with a modified AFM. In combination with 3D segregation experiments in droplet cultures we try to clarify the role of surface tension in tumor spreading.
Achour, Imène; Arel-Dubeau, Anne-Marie; Renaud, Justine; Legrand, Manon; Attard, Everaldo; Germain, Marc; Martinoli, Maria-Grazia
2016-01-01
Parkinson's disease (PD) is a progressive neurodegenerative disorder, primarily affecting dopaminergic neurons in the substantia nigra. There is currently no cure for PD and present medications aim to alleviate clinical symptoms, thus prevention remains the ideal strategy to reduce the prevalence of this disease. The goal of this study was to investigate whether oleuropein (OLE), the major phenolic compound in olive derivatives, may prevent neuronal degeneration in a cellular dopaminergic model of PD, differentiated PC12 cells exposed to the potent parkinsonian toxin 6-hydroxydopamine (6-OHDA). We also investigated OLE's ability to mitigate mitochondrial oxidative stress and modulate the autophagic flux. Our results obtained by measuring cytotoxicity and apoptotic events demonstrate that OLE significantly decreases neuronal death. OLE could also reduce mitochondrial production of reactive oxygen species resulting from blocking superoxide dismutase activity. Moreover, quantification of autophagic and acidic vesicles in the cytoplasm alongside expression of specific autophagic markers uncovered a regulatory role for OLE against autophagic flux impairment induced by bafilomycin A1. Altogether, our results define OLE as a neuroprotective, anti-oxidative and autophagy-regulating molecule, in a neuronal dopaminergic cellular model. PMID:27517912
Directory of Open Access Journals (Sweden)
Imène Achour
2016-08-01
Full Text Available Parkinson’s disease (PD is a progressive neurodegenerative disorder, primarily affecting dopaminergic neurons in the substantia nigra. There is currently no cure for PD and present medications aim to alleviate clinical symptoms, thus prevention remains the ideal strategy to reduce the prevalence of this disease. The goal of this study was to investigate whether oleuropein (OLE, the major phenolic compound in olive derivatives, may prevent neuronal degeneration in a cellular dopaminergic model of PD, differentiated PC12 cells exposed to the potent parkinsonian toxin 6-hydroxydopamine (6-OHDA. We also investigated OLE’s ability to mitigate mitochondrial oxidative stress and modulate the autophagic flux. Our results obtained by measuring cytotoxicity and apoptotic events demonstrate that OLE significantly decreases neuronal death. OLE could also reduce mitochondrial production of reactive oxygen species resulting from blocking superoxide dismutase activity. Moreover, quantification of autophagic and acidic vesicles in the cytoplasm alongside expression of specific autophagic markers uncovered a regulatory role for OLE against autophagic flux impairment induced by bafilomycin A1. Altogether, our results define OLE as a neuroprotective, anti-oxidative and autophagy-regulating molecule, in a neuronal dopaminergic cellular model.
Topol, Igor A.; Nemukhin, Alexander V.; Burt, Stanley K.
Interactions of 1,2-dithiolane species with zinc-containing sites, which mimic the zinc finger domains of retroviral and the cellular zinc finger proteins, have been investigated by quantum chemistry tools. According to the calculations, the immediate domains of zinc binding sites in the cellular and retroviral zinc fingers interact differently with such agents of the disulphide family. Thus, when approaching the model cellular-type domains, the molecules of 1,2-dithiolanes experience considerable potential barriers along the reaction path. However, these species react practically barrier-less with the model retroviral-type domains at the correlated DFT level. The results of the quantum chemical modelling provide firm support to the selectivity of 1,2-dithiolanes towards retroviral and cellular zinc fingers. This can be of great practical importance for the design of therapeutics that accomplish functional inactivation of the zinc fingers of the human immunodeficiency virus (HIV-1) retroviral type nucleocapsid protein NCp7.
Directory of Open Access Journals (Sweden)
Megan Olsen
Full Text Available Computational models in the field of cancer research have focused primarily on estimates of biological events based on laboratory generated data. We introduce a novel in-silico technology that takes us to the next level of prediction models and facilitates innovative solutions through the mathematical system. The model's building blocks are cells defined phenotypically as normal or tumor, with biological processes translated into equations describing the life protocols of the cells in a quantitative and stochastic manner. The essentials of communication in a society composed of normal and tumor cells are explored to reveal "protocols" for selective tumor eradication. Results consistently identify "citizenship properties" among cells that are essential for the induction of healing processes in a healthy system invaded by cancer. These properties act via inter-cellular communication protocols that can be optimized to induce tumor eradication along with system recovery. Within the computational systems, the protocols universally succeed in removing a wide variety of tumors defined by proliferation rates, initial volumes, and apoptosis resistant phenotypes; they show high adaptability for biological details and allow incorporation of population heterogeneity. These protocols work as long as at least 32% of cells obey extra-cellular commands and at least 28% of cancer cells report their deaths. This low percentage implies that the protocols are resilient to the suboptimal situations often seen in biological systems. We conclude that our in-silico model is a powerful tool to investigate, to propose, and to exercise logical anti-cancer solutions. Functional results should be confirmed in a biological system and molecular findings should be loaded into the computational model for the next level of directed experiments.
A Modified Cellular Automaton Approach for Mixed Bicycle Traffic Flow Modeling
Directory of Open Access Journals (Sweden)
Xiaonian Shan
2015-01-01
Full Text Available Several previous studies have used the Cellular Automaton (CA for the modeling of bicycle traffic flow. However, previous CA models have several limitations, resulting in differences between the simulated and the observed traffic flow features. The primary objective of this study is to propose a modified CA model for simulating the characteristics of mixed bicycle traffic flow. Field data were collected on physically separated bicycle path in Shanghai, China, and were used to calibrate the CA model using the genetic algorithm. Traffic flow features between simulations of several CA models and field observations were compared. The results showed that our modified CA model produced more accurate simulation for the fundamental diagram and the passing events in mixed bicycle traffic flow. Based on our model, the bicycle traffic flow features, including the fundamental diagram, the number of passing events, and the number of lane changes, were analyzed. We also analyzed the traffic flow features with different traffic densities, traffic components on different travel lanes. Results of the study can provide important information for understanding and simulating the operations of mixed bicycle traffic flow.
Idealized Mesoscale Model Simulations of Open Cellular Convection Over the Sea
DEFF Research Database (Denmark)
Vincent, Claire Louise; Hahmann, Andrea N.; Kelly, Mark C.
2012-01-01
important terms in the budgets were buoyancy, pressure balance and inter-scale transfer to subgrid scales. Cells were also composited to calculate the average cell-scale flow and each of the budget terms on two-dimensional cross-sections through the cells, parallel and perpendicular to the mean wind......The atmospheric conditions during an observed case of open cellular convection over the North Sea were simulated using the Weather Research and Forecasting (WRF) numerical model. Wind, temperature and water vapour mixing ratio profiles from the WRF simulation were used to initialize an idealized...... version of the model, which excluded the effects of topography, surface inhomogeneities and large-scale weather forcing. Cells with an average diameter of 17.4 km developed. Simulations both with and without a capping inversion were made, and the cell-scale kinetic energy budget was calculated for each...
Modeling and Simulation for Urban Rail Traffic Problem Based on Cellular Automata
Institute of Scientific and Technical Information of China (English)
许琰; 曹成铉; 李明华; 罗金龙
2012-01-01
Based on the Nagel-Schreckenberg model, we propose a new cellular automata model to simulate the urban rail traffic flow under moving block system and present a new minimum instantaneous distance formula under pure moving block. We also analyze the characteristics of the urban rail traffic flow under the influence of train density, station dwell times, the length of train, and the train velocity. Train delays can be decreased effectively through flexible departure intervals according to the preceding train type before its departure. The results demonstrate that a suitable adjustment of the current train velocity based on the following train velocity can greatly shorten the minimum departure intervals and then increase the capacity of rail transit.
Hoganson, David M; Owens, Gwen E; Meppelink, Amanda M; Bassett, Erik K; Bowley, Chris M; Hinkel, Cameron J; Finkelstein, Eric B; Goldman, Scott M; Vacanti, Joseph P
2016-07-01
Extracellular matrix (ECM) materials from animal and human sources have become important materials for soft tissue repair. Microparticles of ECM materials have increased surface area and exposed binding sites compared to sheet materials. Decellularized porcine peritoneum was mechanically dissociated into 200 µm microparticles, seeded with fibroblasts and cultured in a low gravity rotating bioreactor. The cells avidly attached and maintained excellent viability on the microparticles. When the seeded microparticles were placed in a collagen gel, the cells quickly migrated off the microparticles and through the gel. Cells from seeded microparticles migrated to and across an in vitro anastomosis model, increasing the tensile strength of the model. Cell seeded microparticles of ECM material have potential for paracrine and cellular delivery therapies when delivered in a gel carrier. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 104A: 1728-1735, 2016. PMID:26946064
Driver’s Awareness and Lane Changing Maneuver in Traffic Flow based on Cellular Automaton Model
Directory of Open Access Journals (Sweden)
Kohei Arai
2015-08-01
Full Text Available Effect of driver’s awareness (e.g., to estimate the speed and arrival time of another vehicle on the lane changing maneuver is discussed. “Scope awareness” is defined as the visibility which is required for the driver to make a visual perception about road condition and the speed of vehicle that appears in the target lane for lane changing in the road. Cellular automaton based simulation model is created and applied to simulation studies for driver awareness behavior. This study clarifies relations between the lane changing behavior and the scope awareness parameter that reflects driver behavior. Simulation results show that the proposed model is valid for investigation of the important features of lane changing maneuver.
Genome editing of human pluripotent stem cells to generate human cellular disease models
Directory of Open Access Journals (Sweden)
Kiran Musunuru
2013-07-01
Full Text Available Disease modeling with human pluripotent stem cells has come into the public spotlight with the awarding of the Nobel Prize in Physiology or Medicine for 2012 to Drs John Gurdon and Shinya Yamanaka for the discovery that mature cells can be reprogrammed to become pluripotent. This discovery has opened the door for the generation of pluripotent stem cells from individuals with disease and the differentiation of these cells into somatic cell types for the study of disease pathophysiology. The emergence of genome-editing technology over the past few years has made it feasible to generate and investigate human cellular disease models with even greater speed and efficiency. Here, recent technological advances in genome editing, and its utility in human biology and disease studies, are reviewed.
An improved cellular automaton model considering the effect of traffic lights and driving behaviour
He, Hong-Di; Lu, Wei-Zhen; Dong, Li-Yun
2011-04-01
This paper proposes an improved cellular automaton model to describe the urban traffic flow with the consideration of traffic light and driving behaviour effects. Based on the model, the characteristics of the urban traffic flow on a single-lane road are investigated under three different control strategies, i.e., the synchronized, the green wave and the random strategies. The fundamental diagrams and time-space patterns of the traffic flows are provided for these strategies respectively. It finds that the dynamical transition to the congested flow appears when the vehicle density is higher than a critical level. The saturated flow is less dependent on the cycle time and the strategies of the traffic light control, while the critical vehicle density varies with the cycle time and the strategies. Simulated results indicate that the green wave strategy is proven to be the most effective one among the above three control strategies.
The Aldous-Shields model revisited (with application to cellular ageing)
Best, Katharina
2010-01-01
In Aldous and Shields (1988), a model for a rooted, growing random binary tree was presented. For some c>0, an external vertex splits at rate c^(-i) (and becomes internal) if its distance from the root (depth) is i. For c>1, we reanalyse the tree profile, i.e. the numbers of external vertices in depth i=1,2,.... Our main result are concrete formulas for the expectation and covariance-structure of the profile. In addition, we present the application of the model to cellular ageing. Here, we assume that nodes in depth h+1 are senescent, i.e. do not split. We obtain a limit result for the proportion of non-senescent vertices for large h.
A cellular automation model for the change of public attitude regarding nuclear energy
International Nuclear Information System (INIS)
A cellular automation model was constructed to investigate how public opinion on nuclear energy in Japan depends upon the information environment and personal communication between people. From simulation with this model, the following become clear; (i) society is a highly non-linear system with a self-organizing potential: (ii) in a society composed of one type of constituent member with homogeneous characteristics, the trend of public opinion is substantially changed only when the effort to ameliorate public acceptance over a long period of time, by means such as education, persuasion and advertisement, exceeds a certain threshold, and (iii) in the case when the amount of information on nuclear risk released from the newsmedia is reduced continuously from now on, the acceptability of nuclear energy is significantly improved so far as the extent of the reduction exceeds a certain threshold. (author)
A nanoflare based cellular automaton model and the observed properties of the coronal plasma
Fuentes, Marcelo López
2016-01-01
We use the cellular automaton model described in L\\'opez Fuentes \\& Klimchuk (2015, ApJ, 799, 128) to study the evolution of coronal loop plasmas. The model, based on the idea of a critical misalignment angle in tangled magnetic fields, produces nanoflares of varying frequency with respect to the plasma cooling time. We compare the results of the model with active region (AR) observations obtained with the Hinode/XRT and SDO/AIA instruments. The comparison is based on the statistical properties of synthetic and observed loop lightcurves. Our results show that the model reproduces the main observational characteristics of the evolution of the plasma in AR coronal loops. The typical intensity fluctuations have an amplitude of 10 to 15\\% both for the model and the observations. The sign of the skewness of the intensity distributions indicates the presence of cooling plasma in the loops. We also study the emission measure (EM) distribution predicted by the model and obtain slopes in log(EM) versus log(T) betw...
CellLab-CTS 2015: continuous-time stochastic cellular automaton modeling using Landlab
Tucker, Gregory E.; Hobley, Daniel E. J.; Hutton, Eric; Gasparini, Nicole M.; Istanbulluoglu, Erkan; Adams, Jordan M.; Siddartha Nudurupati, Sai
2016-02-01
CellLab-CTS 2015 is a Python-language software library for creating two-dimensional, continuous-time stochastic (CTS) cellular automaton models. The model domain consists of a set of grid nodes, with each node assigned an integer state code that represents its condition or composition. Adjacent pairs of nodes may undergo transitions to different states, according to a user-defined average transition rate. A model is created by writing a Python code that defines the possible states, the transitions, and the rates of those transitions. The code instantiates, initializes, and runs one of four object classes that represent different types of CTS models. CellLab-CTS provides the option of using either square or hexagonal grid cells. The software provides the ability to treat particular grid-node states as moving particles, and to track their position over time. Grid nodes may also be assigned user-defined properties, which the user can update after each transition through the use of a callback function. As a component of the Landlab modeling framework, CellLab-CTS models take advantage of a suite of Landlab's tools and capabilities, such as support for standardized input and output.
Modelling urban growth in the Indo-Gangetic plain using nighttime OLS data and cellular automata
Roy Chowdhury, P. K.; Maithani, Sandeep
2014-12-01
The present study demonstrates the applicability of the Operational Linescan System (OLS) sensor in modelling urban growth at regional level. The nighttime OLS data provides an easy, inexpensive way to map urban areas at a regional scale, requiring a very small volume of data. A cellular automata (CA) model was developed for simulating urban growth in the Indo-Gangetic plain; using OLS data derived maps as input. In the proposed CA model, urban growth was expressed in terms of causative factors like economy, topography, accessibility and urban infrastructure. The model was calibrated and validated based on OLS data of year 2003 and 2008 respectively using spatial metrics measures and subsequently the urban growth was predicted for the year 2020. The model predicted high urban growth in North Western part of the study area, in south eastern part growth would be concentrated around two cities, Kolkata and Howrah. While in the middle portion of the study area, i.e., Jharkhand, Bihar and Eastern Uttar Pradesh, urban growth has been predicted in form of clusters, mostly around the present big cities. These results will not only provide an input to urban planning but can also be utilized in hydrological and ecological modelling which require an estimate of future built up areas especially at regional level.
Open boundaries in a cellular automaton model for traffic flow with metastable states
Barlovic, Robert; Huisinga, Torsten; Schadschneider, Andreas; Schreckenberg, Michael
2002-10-01
The effects of open boundaries in the velocity-dependent randomization (VDR) model, a modified version of the well-known Nagel-Schreckenberg (NaSch) cellular automaton model for traffic flow, are investigated. In contrast to the NaSch model, the VDR model exhibits metastable states and phase separation in a certain density regime. A proper insertion strategy allows us to investigate the whole spectrum of possible system states and the structure of the phase diagram by Monte Carlo simulations. We observe an interesting microscopic structure of the jammed phases, which is different from the one of the NaSch model. For finite systems, the existence of high flow states in a certain parameter regime leads to a special structure of the fundamental diagram measured in the open system. Apart from that, the results are in agreement with an extremal principle for the flow, which has been introduced for models with a unique flow-density relation. Finally, we discuss the application of our findings for a systematic flow optimization. Here some surprising results are obtained, e.g., a restriction of the inflow can lead to an improvement of the total flow through a bottleneck.
Qian, Linghui; Zhang, Cheng-Wu; Mao, Yanli; Li, Lin; Gao, Nengyue; Lim, Kah-Leong; Xu, Qing-Hua; Yao, Shao Q
2016-01-01
Caspases work as a double-edged sword in maintaining cell homeostasis. Highly regulated caspase activities are essential during animal development, but dysregulation might lead to different diseases, e.g. extreme caspase activation is known to promote neurodegeneration. At present, visualization of caspase activation has mostly remained at the cellular level, in part due to a lack of cell-permeable imaging probes capable of direct, real-time investigations of endogenous caspase activities in deep tissues. Herein, we report a suite of two-photon, small molecule/peptide probes which enable sensitive and dynamic imaging of individual caspase activities in neurodegenerative models under physiological conditions. With no apparent toxicity and the ability of imaging endogenous caspases both in different subcellular organelles of mammalian cells and in brain tissues, these probes serve as complementary tools to conventional histological analysis. They should facilitate future explorations of caspases at molecular, cellular and organism levels and inspire development of novel two-photon probes against other enzymes. PMID:27210613
Directory of Open Access Journals (Sweden)
Marko eUutela
2014-05-01
Full Text Available Fluoxetine is used as a therapeutic agent for autism spectrum disorder (ASD, including Fragile X syndrome (FXS. The treatment often associates with disruptive behaviors such as agitation and disinhibited behaviors in FXS. To identify mechanisms that increase the risk to poor treatment outcome, we investigated the behavioral and cellular effects of fluoxetine on adult Fmr1 knockout (KO mice, a mouse model for FXS. We found that fluoxetine reduced anxiety-like behavior of both wild type and Fmr1 KO mice seen as shortened latency to enter the center area in the open field test. In Fmr1 KO mice, fluoxetine normalized locomotor hyperactivity but abnormally increased exploratory activity. Reduced Brain-derived neurotrophic factor (BDNF and increased TrkB receptor expression levels in the hippocampus of Fmr1 KO mice associated with inappropriate coping responses under stressful condition and abolished antidepressant activity of fluoxetine. Fluoxetine response in the cell proliferation was also missing in the hippocampus of Fmr1 KO mice when compared with wild type controls. The postnatal expression of serotonin transporter was reduced in the thalamic nuclei of Fmr1 KO mice during the time of transient innervation of somatosensory neurons suggesting that developmental changes of serotonin transporter (SERT expression were involved in the differential cellular and behavioral responses to fluoxetine in wild type and Fmr1 mice. The results indicate that changes of BDNF/TrkB signaling contribute to differential behavioral responses to fluoxetine among individuals with ASD.
DEFF Research Database (Denmark)
Osmanagic, Azra; Emamifar, Amir; Christian Bang, Jacob;
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...
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
Sakr, Ahmed Hamdi; Hossain, Ekram
2014-01-01
While cognitive radio enables spectrum-efficient wireless communication, radio frequency (RF) energy harvesting from ambient interference is an enabler for energy-efficient wireless communication. In this paper, we model and analyze cognitive and energy harvesting-based D2D communication in cellular networks. The cognitive D2D transmitters harvest energy from ambient interference and use one of the channels allocated to cellular users (in uplink or downlink), which is referred to as the D2D c...
Cheng, Y; Kekenes-Huskey, P; Hake, JE; Holst, MJ; McCammon, JA; Michailova, AP
2012-01-01
This article provides a brief review of multi-scale modeling at the molecular to cellular scale, with new results for heart muscle cells. A finite element-based simulation package (SMOL) was used to investigate the signaling transduction at molecular and sub-cellular scales (http://mccammon.ucsd.edu/smol/, http://FETK.org) by numerical solution of time-dependent Smoluchowski equations and a reaction-diffusion system. At the molecular scale, SMOL has yielded experimentally-validated estimates ...
Developing an Abaqus *HYPERFOAM Model for M9747 (4003047) Cellular Silicone Foam
Energy Technology Data Exchange (ETDEWEB)
Siranosian, Antranik A. [Los Alamos National Laboratory; Stevens, R. Robert [Los Alamos National Laboratory
2012-04-26
This report documents work done to develop an Abaqus *HYPERFOAM hyperelastic model for M9747 (4003047) cellular silicone foam for use in quasi-static analyses at ambient temperature. Experimental data, from acceptance tests for 'Pad A' conducted at the Kansas City Plant (KCP), was used to calibrate the model. The data includes gap (relative displacement) and load measurements from three locations on the pad. Thirteen sets of data, from pads with different serial numbers, were provided. The thirty-nine gap-load curves were extracted from the thirteen supplied Excel spreadsheets and analyzed, and from those thirty-nine one set of data, representing a qualitative mean, was chosen to calibrate the model. The data was converted from gap and load to nominal (engineering) strain and nominal stress in order to implement it in Abaqus. Strain computations required initial pad thickness estimates. An Abaqus model of a right-circular cylinder was used to evaluate and calibrate the *HYPERFOAM model.
International Nuclear Information System (INIS)
We present a two-dimensional continuous cellular automaton that is equivalent to a driven spring-block model. Both the conservation and the anisotropy in the model are controllable quantities. Above a critical level of conservation, the model exhibits self-organized criticality. The self-organization of this system and hence the critical exponents depend on the conservation and the boundary conditions. In the critical isotropic nonconservative phase, the exponents change continuously as a function of conservation. Furthermore, the exponents vary continuously when changing the boundary conditions smoothly. Consequently, there is no universality of the critical exponents. We discuss the relevance of this for earthquakes. Introducing anisotropy changes the scaling of the distribution function, but not the power-law exponent. We explore the phase diagram of this model. We find that at low conservation levels a localization transition occurs. We see two additional phase transitions. The first is seen when moving from the conservative into the nonconservative model. The second appears when passing from the anisotropic two-dimensional system to the purely one-dimensional system
Vassiliadis, D.; Anastasiadis, A.; Georgoulis, M.; Vlahos, L.
1998-12-01
Cellular automata (CA) models account for the power-law distributions found for solar flare hard X-ray observations, but their physics has been unclear. We examine four of these models and show that their criteria and magnetic field distribution rules can be derived by discretizing the MHD diffusion equation as obtained from a simplified Ohm's law. Identifying the discrete MHD with the CA models leads to an expression for the resistivity as a function of the current on the flux tube boundary, as may be expected from current-driven instabilities. Anisotropic CA models correspond to a nonlinear resistivity η(J), while isotropic ones are associated with hyperresistivity η(▽2J). The discrete equations satisfy the necessary conditions for self-organized criticality (Lu): there is local conservation of a field (magnetic flux), while the nonlinear resistivity provides a rapid dissipation and relaxation mechanism. The approach justifies many features of the CA models that were originally based on intuition.
A multi-objective model for designing a group layout of a dynamic cellular manufacturing system
Kia, Reza; Shirazi, Hossein; Javadian, Nikbakhsh; Tavakkoli-Moghaddam, Reza
2013-04-01
This paper presents a multi-objective mixed-integer nonlinear programming model to design a group layout of a cellular manufacturing system in a dynamic environment, in which the number of cells to be formed is variable. Cell formation (CF) and group layout (GL) are concurrently made in a dynamic environment by the integrated model, which incorporates with an extensive coverage of important manufacturing features used in the design of CMSs. Additionally, there are some features that make the presented model different from the previous studies. These features include the following: (1) the variable number of cells, (2) the integrated CF and GL decisions in a dynamic environment by a multi-objective mathematical model, and (3) two conflicting objectives that minimize the total costs (i.e., costs of intra and inter-cell material handling, machine relocation, purchasing new machines, machine overhead, machine processing, and forming cells) and minimize the imbalance of workload among cells. Furthermore, the presented model considers some limitations, such as machine capability, machine capacity, part demands satisfaction, cell size, material flow conservation, and location assignment. Four numerical examples are solved by the GAMS software to illustrate the promising results obtained by the incorporated features.
Molecular modeling of the conformational dynamics of the cellular prion protein
Nguyen, Charles; Colling, Ian; Bartz, Jason; Soto, Patricia
2014-03-01
Prions are infectious agents responsible for transmissible spongiform encephalopathies (TSEs), a type of fatal neurodegenerative disease in mammals. Prions propagate biological information by conversion of the non-pathological version of the prion protein to the infectious conformation, PrPSc. A wealth of knowledge has shed light on the nature and mechanism of prion protein conversion. In spite of the significance of this problem, we are far from fully understanding the conformational dynamics of the cellular isoform. To remedy this situation we employ multiple biomolecular modeling techniques such as docking and molecular dynamics simulations to map the free energy landscape and determine what specific regions of the prion protein are most conductive to binding. The overall goal is to characterize the conformational dynamics of the cell form of the prion protein, PrPc, to gain insight into inhibition pathways against misfolding. NE EPSCoR FIRST Award to Patricia Soto.
Jiao, Yang
2011-01-01
Understanding tumor invasion and metastasis is of crucial importance for both fundamental cancer research and clinical practice. In vitro experiments have established that the invasive growth of malignant tumors is characterized by the dendritic invasive branches composed of chains of tumor cells emanating from the primary tumor mass. The preponderance of previous tumor simulations focused on non-invasive (or proliferative) growth. The formation of the invasive cell chains and their interactions with the primary tumor mass and host microenvironment are not well understood. Here, we present a novel cellular automaton (CA) model that enables one to efficiently simulate invasive tumor growth in a heterogeneous host microenvironment. By taking into account a variety of microscopic-scale tumor-host interactions, including the short-range mechanical interactions between tumor cells and tumor stroma, degradation of extracellular matrix by the invasive cells and oxygen/nutrient gradient driven cell motions, our CA mo...
Fatigue design of a cellular phone folder using regression model-based multi-objective optimization
Kim, Young Gyun; Lee, Jongsoo
2016-08-01
In a folding cellular phone, the folding device is repeatedly opened and closed by the user, which eventually results in fatigue damage, particularly to the front of the folder. Hence, it is important to improve the safety and endurance of the folder while also reducing its weight. This article presents an optimal design for the folder front that maximizes its fatigue endurance while minimizing its thickness. Design data for analysis and optimization were obtained experimentally using a test jig. Multi-objective optimization was carried out using a nonlinear regression model. Three regression methods were employed: back-propagation neural networks, logistic regression and support vector machines. The AdaBoost ensemble technique was also used to improve the approximation. Two-objective Pareto-optimal solutions were identified using the non-dominated sorting genetic algorithm (NSGA-II). Finally, a numerically optimized solution was validated against experimental product data, in terms of both fatigue endurance and thickness index.
Phase transition in the economically modeled growth of a cellular nervous system
Nicosia, Vincenzo; Schafer, William R; Latora, Vito; Bullmore, Edward T; 10.1073/pnas.1300753110
2013-01-01
Spatially-embedded complex networks, such as nervous systems, the Internet and transportation networks, generally have non-trivial topological patterns of connections combined with nearly minimal wiring costs. However the growth rules shaping these economical trade-offs between cost and topology are not well understood. Here we study the cellular nervous system of the nematode worm C. elegans, together with information on the birth times of neurons and on their spatial locations. We find that the growth of this network undergoes a transition from an accelerated to a constant increase in the number of links (synaptic connections) as a function of the number of nodes (neurons). The time of this phase transition coincides closely with the observed moment of hatching, when development switches metamorphically from oval to larval stages. We use graph analysis and generative modelling to show that the transition between different growth regimes, as well as its coincidence with the moment of hatching, can be explain...
Phase transitions in a cellular automaton model of a highway on-ramp
Belitsky, Vladimir; Maric, Nevena; Schütz, Gunter M.
2007-09-01
We introduce a lattice gas model for the merging of two single-lane automobile highways. The merging rules for traffic on the two lanes are deterministic, but the inflow on both lanes is stochastic. Analysing the stationary distribution of this stochastic cellular automaton, we find a discontinuous phase transition from a free-flow phase which depends on the initial state of the road to a jammed phase where all memory of the initial state is lost. Inside the jammed phase we identify dynamical phase transitions in the approach to stationarity. Each dynamical phase is characterized by a fixed number of relaxation cycles which is decreasing as one moves deeper into the jammed phase. In each cycle step, the number of 'desperate' drivers who force their way onto the main road when they reach the end of the on-ramp increases until stationarity.
Phase transitions in a cellular automaton model of a highway on-ramp
International Nuclear Information System (INIS)
We introduce a lattice gas model for the merging of two single-lane automobile highways. The merging rules for traffic on the two lanes are deterministic, but the inflow on both lanes is stochastic. Analysing the stationary distribution of this stochastic cellular automaton, we find a discontinuous phase transition from a free-flow phase which depends on the initial state of the road to a jammed phase where all memory of the initial state is lost. Inside the jammed phase we identify dynamical phase transitions in the approach to stationarity. Each dynamical phase is characterized by a fixed number of relaxation cycles which is decreasing as one moves deeper into the jammed phase. In each cycle step, the number of 'desperate' drivers who force their way onto the main road when they reach the end of the on-ramp increases until stationarity
Cellular and circuit models of increased resting-state network gamma activity in schizophrenia.
White, R S; Siegel, S J
2016-05-01
Schizophrenia (SCZ) is a disorder characterized by positive symptoms (hallucinations, delusions), negative symptoms (blunted affect, alogia, reduced sociability, and anhedonia), as well as persistent cognitive deficits (memory, concentration, and learning). While the biology underlying subjective experiences is difficult to study, abnormalities in electroencephalographic (EEG) measures offer a means to dissect potential circuit and cellular changes in brain function. EEG is indispensable for studying cerebral information processing due to the introduction of techniques for the decomposition of event-related activity into its frequency components. Specifically, brain activity in the gamma frequency range (30-80Hz) is thought to underlie cognitive function and may be used as an endophenotype to aid in diagnosis and treatment of SCZ. In this review we address evidence indicating that there is increased resting-state gamma power in SCZ. We address how modeling this aspect of the illness in animals may help treatment development as well as providing insights into the etiology of SCZ. PMID:26577758
A Discrete/continuous Coupled Approach for Modeling Impacts on Cellular Geostructures
Breugnot, A.; Lambert, S.; Villard, P.; Gotteland, P.
2016-05-01
This article presents a numerical model coupling the finite difference method and discrete element methods (FDM, DEM) for simulating the response of cellular geostructures to impacts. DEM is used in the vicinity of the impacted area while FDM is used far away. The continuity between the DEM and FDM domains is insured using the edge-to-edge method. The numerical parameters are calibrated based on compression and impact experiments conducted on elementary cells. Numerical simulations at the structure scale are compared with real-scale experimental data. The response of the structure is addressed varying the impact conditions. The projectile shape and the position of the impact point appear to be the most influential parameters.
Cellular Automata Models of Traffic Behavior in Presence of Speed Breaking Structures
International Nuclear Information System (INIS)
In this article, we study traffic flow in the presence of speed breaking structures. The speed breakers are typically used to reduce the local speed of vehicles near certain institutions such as schools and hospitals. Through a cellular automata model we study the impact of such structures on global traffic characteristics. The simulation results indicate that the presence of speed breakers could reduce the global flow under moderate global densities. However, under low and high global density traffic regime the presence of speed breakers does not have an impact on the global flow. Further the speed limit enforced by the speed breaker creates a phase distinction. For a given global density and slowdown probability, as the speed limit enforced by the speed breaker increases, the traffic moves from the reduced flow phase to maximum flow phase. This underlines the importance of proper design of these structures to avoid undesired flow restrictions. (general)
Computer simulation of a cellular automata model for the immune response in a retrovirus system
International Nuclear Information System (INIS)
Immune response in a retrovirus system is modeled by a network of three binary cell elements to take into account some of the main functional features of T4 cells, T8 cells, and viruses. Two different intercell interactions are introduced, one of which leads to three fixed points while the other yields bistable fixed points oscillating between a healthy state and a sick state in a mean field treatment. Evolution of these cells is studied for quenched and annealed random interactions on a simple cubic lattice with a nearest neighbor interaction using inhomogenous cellular automata. Populations of T4 cells and viral cells oscillate together with damping (with constant amplitude) for annealed (quenched) interaction on increasing the value of mixing probability B from zero to a characteristic value Bca (Bcq). For higher B, the average number of T4 cells increases while that of the viral infected cells decreases monotonically on increasing B, suggesting a phase transition at Bca (Bcq)
Directory of Open Access Journals (Sweden)
Tamaddon AM.
2007-05-01
Full Text Available Cationic liposomes are used for cellular delivery of antisense oligodeoxynucleotide (AsODN, where release of encapsulated AsODN is mainly controlled by endocytosis and fusion mechanisms. In this investigation, it was tried to model such a release process that is difficult to evaluate in cell culture. For this purpose, an AsODN model (against protein kinase C-α was encapsulated in a DODAP-containing cationic liposome and evaluated for size, zeta-potential, encapsulation and ODN stability. Vesicular models of outer layer and total plasma membranes and early and late endosomal membranes were developed, based on lipid content and pH, using ether injection method. ODN release was determined by the fluorescence dequenching of encapsulated FITC-ODN. Zeta potential, size and ODN encapsulation efficiency of the prepared liposomes were -2.49 ± 7.15 mV, 108.4 nm and 73% respectively. ODN protection was 3-4 times more than that of conventional liposome/ODN complexation method. There was a correlation between model concentration and percent of ODN release. At 7.5 µM, the percent of released ODN was 76% for the cholesterol-free model of the late endosome and 16% for the early endosomal membrane; while the release was less than 11% for the models of plasma membrane. ODN release increased with temperature in the range of 4-37◦C for the late endosomal model, but not for others, possibly due to their high cholesterol contents or acidic pH. The interaction was fast and completed within 5 minutes and didn’t change in the range of 5-60 minutes. Our data are in agreement with published cell culture studies and reveal that cell-liposomes interaction can be modeled by lamellar membranes.
Directory of Open Access Journals (Sweden)
Xin Zhao
Full Text Available Protocatechuic aldehyde (PAL has been reported to bind to DJ-1, a key protein involved in Parkinson's disease (PD, and exerts potential neuroprotective effects via DJ-1 in SH-SY5Y cells. In this study, we investigated the neuroprotective pharmacological effects of PAL against neurotoxin-induced cell and animal models of PD. In cellular models of PD, PAL markedly increased cell viability rates, mitochondrial oxidation-reduction activity and mitochondrial membrane potential, and reduced intracellular ROS levels to prevent neurotoxicity in PC12 cells. In animal models of PD, PAL reduced the apomorphine injection, caused turning in 6-OHDA treated rats, and increased the motor coordination and stride decreases in MPTP treated mice. Meanwhile, in an MPTP mouse model, PAL prevented a decrease of the contents of dopamine (DA and its metabolites in the striatum and TH-positive dopaminergic neuron loss in the substantia nigra (SN. In addition, PAL increased the protein expression of DJ-1 and reduced the level of α-synuclein in the SN of MPTP lesioned mice. PAL also increased the spine density in hippocampal CA1 neurons. The current study demonstrates that PAL can efficiently protect dopaminergic neurons against neurotoxin injury in vitro and in vivo, and that the potential mechanisms may be related to its effects in increasing DJ-1, decreasing α-synuclein and its growth-promoting effect on spine density.
Lattice gas cellular automation model for rippling and aggregation in myxobacteria
Alber, Mark S.; Jiang, Yi; Kiskowski, Maria A.
2004-05-01
A lattice gas cellular automation (LGCA) model is used to simulate rippling and aggregation in myxobacteria. An efficient way of representing cells of different cell size, shape and orientation is presented that may be easily extended to model later stages of fruiting body formation. This LGCA model is designed to investigate whether a refractory period, a minimum response time, a maximum oscillation period and non-linear dependence of reversals of cells on C-factor are necessary assumptions for rippling. It is shown that a refractory period of 2-3 min, a minimum response time of up to 1 min and no maximum oscillation period best reproduce rippling in the experiments of Myxococcus xanthus. Non-linear dependence of reversals on C-factor is critical at high cell density. Quantitative simulations demonstrate that the increase in wavelength of ripples when a culture is diluted with non-signaling cells can be explained entirely by the decreased density of C-signaling cells. This result further supports the hypothesis that levels of C-signaling quantitatively depend on and modulate cell density. Analysis of the interpenetrating high density waves shows the presence of a phase shift analogous to the phase shift of interpenetrating solitons. Finally, a model for swarming, aggregation and early fruiting body formation is presented.
Cellular replication limits in the Luria-Delbrück mutation model
Rodriguez-Brenes, Ignacio A.; Wodarz, Dominik; Komarova, Natalia L.
2016-08-01
Originally developed to elucidate the mechanisms of natural selection in bacteria, the Luria-Delbrück model assumed that cells are intrinsically capable of dividing an unlimited number of times. This assumption however, is not true for human somatic cells which undergo replicative senescence. Replicative senescence is thought to act as a mechanism to protect against cancer and the escape from it is a rate-limiting step in cancer progression. Here we introduce a Luria-Delbrück model that explicitly takes into account cellular replication limits in the wild type cell population and models the emergence of mutants that escape replicative senescence. We present results on the mean, variance, distribution, and asymptotic behavior of the mutant population in terms of three classical formulations of the problem. More broadly the paper introduces the concept of incorporating replicative limits as part of the Luria-Delbrück mutational framework. Guidelines to extend the theory to include other types of mutations and possible applications to the modeling of telomere crisis and fluctuation analysis are also discussed.
Stability Analysis of a Hybrid Cellular Automaton Model of Cell Colony Growth
Gerlee, P
2007-01-01
Cell colonies of bacteria, tumour cells and fungi, under nutrient limited growth conditions, exhibit complex branched growth patterns. In order to investigate this phenomenon we present a simple hybrid cellular automaton model of cell colony growth. In the model the growth of the colony is limited by a nutrient that is consumed by the cells and which inhibits cell division if it falls below a certain threshold. Using this model we have investigated how the nutrient consumption rate of the cells affects the growth dynamics of the colony. We found that for low consumption rates the colony takes on a Eden-like morphology, while for higher consumption rates the morphology of the colony is branched with a fractal geometry. These findings are in agreement with previous results, but the simplicity of the model presented here allows for a linear stability analysis of the system. By observing that the local growth of the colony is proportional to the flux of the nutrient we derive an approximate dispersion relation fo...
A mathematical model of cortical bone remodeling at cellular level under mechanical stimulus
Institute of Scientific and Technical Information of China (English)
Qing-Hua Qin; Ya-Nan Wang
2012-01-01
A bone cell population dynamics model for cortical bone remodeling under mechanical stimulus is developed in this paper.The external experiments extracted from the literature which have not been used in the creation of the model are used to test the validity of the model.Not only can the model compare reasonably well with these experimental results such as the increase percentage of final values of bone mineral content (BMC) and bone fracture energy (BFE) among different loading schemes (which proves the validity of the model),but also predict the realtime development pattern of BMC and BFE,as well as the dynamics of osteoblasts (OBA),osteoclasts (OCA),nitric oxide (NO) and prostaglandin E2 (PGE2) for each loading scheme,which can hardly be monitored through experiment.In conclusion,the model is the first of its kind that is able to provide an insight into the quantitative mechanism of bone remodeling at cellular level by which bone cells are activated by mechanical stimulus in order to start resorption/formation of bone mass.More importantly,this model has laid a solid foundation based on which future work such as systemic control theory analysis of bone remodeling under mechanical stimulus can be investigated.The to-be identified control mechanism will help to develop effective drugs and combined nonpharmacological therapies to combat bone loss pathologies.Also this deeper understanding of how mechanical forces quantitatively interact with skeletal tissue is essential for the generation of bone tissue for tissue replacement purposes in tissue engineering.
Large-scale parallel lattice Boltzmann-cellular automaton model of two-dimensional dendritic growth
Jelinek, Bohumir; Eshraghi, Mohsen; Felicelli, Sergio; Peters, John F.
2014-03-01
An extremely scalable lattice Boltzmann (LB)-cellular automaton (CA) model for simulations of two-dimensional (2D) dendritic solidification under forced convection is presented. The model incorporates effects of phase change, solute diffusion, melt convection, and heat transport. The LB model represents the diffusion, convection, and heat transfer phenomena. The dendrite growth is driven by a difference between actual and equilibrium liquid composition at the solid-liquid interface. The CA technique is deployed to track the new interface cells. The computer program was parallelized using the Message Passing Interface (MPI) technique. Parallel scaling of the algorithm was studied and major scalability bottlenecks were identified. Efficiency loss attributable to the high memory bandwidth requirement of the algorithm was observed when using multiple cores per processor. Parallel writing of the output variables of interest was implemented in the binary Hierarchical Data Format 5 (HDF5) to improve the output performance, and to simplify visualization. Calculations were carried out in single precision arithmetic without significant loss in accuracy, resulting in 50% reduction of memory and computational time requirements. The presented solidification model shows a very good scalability up to centimeter size domains, including more than ten million of dendrites. Catalogue identifier: AEQZ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEQZ_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, UK Licensing provisions: Standard CPC license, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 29,767 No. of bytes in distributed program, including test data, etc.: 3131,367 Distribution format: tar.gz Programming language: Fortran 90. Computer: Linux PC and clusters. Operating system: Linux. Has the code been vectorized or parallelized?: Yes. Program is parallelized using MPI
Hung, Shih-Han; Su, Chin-Hui; Tseng, How
2016-08-01
It is important to have a standardized tympanic membrane (TM) perforation platform to evaluate the various myringoplasty materials that have been studied and developed extensively during recent years. However, currently there are no cellular models specifically designed for this purpose, and animal models remain unsatisfactory. The purpose of this study is to propose an inexpensive, readily available, well-controlled, and easy-to-create cellular model as a substitute for use in the evaluation of TM repairing materials. A trans-well model was created using a cell culture insert with a round hole created at the center of the polycarbonate membrane. HaCaT cells were cultured on the fenestrated culture insert, and the desired myringoplasty graft was placed at the center of the window for one week and observed by fluorescent microscopy under vital staining. Under this cellular model, there was notable migration of HaCaT cells onto the positive control graft (rabbit fascia), while only a few cell clusters were observed on the negative control graft (paper). Model validation showed that the cell migration ratio for the PLLA + 1% hyaluronic acid (HA) graft is significantly higher than using myringoplasty paper, poly L-lactide (PLLA), or PLLA + 0.5% HA (p < 0.05). This trans-well-based cellular model might be a useful pre-evaluation platform for the evaluation of TM repairing materials. The model is inexpensive, readily available, easy to create, and standardized for use. PMID:26335291
Development of novel cellular model for affinity studies of histamine H(4) receptor ligands.
Karcz, Tadeusz; Kieć-Kononowicz, Katarzyna
2013-01-01
The G protein-coupled histamine H4 receptor (H4R) is the last member of histamine receptors family discovered so far. Its expression pattern, together with postulated involvement in a wide variety of immunological and inflammatory processes make histamine H4 receptor an interesting target for drug development. Potential H4R ligands may provide an innovative therapies for different immuno-based diseases, including allergy, asthma, pruritus associated with allergy or autoimmune skin conditions, rheumatoid arthritis and pain. However, none of successfully developed selective and potent histamine H4 receptor ligands have been introduced to the market up to date. For that reason there is still a strong demand for pharmacological models to be used in studies on potent H4R ligands. In current work we present the development of novel mammalian cell line, stably expressing human histamine H4 receptor, with use of retroviral transduction approach. Obtained cell line was pharmacologically characterized in radioligand binding studies and its utility for affinity testing of potent receptor ligands was confirmed in comparative studies with the use of relevant insect cells expression model. Obtained results allow for statement that developed cellular model may be successfully employed in search for new compounds active at histamine H4 receptor. PMID:24432340
Effect of Driver Scope Awareness in the Lane Changing Maneuvers Using Cellular Automaton Model
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Kohei Arai
2013-07-01
Full Text Available This paper investigated the effect of drivers’ visibility and their perception (e.g., to estimate the speed and arrival time of another vehicle on the lane changing maneuver. The term of scope awareness was used to describe the visibility required by the driver to make a perception about road condition and the speed of vehicle that exist in that road. A computer simulation model was conducted to show this driver awareness behavior. This studying attempt to precisely catching the lane changing behavior and illustrate the scope awareness parameter that reflects driver behavior. This paper proposes a simple cellular automata model for studying driver visibility effects of lane changing maneuver and driver perception of estimated speed. Different values of scope awareness were examined to capture its effect on the traffic flow. Simulation results show the ability of this model to capture the important features of lane changing maneuver and revealed the appearance of the short-thin solid line jam and the wide solid line jam in the traffic flow as the consequences of lane changing maneuver.
Idealists in the Ruhr region; Idealisten im Pott
Energy Technology Data Exchange (ETDEWEB)
Meyer, J.P.
2001-07-01
In spite of a reimbursement of 99 DPf/kWh, installation of private PV systems still requires idealism. A model project was initiated by the local authorities of the town of Schwerte near Dortmund: It all started in 1991 with the carbon dioxide emissions reduction concept of the town of Schwerte. Private builder-owners were to be informed on alternative energy sources. In 1993, regular meetings were introduced with the aim of informing the public (including the use of tools like the web) and of getting as many PV systems as possible going on Schwerte roofs. [German] Trotz der 99 Pf/kWh braucht die Installation von privaten PV-Anlagen immer noch viel Engagement. Ein vorbildliches Projekt ist auf Initiative der Stadt Schwerte bei Dortmund entstanden und lebt heute dank der unermuedlichen Arbeit einzelner PV-Begeisterter weiter: der Schwerter Solarstammtisch. Begonnen hat es 1991 mit dem CO{sub 2}-Minderungskonzept der Stadt Schwerte. Private Bauherren sollten auf den Einsatz alternativer Energien hingewiesen werden. Aus dieser Idee entwickelte sich 1993 ein regelmaessiges Treffen mit dem Ziel 'die Menschen zu informieren (auch ueber das Internet) und moeglichst viele Anlagen auf Schwerter Daecher zu bekommen'. (orig.)
Chen, Qingcai; Shi, Jianghong; Liu, Xiaowei; Wu, Wei; Liu, Bo; Zhang, Hui
2013-03-01
A cellular automata model (CA model) was used to simulate the soil column leaching process of estrogens during the processes of migration and transformation. The results of the simulated leaching experiment showed that the first-order degradation rates of 17α-ethynylestradiol (EE2), 17β-estradiol (E2) and estrone (E1) were 0.131 h- 1 for E2, 0.099 h- 1 for E1 and 0.064 h- 1 for EE2 in the EE2 and E2 leaching process, and the first-order sorption rates were 5.94 h- 1 for E2, 5.63 h- 1 for EE2, 3.125 h- 1 for E1. Their sorption rates were positively correlated with the n-octanol/water partition coefficients. When the diffusion rate was low, its impact on the simulation results was insignificant. The increase in sorption and degradation rates caused the decrease in the total estrogens that leached. In addition, increasing the sorption rate could delay the emerging time of the maximum concentration of estrogen that leached, whereas increasing the degradation rate could shorten the emerging time of the maximum concentration of estrogen that leached. The comparison made between the experimental data and the simulation results of the CA model and the HYDRUS-1D software showed that the establishment of one-component and multi-component CA models could simulate EE2 and E2 soil column leaching processes, and the CA models achieve an intuitive, dynamic, and visual simulation.
Load-aware modeling for uplink cellular networks in a multi-channel environment
Alammouri, Ahmad Mohammad Abdel-Karim
2014-09-01
We exploit tools from stochastic geometry to develop a tractable analytical approach for modeling uplink cellular networks. The developed model is load aware and accounts for per-user power control as well as the limited transmit power constraint for the users\\' equipment (UEs). The proposed analytical paradigm is based on a simple per-user power control scheme in which each user inverts his path-loss such that the signal is received at his serving base station (BS) with a certain power threshold ρ Due to the limited transmit power of the UEs, users that cannot invert their path-loss to their serving BSs are allowed to transmit with their maximum transmit power. We show that the proposed power control scheme not only provides a balanced cell center and cell edge user performance, it also facilitates the analysis when compared to the state-of-the-art approaches in the literature. To this end, we discuss how to manipulate the design variable ρ in response to the network parameters to optimize one or more of the performance metrics such as the outage probability, the network capacity, and the energy efficiency.
International Nuclear Information System (INIS)
Repeated injury to the stratum corneum of mammalian skin (caused by friction, soaps, or organic solvents) elicits hyperkeratosis and epidermal thickening. Functionally, these changes serve to restore the cutaneous barrier and protect the organism. To better understand the molecular and cellular basis of this response, we have engineered an in vitro model of acetone-induced injury using organotypic epidermal cultures. Rat epidermal keratinocytes (REKs), grown on a collagen raft in the absence of any feeder fibroblasts, developed all the hallmarks of a true epidermis including a well-formed cornified layer. To induce barrier injury, REK cultures were treated with intermittent 30-s exposures to acetone then were fixed and paraffin-sectioned. After two exposures, increased proliferation (Ki67 and BrdU staining) was observed in basal and suprabasal layers. After three exposures, proliferation became confined to localized buds in the basal layer and increased terminal differentiation was observed (compact hyperkeratosis of the stratum corneum, elevated levels of K10 and filaggrin, and heightened transglutaminase activity). Thus, barrier disruption causes epidermal hyperplasia and/or enhances differentiation, depending upon the extent and duration of injury. Given that no fibroblasts are present in the model, the ability to mount a hyperplastic response to barrier injury is an inherent property of keratinocytes
Ballarini, F.; Alloni, D.; Facoetti, A.; Mairani, A.; Nano, R.; Ottolenghi, A.
Astronauts in space are continuously exposed to low doses of ionizing radiation from Galactic Cosmic Rays During the last ten years the effects of low radiation doses have been widely re-discussed following a large number of observations on the so-called non targeted effects in particular bystander effects The latter consist of induction of cytogenetic damage in cells not directly traversed by radiation most likely as a response to molecular messengers released by directly irradiated cells Bystander effects which are observed both for lethal endpoints e g clonogenic inactivation and apoptosis and for non-lethal ones e g mutations and neoplastic transformation tend to show non-linear dose responses This might have significant consequences in terms of low-dose risk which is generally calculated on the basis of the Linear No Threshold hypothesis Although the mechanisms underlying bystander effects are still largely unknown it is now clear that two types of cellular communication i e via gap junctions and or release of molecular messengers into the extracellular environment play a fundamental role Theoretical models and simulation codes can be of help in elucidating such mechanisms In the present paper we will review different available modelling approaches including one that is being developed at the University of Pavia The focus will be on the different assumptions adopted by the various authors and on the implications of such assumptions in terms of non-targeted radiobiological damage and more generally low-dose
Detection and Projection of Forest Changes by Using the Markov Chain Model and Cellular Automata
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Griselda Vázquez-Quintero
2016-03-01
Full Text Available The spatio-temporal analysis of land use changes could provide basic information for managing the protection, conservation and production of forestlands, which promotes a sustainable resource use of temperate ecosystems. In this study we modeled and analyzed the spatial and temporal dynamics of land use of a temperate forests in the region of Pueblo Nuevo, Durango, Mexico. Data from the Landsat images Multispectral Scanner (MSS 1973, Thematic Mapper (TM 1990, and Operational Land Imager (OLI 2014 were used. Supervised classification methods were then applied to generate the land use for these years. To validate the land use classifications on the images, the Kappa coefficient was used. The resulting Kappa coefficients were 91%, 92% and 90% for 1973, 1990 and 2014, respectively. The analysis of the change dynamics was assessed with Markov Chains and Cellular Automata (CA, which are based on probabilistic modeling techniques. The Markov Chains and CA show constant changes in land use. The class most affected by these changes is the pine forest. Changes in the extent of temperate forest of the study area were further projected until 2028, indicating that the area of pine forest could be continuously reduced. The results of this study could provide quantitative information, which represents a base for assessing the sustainability in the management of these temperate forest ecosystems and for taking actions to mitigate their degradation.
Effects of Mechanical Properties on Tumor Invasion: Insights from a Cellular Model
Li, YZ
2014-08-01
Understanding the regulating mechanism of tumor invasion is of crucial importance for both fundamental cancer research and clinical applications. Previous in vivo experiments have shown that invasive cancer cells dissociate from the primary tumor and invade into the stroma, forming an irregular invasive morphology. Although cell movements involved in tumor invasion are ultimately driven by mechanical forces of cell-cell interactions and tumor-host interactions, how these mechanical properties affect tumor invasion is still poorly understood. In this study, we use a recently developed two-dimensional cellular model to study the effects of mechanical properties on tumor invasion. We study the effects of cell-cell adhesions as well as the degree of degradation and stiffness of extracellular matrix (ECM). Our simulation results show that cell-cell adhesion relationship must be satisfied for tumor invasion. Increased adhesion to ECM and decreased adhesion among tumor cells result in invasive tumor behaviors. When this invasive behavior occurs, ECM plays an important role for both tumor morphology and the shape of invasive cancer cells. Increased stiffness and stronger degree of degradation of ECM promote tumor invasion, generating more aggressive tumor invasive morphologies. It can also generate irregular shape of invasive cancer cells, protruding towards ECM. The capability of our model suggests it a useful tool to study tumor invasion and might be used to propose optimal treatment in clinical applications.
Tectonic modeling of Konya-Beysehir Region (Turkey using cellular neural networks
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D. Aydogan
2007-06-01
Full Text Available In this paper, to separate regional-residual anomaly maps and to detect borders of buried geological bodies, we applied the Cellular Neural Network (CNN approach to gravity and magnetic anomaly maps. CNN is a stochastic image processing technique, based optimization of templates, which imply relationships of neighborhood pixels in 2-Dimensional (2D potential anomalies. Here, CNN performance in geophysics, tested by various synthetic examples and the results are compared to classical methods such as boundary analysis and second vertical derivatives. After we obtained satisfactory results in synthetic models, we applied CNN to Bouguer anomaly map of Konya-Beysehir Region, which has complex tectonic structure with various fault combinations. We evaluated CNN outputs and 2D/3D models, which are constructed using forward and inversion methods. Then we presented a new tectonic structure of Konya-Beysehir Region. We have denoted (F1, F2, , F7 and (Konya1, Konya2 faults according to our evaluations of CNN outputs. Thus, we have concluded that CNN is a compromising stochastic image processing technique in geophysics.
Renal Contrast-Enhanced Sonography Findings in a Model of Acute Cellular Allograft Rejection.
Grabner, A; Kentrup, D; Pawelski, H; Mühlmeister, M; Biermann, C; Edemir, B; Heitplatz, B; Van Marck, V; Bettinger, T; Pavenstädt, H; Schlatter, E; Stypmann, J; Tiemann, K; Reuter, S
2016-05-01
Noninvasive methods to diagnose and differentiate acute cellular rejection from acute tubular necrosis or acute calcineurin inhibitor toxicity are still missing. Because T lymphocytes play a decisive role in early states of rejection, we investigated the suitability and feasibility of antibody-mediated contrast-enhanced ultrasound by using microbubbles targeted to CD3(+) , CD4(+) , or CD8(+) T cells in different models of renal disease. In an established rat renal transplantation model, CD3-mediated ultrasound allows the detection of acute rejection as early as on postoperative day 2. Ultrasound signal intensities increased with the severity of inflammation. Further, an early response to therapy could be monitored by using contrast-enhanced sonography. Notably, acute tubular necrosis occurring after ischemia-reperfusion injury as well as acute calcineurin inhibitor toxicity could easily be differentiated. Finally, the quantified ultrasound signal correlated significantly with the number of infiltrating T cells obtained by histology and with CD3 mRNA levels, as well as with chemokine CXCL9, CXCL11, and CCL19 mRNA but not with KIM-1 mRNA expression, thereby representing the severity of graft inflammation but not the degree of kidney injury. In summary, we demonstrate that antibody-mediated contrast-enhanced ultrasound targeting T lymphocytes could be a promising tool for an easy and reproducible assessment of acute rejection after renal transplantation. PMID:26613381
Model of Handover and Traffic Based on Cellular Geometry with Smart Antenna
Zufan Zhang; Jie Zhang; Shaohui Sun
2014-01-01
Based on the application of smart antennas in cellular mobile communications, this paper introduces the impact of the width of the antenna beams playing on the dwell time probability density function in cellular geometry with smart antenna. The research results indicate that the smart cell structure can improve the dwell time of users within the cell and improve the traffic system performance.
Simulating debris flows through a hexagonal cellular automata model: SCIDDICA S3–hex
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D. D’Ambrosio
2003-01-01
Full Text Available Cellular Automata (CA represent a formal frame for dynamical systems, which evolve on the base of local interactions. Some types of landslide, such as debris flows, match well this requirement. The latest hexagonal release (S3–hex of the deterministic model SCIDDICA, specifically developed for simulating debris flows, is described. For CA simulation purposes, landslides can be viewed as a dynamical system, subdivided into elementary parts, whose state evolves exclusively as a consequence of local interactions within a spatial and temporal discretum. Space is the world of the CA, here constituted by hexagonal cells. The attributes of each cell ("substates" describe physical characteristics. For computational reasons, the natural phenomenon is "decomposed" into a number of elementary processes, whose proper composition makes up the "transition function" of the CA. By simultaneously applying this function to all the cells, the evolution of the phenomenon can be simulated in terms of modifications of the substates. SCIDDICA S3–hex exhibits a great flexibility in modelling debris flows. With respect to the previous releases of the model, the mechanism of progressive erosion of the soil cover has been added to the transition function. Considered substates are: altitude; thickness and energy of landslide debris; depth of erodable soil cover; debris outflows. Considered elementary processes are: mobilisation triggering and effect (T1, debris outflows (I1, update of landslide debris thickness and energy (I2, and energy loss (T2. Simulations of real debris flows, occurred in Campania (Southern Italy in May 1998 (Sarno and December 1999 (San Martino V.C. and Cervinara, have been performed for model calibration purposes; some examples of analysis are briefly described. Possible applications of the method are: risk mapping, also based on a statistical approach; evaluating the effects of mitigation actions (e.g. stream deviations, topographic
Evolving Transport Networks With Cellular Automata Models Inspired by Slime Mould.
Tsompanas, Michail-Antisthenis I; Sirakoulis, Georgios Ch; Adamatzky, Andrew I
2015-09-01
Man-made transport networks and their design are closely related to the shortest path problem and considered amongst the most debated problems of computational intelligence. Apart from using conventional or bio-inspired computer algorithms, many researchers tried to solve this kind of problem using biological computing substrates, gas-discharge solvers, prototypes of a mobile droplet, and hot ice computers. In this aspect, another example of biological computer is the plasmodium of acellular slime mould Physarum polycephalum (P. polycephalum), which is a large single cell visible by an unaided eye and has been proven as a reliable living substrate for implementing biological computing devices for computational geometry, graph-theoretical problems, and optimization and imitation of transport networks. Although P. polycephalum is easy to experiment with, computing devices built with the living slime mould are extremely slow; it takes slime mould days to execute a computation. Consequently, mapping key computing mechanisms of the slime mould onto silicon would allow us to produce efficient bio-inspired computing devices to tackle with hard to solve computational intelligence problems like the aforementioned. Toward this direction, a cellular automaton (CA)-based, Physarum-inspired, network designing model is proposed. This novel CA-based model is inspired by the propagating strategy, the formation of tubular networks, and the computing abilities of the plasmodium of P. polycephalum. The results delivered by the CA model demonstrate a good match with several previously published results of experimental laboratory studies on imitation of man-made transport networks with P. polycephalum. Consequently, the proposed CA model can be used as a virtual, easy-to-access, and biomimicking laboratory emulator that will economize large time periods needed for biological experiments while producing networks almost identical to the tubular networks of the real-slime mould. PMID
fA cellular automaton model of crystalline cellulose hydrolysis by cellulases
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Little Bryce A
2011-10-01
Full Text Available Abstract Background Cellulose from plant biomass is an abundant, renewable material which could be a major feedstock for low emissions transport fuels such as cellulosic ethanol. Cellulase enzymes that break down cellulose into fermentable sugars are composed of different types - cellobiohydrolases I and II, endoglucanase and β-glucosidase - with separate functions. They form a complex interacting network between themselves, soluble hydrolysis product molecules, solution and solid phase substrates and inhibitors. There have been many models proposed for enzymatic saccharification however none have yet employed a cellular automaton approach, which allows important phenomena, such as enzyme crowding on the surface of solid substrates, denaturation and substrate inhibition, to be considered in the model. Results The Cellulase 4D model was developed de novo taking into account the size and composition of the substrate and surface-acting enzymes were ascribed behaviors based on their movements, catalytic activities and rates, affinity for, and potential for crowding of, the cellulose surface, substrates and inhibitors, and denaturation rates. A basic case modeled on literature-derived parameters obtained from Trichoderma reesei cellulases resulted in cellulose hydrolysis curves that closely matched curves obtained from published experimental data. Scenarios were tested in the model, which included variation of enzyme loadings, adsorption strengths of surface acting enzymes and reaction periods, and the effect on saccharide production over time was assessed. The model simulations indicated an optimal enzyme loading of between 0.5 and 2 of the base case concentrations where a balance was obtained between enzyme crowding on the cellulose crystal, and that the affinities of enzymes for the cellulose surface had a large effect on cellulose hydrolysis. In addition, improvements to the cellobiohydrolase I activity period substantially improved overall
Satoh, Kazuhiro
1989-10-01
Numerical studies are made on the complex behavior of a cellular automaton which serves as a phenomenological model for an ecosystem. The ecosystem is assumed to contain only three populations, i.e., a population of plants, of herbivores, and of carnivores. A two-dimensional region where organisms live is divided into square cells and the population density in each cell is regarded as a discrete variable. The influence of the physical environment and the interactions between organisms are reduced to a simple rule of cellular automaton evolution. It is found that the time dependent spatial distribution of organisms is, in general, very random and complex. However, under certain conditions, the self-organization of ordered patterns such as rotating spirals or concentric circles takes place. The relevance of the cellular automaton as a model for the ecosystem is discussed.
Yao Xiao; Jing Shi
2015-01-01
This paper aimed to analyze the influence of drivers’ behavior of phone use while driving on traffic flow, including both traffic efficiency and traffic safety. An improved cellular automaton model was proposed to simulate traffic flow with distracted drivers based on the Nagel-Schreckenberg model. The driving characters of drivers using a phone were first discussed and a value representing the probability to use a phone while driving was put into the CA model. Simulation results showed that ...
Huang, Hua-mei; Zhang, Li-quan; Guan, Yu-juan; Wang, Dong-hui
2008-03-01
Biological invasion has received considerable attention recently because of increasing impacts on local ecosystems. Expansion of Spartina alterniflora, a non-native species, on the intertidal mudflats of Jiuduansha Shoals at the Yangtze River Estuary is a prime example of a spatially-structured invasion in a relatively simple habitat, for which strategic control efforts can be modeled and applied. Here, we developed a Cellular Automata (CA) model, in conjunction with Remote Sensing and Geographical Information Systems, to simulate the expanding process of S. alterniflora for a period of 8 years after being introduced to the new shoals, and to study the interactions between spatial pattern and ecosystem processes for the saltmarsh vegetation. The results showed that the CA model could simulate the population dynamics of S. alterniflora and Phragmites australis on the Jiuduansha Shoals successfully. The results strongly support the hypothesis of space pre-emption as well as range expansion with simple advancing wave fronts for these two species. In the Yangtze River Estuary, the native species P. australis shares the same niche with the exotic species S. alterniflora. However, the range expansion rate of P. australis was much slower than that of S. alterniflora. With the accretion of the Jiuduansha Shoals due to the large quantity of sediments deposited by the Yangtze River, a rapid range expansion of S. alterniflora is predicted to last for a long period into future. This study indicated the potential for this approach to provide valuable insights into population and community ecology of invasive species, which could be very important for wetland biodiversity conservation and resource management in the Yangtze River Estuary and other such impacted areas.
Modeling and Simulation of Polarization in Internet Group Opinions Based on Cellular Automata
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Yaofeng Zhang
2015-01-01
Full Text Available Hot events on Internet always attract many people who usually form one or several opinion camps through discussion. For the problem of polarization in Internet group opinions, we propose a new model based on Cellular Automata by considering neighbors, opinion leaders, and external influences. Simulation results show the following: (1 It is easy to form the polarization for both continuous opinions and discrete opinions when we only consider neighbors influence, and continuous opinions are more effective in speeding the polarization of group. (2 Coevolution mechanism takes more time to make the system stable, and the global coupling mechanism leads the system to consensus. (3 Opinion leaders play an important role in the development of consensus in Internet group opinions. However, both taking the opinion leaders as zealots and taking some randomly selected individuals as zealots are not conductive to the consensus. (4 Double opinion leaders with consistent opinions will accelerate the formation of group consensus, but the opposite opinions will lead to group polarization. (5 Only small external influences can change the evolutionary direction of Internet group opinions.
Directory of Open Access Journals (Sweden)
Alejandro Martínez-Herrera
2015-09-01
Full Text Available Dystrophin Dp40 is the shortest protein encoded by the DMD (Duchenne muscular dystrophy gene. This protein is unique since it lacks the C-terminal end of dystrophins. In this data article, we describe the subcellular localization, nuclear export signals and the three-dimensional structure modeling of putative Dp40 proteins using bioinformatics tools. The Dp40 wild type protein was predicted as a cytoplasmic protein while the Dp40n4 was predicted to be nuclear. Changes L93P and L170P are involved in the nuclear localization of Dp40n4 protein. A close analysis of Dp40 protein scored that amino acids 93LEQEHNNLV101 and 168LLLHDSIQI176 could function as NES sequences and the scores are lost in Dp40n4. In addition, the changes L93/170P modify the tertiary structure of putative Dp40 mutants. The analysis showed that changes of residues 93 and 170 from leucine to proline allow the nuclear localization of Dp40 proteins. The data described here are related to the research article entitled “EF-hand domains are involved in the differential cellular distribution of dystrophin Dp40” (J. Aragón et al. Neurosci. Lett. 600 (2015 115–120 [1].
International Nuclear Information System (INIS)
A numerical implementation of a three-dimensional (3D) cellular automaton (CA)–finite element (FE) model has been developed for the prediction of solidification grain structures. For the first time, it relies on optimized parallel computation to solve industrial-scale problems (centimeter to meter long) while using a sufficiently small CA grid size to predict representative structures. Several algorithm modifications and strategies to maximize parallel efficiency are introduced. Improvements on a real case simulation are measured and discussed. The CA–FE implementation here is demonstrated using 32 computing units to predict grain structure in a 2.08 m × 0.382 m × 0.382 m ingot involving 4.9 billion cells and 1.6 million grains. These numerical improvements permit tracking of local changes in texture and grain size over real-cast parts while integrating interactions with macrosegregation, heat flow and fluid flow. Full 3D is essential in all these analyses, and can be dealt with successfully using the implementation presented here. (paper)
Institute of Scientific and Technical Information of China (English)
A.Yu. SMOLIN; E.V. SHILKO; S.V. ASTAFUROV; I.S. KONOVALENKO; S.P. BUYAKOVA; S.G. PSAKHIE
2015-01-01
Two classes of composite materials are considered: classical metaleceramic composites with reinforcing hard inclusions as well as hard ceramics matrix with soft gel inclusions. Movable cellular automaton method is used for modeling the mechanical behaviors of such different heterogeneous materials. The method is based on particle approach and may be considered as a kind of discrete element method. The main feature of the method is the use of many-body forces of inter-element interaction within the formalism of simply deformable element approximation. It was shown that the strength of reinforcing particles and the width of particle-binder interphase boundaries had determining influence on the service characteristics of metaleceramic composite. In particular, the increasing of strength of carbide inclusions may lead to significant increase in the strength and ultimate strain of composite material. On the example of porous zirconia ceramics it was shown that the change in the mechanical properties of pore surface leads to the corresponding change in effective elastic modulus and strength limit of the ceramic sample. The less is the pore size, the more is this effect. The increase in the elastic properties of pore surface of ceramics may reduce its fracture energy.
Computer simulation of a cellular automata model for the immune response in a retrovirus system
Pandey, R. B.
1989-02-01
Immune response in a retrovirus system is modeled by a network of three binary cell elements to take into account some of the main functional features of T4 cells, T8 cells, and viruses. Two different intercell interactions are introduced, one of which leads to three fixed points while the other yields bistable fixed points oscillating between a healthy state and a sick state in a mean field treatment. Evolution of these cells is studied for quenched and annealed random interactions on a simple cubic lattice with a nearest neighbor interaction using inhomogenous cellular automata. Populations of T4 cells and viral cells oscillate together with damping (with constant amplitude) for annealed (quenched) interaction on increasing the value of mixing probability B from zero to a characteristic value B ca ( B cq). For higher B, the average number of T4 cells increases while that of the viral infected cells decreases monotonically on increasing B, suggesting a phase transition at B ca ( B cq).
Lateral Drift Behavior Analysis in Mixed Bicycle Traffic: A Cellular Automaton Model Approach
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Xue Feng
2016-01-01
Full Text Available Bicycle movements are always associated with lateral drifts. However, the impacts of lateral drift behavior, as well as variable lateral clearance maintaining behavior due to the variation of drift intensity, on mixed bicycle flow are not clear. This paper establishes a new cellular automata model to study typical characteristics of mixed bicycle traffic induced by lateral drift and its accompanying behavior. Based on derived positive correlation between passing speed and drift speed through survey, the occurrence probability of lateral drift and the degree of maintained lateral clearance are both introduced in accordance with the variance of passing speed. Then, in whole density region, firm conformity between simulation results and actual survey data is reached, which has seldom been achieved in previous studies. It is further verified that speed distortions in intermediate and high density region induced by assumption of constant lateral clearance requirements can be revised by introducing its variability characteristics. In addition, two contrastive impacts of lateral drift behavior are observed. That is, it causes speed fluctuation in low density while alleviating the speed fluctuation in relatively high density. These results are expected to be helpful to improve the simulation performance of mixed bicycle flow as well as depict more realistic vehicle-bicycle conflicts and so on.
Path Loss, Shadow Fading, and Line-Of-Sight Probability Models for 5G Urban Macro-Cellular Scenarios
DEFF Research Database (Denmark)
Sun, Shu; Thomas, Timothy; Rappaport, Theodore S.;
2015-01-01
This paper presents key parameters including the line-of-sight (LOS) probability, large-scale path loss, and shadow fading models for the design of future fifth generation (5G) wireless communication systems in urban macro-cellular (UMa) scenarios, using the data obtained from propagation...
International Nuclear Information System (INIS)
Full text: The Bauschinger effect refers to an observed asymmetry in the forward and reverse loading curves of a metal or an alloy. Typically, the absolute value of the yield stress in reverse loading is lower than the maximum stress imposed on the initial, forward loading. This difference arises from either the presence of a back stress or from the greater strength of obstacles opposing dislocation motion in the forward than in the reverse direction. Thus, the Bauschinger effect contributes to the phenomena referred to as kinematic hardening. In particular dispersion hardened systems, containing strong, non-shearable particles that offer obstacles to dislocation motion, will often exhibit a large kinematic hardening component. When a material is described as a group of parallel elements (a composite) having variable yield stresses and or Young's moduli, kinematic hardening of type KI, is observed when the first element to yield on forward loading is the first element to yield on reverse loading. Kinematic hardening types KII and KIII result when the order of relaxation of the elements is different from the order of their initial yielding. The reverse loading curves for types KII and KIII hardening generally exhibit inflection points at the initiation of yielding on reverse loading. In previous work, a micromechanics model, with a detailed description of the microstructure, was employed to model the effects of plastic inhomogeneity and duplicate the loading and unloading trends observed experimentally. Trends predicted by the model corresponded well to some of the expectations derived from observation, e.g. the effects related to the inclusions of different phases, however in some cases the correlation depended on the assignment of unrealistic properties to microstructural constituents. In the current work, the material is modeled as an array of coupled elements with varying stiffnesses and strengths. A stochastic cellular automaton is then used to simulate the
Recurrence time statistics of landslide events simulated by a cellular automaton model
Piegari, Ester; Di Maio, Rosa; Avella, Adolfo
2014-05-01
The recurrence time statistics of a cellular automaton modelling landslide events is analyzed by performing a numerical analysis in the parameter space and estimating Fano factor behaviors. The model is an extended version of the OFC model, which is a paradigm for SOC in non-conserved systems, but it works differently from the original OFC model as a finite value of the driving rate is applied. By driving the system to instability with different rates, the model exhibits a smooth transition from a correlated to an uncorrelated regime as the effect of a change in predominant mechanisms to propagate instability. If the rate at which instability is approached is small, chain processes dominate the landslide dynamics, and power laws govern probability distributions. However, the power-law regime typical of SOC-like systems is found in a range of return intervals that becomes shorter and shorter by increasing the values of the driving rates. Indeed, if the rates at which instability is approached are large, domino processes are no longer active in propagating instability, and large events simply occur because a large number of cells simultaneously reach instability. Such a gradual loss of the effectiveness of the chain propagation mechanism causes the system gradually enter to an uncorrelated regime where recurrence time distributions are characterized by Weibull behaviors. Simulation results are qualitatively compared with those from a recent analysis performed by Witt et al.(Earth Surf. Process. Landforms, 35, 1138, 2010) for the first complete databases of landslide occurrences over a period as large as fifty years. From the comparison with the extensive landslide data set, the numerical analysis suggests that statistics of such landslide data seem to be described by a crossover region between a correlated regime and an uncorrelated regime, where recurrence time distributions are characterized by power-law and Weibull behaviors for short and long return times
Model of Handover and Traffic Based on Cellular Geometry with Smart Antenna
Directory of Open Access Journals (Sweden)
Zufan Zhang
2014-01-01
Full Text Available Based on the application of smart antennas in cellular mobile communications, this paper introduces the impact of the width of the antenna beams playing on the dwell time probability density function in cellular geometry with smart antenna. The research results indicate that the smart cell structure can improve the dwell time of users within the cell and improve the traffic system performance.
Directory of Open Access Journals (Sweden)
Nathalie Boone
Full Text Available BACKGROUND: Familial dysautonomia (FD is a hereditary neuropathy caused by mutations in the IKBKAP gene, the most common of which results in variable tissue-specific mRNA splicing with skipping of exon 20. Defective splicing is especially severe in nervous tissue, leading to incomplete development and progressive degeneration of sensory and autonomic neurons. The specificity of neuron loss in FD is poorly understood due to the lack of an appropriate model system. To better understand and modelize the molecular mechanisms of IKBKAP mRNA splicing, we collected human olfactory ecto-mesenchymal stem cells (hOE-MSC from FD patients. hOE-MSCs have a pluripotent ability to differentiate into various cell lineages, including neurons and glial cells. METHODOLOGY/PRINCIPAL FINDINGS: We confirmed IKBKAP mRNA alternative splicing in FD hOE-MSCs and identified 2 novel spliced isoforms also present in control cells. We observed a significant lower expression of both IKBKAP transcript and IKAP/hELP1 protein in FD cells resulting from the degradation of the transcript isoform skipping exon 20. We localized IKAP/hELP1 in different cell compartments, including the nucleus, which supports multiple roles for that protein. We also investigated cellular pathways altered in FD, at the genome-wide level, and confirmed that cell migration and cytoskeleton reorganization were among the processes altered in FD. Indeed, FD hOE-MSCs exhibit impaired migration compared to control cells. Moreover, we showed that kinetin improved exon 20 inclusion and restores a normal level of IKAP/hELP1 in FD hOE-MSCs. Furthermore, we were able to modify the IKBKAP splicing ratio in FD hOE-MSCs, increasing or reducing the WT (exon 20 inclusion:MU (exon 20 skipping ratio respectively, either by producing free-floating spheres, or by inducing cells into neural differentiation. CONCLUSIONS/SIGNIFICANCE: hOE-MSCs isolated from FD patients represent a new approach for modeling FD to better
Franz, Michael G.; Payne, Wyatt G.; Xing, Liyu; Naidu, D. K; Salas, R. E; Marshall, Vivienne S.; Trumpower, C. J; Smith, Charlotte A; Steed, David L.; Robson, M. C.
2008-01-01
Objective: Growth factors demonstrate mixed results improving wound healing. Amnion-derived multipotent cells release physiologic levels of growth factors and tissue inhibitors of metalloproteinases. This solution was tested in models of acute and chronic wound healing. Methods: Acute model: Sprague-Dawley rats underwent laparotomy incisions. The midline fascia was primed with phosphate-buffered saline, unconditioned media, or amnion-derived cellular cytokine suspension prior to incision. Bre...
Secure D2D Communication in Large-Scale Cognitive Cellular Networks: A Wireless Power Transfer Model
Liu, Yuanwei; Wang, Lifeng; Zaidi, Syed Ali Raza; Elkashlan, Maged; Duong, Trung Q.
2015-01-01
In this paper, we investigate secure device-to-device (D2D) communication in energy harvesting large-scale cognitive cellular networks. The energy constrained D2D transmitter harvests energy from multiantenna equipped power beacons (PBs), and communicates with the corresponding receiver using the spectrum of the primary base stations (BSs). We introduce a power transfer model and an information signal model to enable wireless energy harvesting and secure information transmission. In the power...
Effect of preoperative immunonutrition and other nutrition models on cellular immune parameters
Institute of Scientific and Technical Information of China (English)
Yusuf Gunerhan; Neset Koksal; Umit Yasar Sahin; Mehmet Ali Uzun; Emel Ek(s)ioglu-Demiralp
2009-01-01
AIM: To evaluate the effects of preoperative immunonutrition and other nutrition models on the cellular immunity parameters of patients with gastrointestinal tumors before surgical intervention. In addition, effects on postoperative complications were examined.METHODS: Patients with gastrointestinal tumors were randomized into 3 groups. The immunonutrition group received a combination of arginine, fatty acids and nucleotides. The second and third group received normal nutrition and standard enteral nutrition,respectively. Nutrition protocols were administered for 7 d prior to the operation. Nutritional parameters,in particular prealbumin levels and lymphocyte subpopulations (CD4+, CD8+, CD16+/56+, and CD69 cells) were evaluated before and after the nutrition protocols. Groups were compared in terms of postoperative complications and duration of hospital stay.RESULTS: Of the 42 patients who completed the study, 16 received immunonutrition, 13 received normal nutrition and 13 received standard enteral nutrition.prealbumin values were low in every group, but this parameter was improved after the nutritional protocol only in the immunonutrition group (13.64 ± 8.83vs 15.98 ± 8.66, P = 0.037). Groups were similar in terms of CD4+, CD16+/56, and CD69+ prior to the nutritional protocol; whereas CD8+ was higher in the standard nutrition group compared to the immunonutrition group. After nutritional protocols,none of the groups had an increase in their lymphocyte subpopulations. Also, groups did not differ in terms of postoperative complications and postoperative durations of hospital stay.CONCLUSION: Preoperative immunonutrition provided a significant increase in prealbumin levels,while it did not significantly alter T lymphocyte subpopulation counts, the rate of postoperative complications and the duration of hospital stay.
Elsawy, Hesham
2014-08-01
Using stochastic geometry, we develop a tractable uplink modeling paradigm for outage probability and spectral efficiency in both single and multi-tier cellular wireless networks. The analysis accounts for per user equipment (UE) power control as well as the maximum power limitations for UEs. More specifically, for interference mitigation and robust uplink communication, each UE is required to control its transmit power such that the average received signal power at its serving base station (BS) is equal to a certain threshold ρo. Due to the limited transmit power, the UEs employ a truncated channel inversion power control policy with a cutoff threshold of ρo. We show that there exists a transfer point in the uplink system performance that depends on the following tuple: BS intensity λ, maximum transmit power of UEs Pu, and ρo. That is, when Pu is a tight operational constraint with respect to (w.r.t.) λ and ρo, the uplink outage probability and spectral efficiency highly depend on the values of λ and ρo. In this case, there exists an optimal cutoff threshold ρ*o, which depends on the system parameters, that minimizes the outage probability. On the other hand, when Pu is not a binding operational constraint w.r.t. λ and ρo, the uplink outage probability and spectral efficiency become independent of λ and ρo. We obtain approximate yet accurate simple expressions for outage probability and spectral efficiency, which reduce to closed forms in some special cases. © 2002-2012 IEEE.
A computational model of cellular mechanisms of temporal coding in the medial geniculate body (MGB.
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Cal F Rabang
Full Text Available Acoustic stimuli are often represented in the early auditory pathway as patterns of neural activity synchronized to time-varying features. This phase-locking predominates until the level of the medial geniculate body (MGB, where previous studies have identified two main, largely segregated response types: Stimulus-synchronized responses faithfully preserve the temporal coding from its afferent inputs, and Non-synchronized responses, which are not phase locked to the inputs, represent changes in temporal modulation by a rate code. The cellular mechanisms underlying this transformation from phase-locked to rate code are not well understood. We use a computational model of a MGB thalamocortical neuron to test the hypothesis that these response classes arise from inferior colliculus (IC excitatory afferents with divergent properties similar to those observed in brain slice studies. Large-conductance inputs exhibiting synaptic depression preserved input synchrony as short as 12.5 ms interclick intervals, while maintaining low firing rates and low-pass filtering responses. By contrast, small-conductance inputs with Mixed plasticity (depression of AMPA-receptor component and facilitation of NMDA-receptor component desynchronized afferent inputs, generated a click-rate dependent increase in firing rate, and high-pass filtered the inputs. Synaptic inputs with facilitation often permitted band-pass synchrony along with band-pass rate tuning. These responses could be tuned by changes in membrane potential, strength of the NMDA component, and characteristics of synaptic plasticity. These results demonstrate how the same synchronized input spike trains from the inferior colliculus can be transformed into different representations of temporal modulation by divergent synaptic properties.
The principles of Katz's cellular track structure radiobiological model
International Nuclear Information System (INIS)
The cellular track structure theory (TST), introduced by Katz in 1968, applies the concept of action cross section as the probability of targets in the radiation detector being activated to elicit the observed endpoint (e.g. cell killing). The ion beam radiation field is specified by the charge Z, speed β (or energy), fluence and linear energy transfer (LET) of the ion, rather than by its total absorbed dose or dose-averaged LET. The detector is represented by radiosensitive elements of size a0 and radiosensitivity D0, its gamma-ray response being represented by c-hit or multi-target expressions rather than by the linear-quadratic formula. Key to TST is the Dδ(r) formula describing the radial distribution of delta-ray dose (RDD) around the ion path. This formula, when folded with the dose response of the detector and radially integrated, yields the 'point target' action cross section value, sPT. The averaged value of the cross section, σ, is obtained by radially integrating the a0-averaged RDD. In the 'track width' regime which may occur at the distal end of the ion's path, the value of s may considerably exceed its geometrical value, πa20. Several scaling principles are applied in TST, resulting in its simple analytic formulation. Multi-target detectors, such as cells, are represented in TST by m, D0, σ0 (the 'saturation value' of the cross section which replaces a0) and k (a 'detector saturation index'), as the fourth model parameter. With increasing LET of the ion, the two-component formulation of TST allows for successive transition from shouldered survival curves at low LET values to exponential ones at radiobiological effectiveness (RBE) maximum, followed by 'thin-down' at the end of the ion track. For a given cell line, having best-fitted the four model parameters (m, D0, σ0 and k) to an available data set of measured survival curves, TST is able to quantitatively predict cell survival and RBE for
International Nuclear Information System (INIS)
By using real space renormalization group methods, bond percolation on d-dimensional hypercubic (d = 2, 3, 4), first - and second - neighbour isotropic square, anisotropic square and 'inhomogeneous' 4-8 lattices is studied. Through some extrapolation methods, critical points and/or frontiers are obtained (as well as the critical exponent ν sub(p) in the isotropic cases) for these lattices that, or agree well with other available results, or are new as far as it is know (first - and second - neighbour isotropic square and 'inhomogeneous' 4-8 lattices). A conjecture concerning approximate (eventually exact) critical points and, in certain situations, critical frontiers of q-state Potts ferromagnets on d-dimensional lattices (d > 1) is formulated. This conjecture is verified within good accuracy for all the lattices whose critical points are known, and it allows the prediction of a great number of new results, some of them it is believed to be exact. Within a real space renomalization group framework, accurate approximations for the critical frontiers associated with the quenched bond-diluted first-neighbour spin-1/2 Ising ferromagnet on triangular and honeycomb lattices are calculated. The best numerical proposals lead, in both pure bond percolation (p = p sub(c)) and pure Ising (p = 1) limits, to the exact critical points and (dt0/dp) sub(p = p sub(c)) (where t0 identical to tanh J/K sub(B) T), and to a 0.15% (0.96%) error in (dt0/dp) sub(p = 1) for the triangular (honeycomb) lattice; for p sub(c) 0 (for fixed p) of 0.27% (0.14%) is estimated for the triangular (honeycomb) lattice. It is exhibited, for many star-triangle graph pairs with any number of terminals and different sizes, that the exact q = 1, 2, 3, 4 critical points of Potts ferromagnets can aZZ of them, be obtained from any one of such graph pairs. (Author)
Hui Guo; Dongmei Liu; Bin Gao; Xiaohui Zhang; Minli You; Hui Ren; Hongbo Zhang; Santos, Hélder A.; Feng Xu
2016-01-01
Evodiamine (EVO) and rutaecarpine (RUT) are promising anti-tumor drug candidates. The evaluation of the anti-proliferative activity and cellular uptake of EVO and RUT in 3D multicellular spheroids of cancer cells would better recapitulate the native situation and thus better reflect an in vivo response to the treatment. Herein, we employed the 3D culture of MCF-7 and SMMC-7721 cells based on hanging drop method and evaluated the anti-proliferative activity and cellular uptake of EVO and RUT i...
DEFF Research Database (Denmark)
Mahshid, Rasoul; Hansen, Hans Nørgaard; Loft Højbjerre, Klaus
2016-01-01
Additive manufacturing is rapidly developing and gaining popularity for direct metal fabrication systems like selective laser melting (SLM). The technology has shown significant improvement for high-quality fabrication of lightweight design-efficient structures such as conformal cooling channels in...... injection molding tools and lattice structures. This research examines the effect of cellular lattice structures on the strength of workpieces additively manufactured from ultra high-strength steel powder. Two commercial SLM machines are used to fabricate cellular samples based on four architectures— solid...
Cheng, Y.; Kekenes-Huskey, P.; Hake, J. E.; Holst, M. J.; McCammon, J. A.; Michailova, A. P.
2012-01-01
This paper presents a brief review of multi-scale modeling at the molecular to cellular scale, with new results for heart muscle cells. A finite element-based simulation package (SMOL) was used to investigate the signaling transduction at molecular and sub-cellular scales (http://mccammon.ucsd.edu/smol/, http://FETK.org) by numerical solution of the time-dependent Smoluchowski equations and a reaction-diffusion system. At the molecular scale, SMOL has yielded experimentally validated estimates of the diffusion-limited association rates for the binding of acetylcholine to mouse acetylcholinesterase using crystallographic structural data. The predicted rate constants exhibit increasingly delayed steady-state times, with increasing ionic strength, and demonstrate the role of an enzyme's electrostatic potential in influencing ligand binding. At the sub-cellular scale, an extension of SMOL solves a nonlinear, reaction-diffusion system describing Ca2+ ligand buffering and diffusion in experimentally derived rodent ventricular myocyte geometries. Results reveal the important role of mobile and stationary Ca2+ buffers, including Ca2+ indicator dye. We found that alterations in Ca2+-binding and dissociation rates of troponin C (TnC) and total TnC concentration modulate sub-cellular Ca2+ signals. The model predicts that reduced off-rate in the whole troponin complex (TnC, TnI, TnT) versus reconstructed thin filaments (Tn, Tm, actin) alters cytosolic Ca2+ dynamics under control conditions or in disease-linked TnC mutations. The ultimate goal of these studies is to develop scalable methods and theories for the integration of molecular-scale information into simulations of cellular-scale systems.
International Nuclear Information System (INIS)
This paper presents a brief review of multi-scale modeling at the molecular to cellular scale, with new results for heart muscle cells. A finite element-based simulation package (SMOL) was used to investigate the signaling transduction at molecular and sub-cellular scales (http://mccammon.ucsd.edu/smol/, http://FETK.org) by numerical solution of the time-dependent Smoluchowski equations and a reaction-diffusion system. At the molecular scale, SMOL has yielded experimentally validated estimates of the diffusion-limited association rates for the binding of acetylcholine to mouse acetylcholinesterase using crystallographic structural data. The predicted rate constants exhibit increasingly delayed steady-state times, with increasing ionic strength, and demonstrate the role of an enzyme's electrostatic potential in influencing ligand binding. At the sub-cellular scale, an extension of SMOL solves a nonlinear, reaction-diffusion system describing Ca2+ ligand buffering and diffusion in experimentally derived rodent ventricular myocyte geometries. Results reveal the important role of mobile and stationary Ca2+ buffers, including Ca2+ indicator dye. We found that alterations in Ca2+-binding and dissociation rates of troponin C (TnC) and total TnC concentration modulate sub-cellular Ca2+ signals. The model predicts that reduced off-rate in the whole troponin complex (TnC, TnI, TnT) versus reconstructed thin filaments (Tn, Tm, actin) alters cytosolic Ca2+ dynamics under control conditions or in disease-linked TnC mutations. The ultimate goal of these studies is to develop scalable methods and theories for the integration of molecular-scale information into simulations of cellular-scale systems.
Chen, Ting-Jung; Wu, Chia-Ching; Su, Fong-Chin
2012-12-01
The cytoskeleton, which is the major mechanical component of cells, supports the cell body and regulates the cellular motility to assist the cell in performing its biological functions. Several cytoskeletal network models have been proposed to investigate the mechanical properties of cells. This review paper summarizes these models with a focus on the prestressed cable network, the semi-flexible chain network, the open-cell foam, the tensegrity, and the granular models. The components, material parameters, types of connection joints, tension conditions, and the advantages and disadvantages of each model are evaluated from a structural and biological point of view. The underlying mechanisms that are associated with the morphological changes of spreading cells are expected to be simulated using a cytoskeletal model; however, it is still paid less attention most likely due to the lack of a suitable cytoskeletal model that can accurately model the spreading process. In this review article, the established cytoskeletal models are hoped to provide useful information for the development of future cytoskeletal models with different degrees of cell attachment for the study of the mechanical mechanisms underlying the cellular behaviors in response to external stimulations. PMID:23062682
Directory of Open Access Journals (Sweden)
H. Wang
2010-03-01
Full Text Available Microphysical and meteorological controls on the formation of open and closed cellular structures in the Southeast Pacific are explored using model simulations based on aircraft observations during the VAMOS Ocean-Cloud-Atmosphere-Land Study Regional Experiment (VOCALS-REx. The effectiveness of factors such as boundary-layer moisture and temperature perturbations, surface heat and moisture fluxes, large-scale vertical motion and solar heating in promoting drizzle and open cell formation for prescribed aerosol number concentrations is explored. For the case considered, drizzle and subsequent open cell formation over a broad region are more sensitive to the observed boundary-layer moisture and temperature perturbations (=0.9 g kg^{−1}; −1 K than to a five-fold decrease in aerosol number concentrations (150 vs. 30 mg^{−1}. When embedding the perturbations in closed cells, local drizzle and pockets of open cells (POCs formation respond faster to the aerosol reduction than to the moisture increase, but the latter generate stronger and more persistent drizzle. The local negative perturbation in temperature drives a mesoscale circulation that prevents local drizzle formation but promotes it in a remote area where lower-level horizontal transport of moisture is blocked and converges to enhance liquid water path. This represents a potential mechanism for POC formation in the Southeast Pacific stratocumulus region whereby the circulation is triggered by strong precipitation in adjacent broad regions of open cells. A simulation that attempts to mimic the influence of a coastally induced upsidence wave results in an increase in cloud water but this alone is insufficient to initiate drizzle. An increase of surface sensible heat flux is also effective in triggering local drizzle and POC formation. Both open and closed cells simulated with observed initial conditions exhibit distinct diurnal variations in cloud properties. A stratocumulus
Alber, M; Glimm, T; Lushnikov, P M; Alber, Mark; Chen, Nan; Glimm, Tilmann; Lushnikov, Pavel M.
2006-01-01
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. In this paper, we derive continuous limit of 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.
[Anterior approach of cervical spine in Pott's disease. Apropos of 7 cases].
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
A case of endometrial tuberculosis complicated by Pott's spine with paraplegia
Directory of Open Access Journals (Sweden)
N. A. Wafai
2014-06-01
Full Text Available Extra-pulmonary tuberculosis has shown an increasing trend in developing countries and accounts for 15-20% of total tuberculosis cases in India. Extra-pulmonary cases are usually diagnosed late due to vague and subtle signs and symptoms at a stage when major irreversible tissue damage had occurred. Tuberculosis is a chronic disease with infection remaining dormant for years in body to get activated whenever the immunity decreases. Spinal and cranial TB has the gravest manifestations, while the abdominal, female genital or pelvic TB poses a challenge because of lack of specific diagnostic tests. Here we are reporting a case of endometrial tuberculosis which was diagnosed very late, followed by treatment default and finally got complicated with Pott's spine with paraplegia due to haematogenous spread. Timely intervention and anti-tubercular treatment improved the symptoms. It stresses on keeping the high suspicion of tuberculosis in unresponsive and persistent general symptoms. [Int J Res Med Sci 2014; 2(3.000: 1157-1160
Medical-surgical treatment of progressive tuberculous (Pott's) paraplegia in Gabon.
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
Calì, Corrado; Baghabra, Jumana; Boges, Daniya J; Holst, Glendon R; Kreshuk, Anna; Hamprecht, Fred A; Srinivasan, Madhusudhanan; Lehväslaiho, Heikki; Magistretti, Pierre J
2016-01-01
Advances in the application of electron microscopy (EM) to serial imaging are opening doors to new ways of analyzing cellular structure. New and improved algorithms and workflows for manual and semiautomated segmentation allow us to observe the spatial arrangement of the smallest cellular features with unprecedented detail in full three-dimensions. From larger samples, higher complexity models can be generated; however, they pose new challenges to data management and analysis. Here we review some currently available solutions and present our approach in detail. We use the fully immersive virtual reality (VR) environment CAVE (cave automatic virtual environment), a room in which we are able to project a cellular reconstruction and visualize in 3D, to step into a world created with Blender, a free, fully customizable 3D modeling software with NeuroMorph plug-ins for visualization and analysis of EM preparations of brain tissue. Our workflow allows for full and fast reconstructions of volumes of brain neuropil using ilastik, a software tool for semiautomated segmentation of EM stacks. With this visualization environment, we can walk into the model containing neuronal and astrocytic processes to study the spatial distribution of glycogen granules, a major energy source that is selectively stored in astrocytes. The use of CAVE was key to the observation of a nonrandom distribution of glycogen, and led us to develop tools to quantitatively analyze glycogen clustering and proximity to other subcellular features. PMID:26179415
Keane, Harriet; Ryan, Brent J.; Jackson, Brendan; Whitmore, Alan; Wade-Martins, Richard
2015-11-01
Neurodegenerative diseases are complex multifactorial disorders characterised by the interplay of many dysregulated physiological processes. As an exemplar, Parkinson’s disease (PD) involves multiple perturbed cellular functions, including mitochondrial dysfunction and autophagic dysregulation in preferentially-sensitive dopamine neurons, a selective pathophysiology recapitulated in vitro using the neurotoxin MPP+. Here we explore a network science approach for the selection of therapeutic protein targets in the cellular MPP+ model. We hypothesised that analysis of protein-protein interaction networks modelling MPP+ toxicity could identify proteins critical for mediating MPP+ toxicity. Analysis of protein-protein interaction networks constructed to model the interplay of mitochondrial dysfunction and autophagic dysregulation (key aspects of MPP+ toxicity) enabled us to identify four proteins predicted to be key for MPP+ toxicity (P62, GABARAP, GBRL1 and GBRL2). Combined, but not individual, knockdown of these proteins increased cellular susceptibility to MPP+ toxicity. Conversely, combined, but not individual, over-expression of the network targets provided rescue of MPP+ toxicity associated with the formation of autophagosome-like structures. We also found that modulation of two distinct proteins in the protein-protein interaction network was necessary and sufficient to mitigate neurotoxicity. Together, these findings validate our network science approach to multi-target identification in complex neurological diseases.
Cali, Corrado
2015-07-14
Advances for application of electron microscopy to serial imaging are opening doors to new ways of analyzing cellular structure. New and improved algorithms and workflows for manual and semiautomated segmentation allow to observe the spatial arrangement of the smallest cellular features with unprecedented detail in full three-dimensions (3D). From larger samples, higher complexity models can be generated; however, they pose new challenges to data management and analysis. Here, we review some currently available solutions and present our approach in detail. We use the fully immersive virtual reality (VR) environment CAVE (cave automatic virtual environment), a room where we are able to project a cellular reconstruction and visualize in 3D, to step into a world created with Blender, a free, fully customizable 3D modeling software with NeuroMorph plug-ins for visualization and analysis of electron microscopy (EM) preparations of brain tissue. Our workflow allows for full and fast reconstructions of volumes of brain neuropil using ilastik, a software tool for semiautomated segmentation of EM stacks. With this visualization environment, we can walk into the model containing neuronal and astrocytic processes to study the spatial distribution of glycogen granules, a major energy source that is selectively stored in astrocytes. The use of CAVE was key to observe a nonrandom distribution of glycogen, and led us to develop tools to quantitatively analyze glycogen clustering and proximity to other subcellular features. This article is protected by copyright. All rights reserved.
Behera, Mukunda D.; Borate, Santosh N.; Panda, Sudhindra N.; Behera, Priti R.; Roy, Partha S.
2012-08-01
Improper practices of land use and land cover (LULC) including deforestation, expansion of agriculture and infrastructure development are deteriorating watershed conditions. Here, we have utilized remote sensing and GIS tools to study LULC dynamics using Cellular Automata (CA)-Markov model and predicted the future LULC scenario, in terms of magnitude and direction, based on past trend in a hydrological unit, Choudwar watershed, India. By analyzing the LULC pattern during 1972, 1990, 1999 and 2005 using satellite-derived maps, we observed that the biophysical and socio-economic drivers including residential/industrial development, road-rail and settlement proximity have influenced the spatial pattern of the watershed LULC, leading to an accretive linear growth of agricultural and settlement areas. The annual rate of increase from 1972 to 2004 in agriculture land, settlement was observed to be 181.96, 9.89 ha/year, respectively, while decrease in forest, wetland and marshy land were 91.22, 27.56 and 39.52 ha/year, respectively. Transition probability and transition area matrix derived using inputs of (i) residential/industrial development and (ii) proximity to transportation network as the major causes. The predicted LULC scenario for the year 2014, with reasonably good accuracy would provide useful inputs to the LULC planners for effective management of the watershed. The study is a maiden attempt that revealed agricultural expansion is the main driving force for loss of forest, wetland and marshy land in the Choudwar watershed and has the potential to continue in future. The forest in lower slopes has been converted to agricultural land and may soon take a call on forests occurring on higher slopes. Our study utilizes three time period changes to better account for the trend and the modelling exercise; thereby advocates for better agricultural practices with additional energy subsidy to arrest further forest loss and LULC alternations.
Tractable Model for Rate in Self-Backhauled Millimeter Wave Cellular Networks
Singh, Sarabjot; Kulkarni, Mandar N.; Ghosh, Amitava; Andrews, Jeffrey G.
2014-01-01
Millimeter wave (mmW) cellular systems will require high gain directional antennas and dense base station (BS) deployments to overcome high near field path loss and poor diffraction. As a desirable side effect, high gain antennas provide interference isolation, providing an opportunity to incorporate self-backhauling--BSs backhauling among themselves in a mesh architecture without significant loss in throughput--to enable the requisite large BS densities. The use of directional antennas and r...
Multi-Scale Modeling of Respiration: Linking External to Cellular Respiration during Exercise
Zhou, Haiying; Lai, Nicola; Saidel, Gerald M.; Cabrera, Marco E.
2009-01-01
In human studies investigating factors that control cellular respiration in working skeletal muscle, pulmonary VO2 dynamics (VO2p) measured at the mouth by indirect calorimetry is typically used to represent muscle O2 consumption (UO2m). Furthermore, measurement of muscle oxygenation using near-infrared spectroscopy has provided information on the dynamic balance between oxygen delivery and oxygen consumption at the microvascular level. To relate these measurements and gain quantitative under...
Phase transition in the economically modeled growth of a cellular nervous system
Nicosia V.; Vertes P.E.; Schafer W.R.; Latora V.; Bullmore E.T.
2013-01-01
Spatially embedded complex networks, such as nervous systems, the Internet, and transportation networks, generally have nontrivial topological patterns of connections combined with nearly minimal wiring costs. However, the growth rules shaping these economical tradeoffs between cost and topology are not well understood. Here, we study the cellular nervous system of the nematode worm Caenorhabditis elegans, together with information on the birth times of neurons and on their spatial locations....
Tectonic modeling of Konya-Beysehir Region (Turkey) using cellular neural networks
D. Aydogan; O. Nuri Uçan; A. Muhittin ALBORA
2007-01-01
In this paper, to separate regional-residual anomaly maps and to detect borders of buried geological bodies, we applied the Cellular Neural Network (CNN) approach to gravity and magnetic anomaly maps. CNN is a stochastic image processing technique, based optimization of templates, which imply relationships of neighborhood pixels in 2-Dimensional (2D) potential anomalies. Here, CNN performance in geophysics, tested by various synthetic examples and the results are compared ...
An integrated cellular model to evaluate cytotoxic effects in mammalian cell lines.
Fernández Freire, P; Peropadre, A; Pérez Martín, J M; Herrero, O; Hazen, M J
2009-12-01
The ever growing anthropogenic pressure to the environment has lead in 2007 to the revision of the existing legislation and the approval of the new European law regarding the production and importation of chemicals, known as REACH. This new legal framework supports the development of alternative methods to animal experimentation encouraging the improvement and/or design of new methodological strategies for the toxicological evaluation of chemical compounds. Even though cytotoxicity studies are a reductionist approach to acute toxicity in vivo, they offer the best agreement between obtaining relevant information about the mechanism of toxic action and the use of alternative methods. Following this trend, this work presents an integrated cellular strategy in order to know the toxicity and mechanism of action of chemical compounds, using simple and reproducible in vitro systems. The experimental procedures are performed in two steps. The first one involves the systematic analysis of the main cellular targets using proliferation, viability and morphological probes. The second step relies upon the results obtained in the first step, including specific assays that focus on the mechanism of toxic action and the cellular response. The benefits of this strategy are exemplified with two real cases: pentachlorophenol and rotenone. PMID:19540333
Codd, E F
1968-01-01
Cellular Automata presents the fundamental principles of homogeneous cellular systems. This book discusses the possibility of biochemical computers with self-reproducing capability.Organized into eight chapters, this book begins with an overview of some theorems dealing with conditions under which universal computation and construction can be exhibited in cellular spaces. This text then presents a design for a machine embedded in a cellular space or a machine that can compute all computable functions and construct a replica of itself in any accessible and sufficiently large region of t
Maerivoet, S; Immers, B; De Moor, B; Maerivoet, Sven; Logghe, Steven; Immers, Ben; Moor, Bart De
2005-01-01
In this paper, we describe a relation between a microscopic traffic cellular automaton (TCA) model (i.e., the stochastic TCA model of Nagel and Schreckenberg) and the macroscopic first-order hydrodynamic model of Lighthill, Whitham, and Richards (LWR). The innovative aspect of our approach, is that we explicitly derive the LWR's fundamental diagram directly from the STCA's rule set, by assuming a stationarity condition that converts the STCA's rules into a set of linear inequalities. In turn, these constraints define the shape of the fundamental diagram, which is then specified to the LWR model. Application of our methodology to a simulation case study, allows us to compare the tempo-spatial behavior of both models. Our results indicate that, in the presence of noise, the capacity flows in the derived fundamental diagram are overestimations of those of the STCA model. Directly specifying the STCA's capacity flows to the LWR fundamental diagram, effectively remedies most of the mismatches between both approach...
International Nuclear Information System (INIS)
We study certain types of Cellular Automata (CA) viewed as an abstraction of large-scale Multi-Agent Systems (MAS). We argue that the classical CA model needs to be modified in several important respects, in order to become a relevant and sufficiently general model for the large-scale MAS, and so that thus generalized model can capture many important MAS properties at the level of agent ensembles and their long-term collective behavior patterns. We specifically focus on the issue of inter-agent communication in CA, and propose sequential cellular automata (SCA) as the first step, and genuinely Asynchronous Cellular Automata (ACA) as the ultimate deterministic CA-based abstract models for large-scale MAS made of simple reactive agents. We first formulate deterministic and nondeterministic versions of sequential CA, and then summarize some interesting configuration space properties (i.e., possible behaviors) of a restricted class of sequential CA. In particular, we compare and contrast those properties of sequential CA with the corresponding properties of the classical (that is, parallel and perfectly synchronous) CA with the same restricted class of update rules. We analytically demonstrate failure of the studied sequential CA models to simulate all possible behaviors of perfectly synchronous parallel CA, even for a very restricted class of non-linear totalistic node update rules. The lesson learned is that the interleaving semantics of concurrency, when applied to sequential CA, is not refined enough to adequately capture the perfect synchrony of parallel CA updates. Last but not least, we outline what would be an appropriate CA-like abstraction for large-scale distributed computing insofar as the inter-agent communication model is concerned, and in that context we propose genuinely asynchronous CA. (author)
Directory of Open Access Journals (Sweden)
Alpaugh Mary L
2009-12-01
Full Text Available Abstract Background The initial step of metastasis in carcinomas, often referred to as the epithelial-mesenchymal transition (EMT, occurs via the loss of adherens junctions (e.g. cadherins by the tumor embolus. This leads to a subsequent loss of cell polarity and cellular differentiation and organization, enabling cells of the embolus to become motile and invasive. However highly malignant inflammatory breast cancer (IBC over-expresses E-cadherin. The human xenograft model of IBC (MARY-X, like IBC, displays the signature phenotype of an exaggerated degree of lymphovascular invasion (LVI in situ by tumor emboli. An intact E-cadherin/α, β-catenin axis mediates the tight, compact clump of cells found both in vitro and in vivo as spheroids and tumor emboli, respectively. Methods Using electron microscopy and focused ion beam milling to acquire in situ sections, we performed ultrastructural analysis of both an IBC and non-IBC, E-cadherin positive cell line to determine if retention of this adhesion molecule contributed to cellular organization. Results Here we report through ultrastructural analysis that IBC exhibits a high degree of cellular organization with polar elements such as apical/lateral positioning of E-cadherin, apical surface microvilli, and tortuous lumen-like (canalis structures. In contrast, agarose-induced spheroids of MCF-7, a weakly invasive E-cadherin positive breast carcinoma cell line, do not exhibit ultrastructural polar features. Conclusions This study has determined that the highly metastatic IBC with an exaggerated malignant phenotype challenges conventional wisdom in that instead of displaying a loss of cellular organization, IBC acquires a highly structured architecture. These findings suggest that the metastatic efficiency might be linked to the formation and maintenance of these architectural features. The comparative architectural features of both the spheroid and embolus of MARY-X provide an in vitro model with
Im, A-Rang; Kim, Yun Hee; Lee, Hye Won; Song, Kwang Hoon
2016-05-01
Nonalcoholic fatty liver disease (NAFLD) is a common chronic liver disease that is rising in prevalence worldwide. Therapeutic strategies for patients with NAFLD are limited by a lack of effective drugs. In this report, we show that Dolichos lablab water extract (DLL-Ex) protects against free fatty acid (FFA)-induced lipid accumulation and attenuates expression of genes involved in lipid droplet accumulation in cellular NAFLD models. The hepatoprotective effects and underlying mechanism of DLL-Ex were assessed using an in vitro cellular model in which NAFLD was simulated by inducing excessive FFA influx into hepatocytes. HepG2 cells were treated with DLL-Ex and FFAs for 24 h, after which intracellular lipid content was observed by using Nile Red and Oil Red O staining. Quantitative real-time polymerase chain reaction was used to measure expression levels of genes related to FFA-mediated cellular energy depletion. Western blotting was used to measure protein levels of phosphorylated c-Jun N-terminal kinase, AMP-activated protein kinase alpha (AMPKα), and peroxisome proliferator-activated receptor γ coactivator 1 alpha. In HepG2 cells, DLL-Ex inhibited expression of CD36, which regulates fatty acid uptake, as well as BODIPY-labeled fatty acid uptake. Additionally, DLL-Ex significantly attenuated FFA-mediated cellular energy depletion and mitochondrial membrane depolarization. Furthermore, DLL-Ex enhanced phosphorylation of AMPK, indicating that AMPK is a critical regulator of DLL-Ex-mediated inhibition of hepatic lipid accumulation, possibly through its antioxidative effect. These results demonstrate that DLL-Ex exerts potent anti-NAFLD activity, suggesting that it could be a potential adjuvant treatment for patients with NAFLD. PMID:27152979
International Nuclear Information System (INIS)
The initial step of metastasis in carcinomas, often referred to as the epithelial-mesenchymal transition (EMT), occurs via the loss of adherens junctions (e.g. cadherins) by the tumor embolus. This leads to a subsequent loss of cell polarity and cellular differentiation and organization, enabling cells of the embolus to become motile and invasive. However highly malignant inflammatory breast cancer (IBC) over-expresses E-cadherin. The human xenograft model of IBC (MARY-X), like IBC, displays the signature phenotype of an exaggerated degree of lymphovascular invasion (LVI) in situ by tumor emboli. An intact E-cadherin/α, β-catenin axis mediates the tight, compact clump of cells found both in vitro and in vivo as spheroids and tumor emboli, respectively. Using electron microscopy and focused ion beam milling to acquire in situ sections, we performed ultrastructural analysis of both an IBC and non-IBC, E-cadherin positive cell line to determine if retention of this adhesion molecule contributed to cellular organization. Here we report through ultrastructural analysis that IBC exhibits a high degree of cellular organization with polar elements such as apical/lateral positioning of E-cadherin, apical surface microvilli, and tortuous lumen-like (canalis) structures. In contrast, agarose-induced spheroids of MCF-7, a weakly invasive E-cadherin positive breast carcinoma cell line, do not exhibit ultrastructural polar features. This study has determined that the highly metastatic IBC with an exaggerated malignant phenotype challenges conventional wisdom in that instead of displaying a loss of cellular organization, IBC acquires a highly structured architecture. These findings suggest that the metastatic efficiency might be linked to the formation and maintenance of these architectural features. The comparative architectural features of both the spheroid and embolus of MARY-X provide an in vitro model with tractable in vivo applications
Vanwalleghem, T.; Jiménez-Hornero, F. J.; Giráldez, J. V.; Laguna, A.
2009-04-01
The process of tillage translocation is well studied and can be described adequately by different existing models. Nevertheless, in complex environments such as olive orchards, characterized by numerous obstacles, application of such conventional tillage erosion models is not straightforward. However, these obstacles have important effects on the spatial pattern of soil redistribution and on resulting soil properties. In this kind of environment, cellular automata could provide a valuable alternative. This study aims at developing a cellular automata model for tillage translocation (CATT) that can take into account such obstacles and at exploring its possibilities and limitations. A simple model was developed, which main parameters are tillage direction, speed and depth. Firstly, the modeĺs outcome was tested against existing 137Cs inventories for a study site in the Belgian loam belt. The observed spatial soil redistribution patterns could be adequately represented by the CATT model. Secondly, a sensitivity analysis was performed to explore the effect of input uncertainty on several selected model outputs. The variance-based extended FAST method was used to determine first and total order sensitivity indices. Tillage depth was identified as the input parameter that determined most of the output variance, followed respectively by tillage direction and speed. The difference between the total and first-order sensitivity indices, between 0.8 and 2, indicated that, in spite of the simple model structure, the model behaves non-linearly with respect to some of the model output variables. Higher-order interactions were especially important for determining the proportion of eroding and deposition cells. Finally, simulations were performed to analyse the model behaviour in complex landscapes, applying it to a field with protruding obstacles (e.g. olive trees). The model adequately represented some morphological features observed in the olive orchards, such as mounds around
Phase-Type Models of Channel-Holding Times in Cellular Communication Systems
DEFF Research Database (Denmark)
Christensen, Thomas Kaare; Nielsen, Bo Friis; Iversen, Villy Bæk
2004-01-01
In this paper, we derive the distribution of the channel-holding time when both cell-residence and call-holding times are phase-type distributed. Furthermore, the distribution of the number of handovers, the conditional channel-holding time distributions, and the channel-holding time when cell re...... residence times are correlated are derived. All distributions are of phase type, making them very general and flexible. The channel-holding times are of importance in performance evaluation and simulation of cellular mobile communication systems....
Energy Technology Data Exchange (ETDEWEB)
Werner, Hofmann; Hatim, Fakir [Salzburg Univ., Div. of Physics and Biophysics, Dept. of Material Science (Austria); Lucia-Adina, Truta-Popa [Babes-Bolyai Univ., Faculty of Physics (Romania)
2006-07-01
To explore the role of the multiplicity of cellular hits by radon progeny alpha particles for lung cancer incidence, the number of single and multiple alpha particle hits were computed for basal and secretory cells in the bronchial epithelium of human airway bifurcations employing Monte Carlo methods. Hot spots of alpha particle hits were observed at the branching points of bronchial airway bifurcations, suggesting that multiple alpha particle hits may occur primarily at carinal ridges. Random alpha particle intersections of bronchial cells during a given exposure period, selected from a Poisson distribution, were simulated by an initiation-promotion model, based on experimentally observed cellular transformation and survival functions. To consider potential bystander effects, which have been observed in cellular in vitro studies, alpha particle interactions were also simulated for larger sensitive target volumes in bronchial epithelium, consisting of a collection of cells. Lung cancer risk simulations indicated that cancer induction for continuous exposures is related to the cycle time of an irradiated cell, thus exhibiting a distinct dose-rate effect. While the dominant role of single hits leads to a linear dose-response relationship at low radon exposure levels, predicted lung cancer risk for a collection of interacting cells exhibits a linear-quadratic response, suggesting that bystander effects, if operating at all under in vivo irradiations, may be restricted to a small number of adjacent cells. (author)
International Nuclear Information System (INIS)
To explore the role of the multiplicity of cellular hits by radon progeny alpha particles for lung cancer incidence, the number of single and multiple alpha particle hits were computed for basal and secretory cells in the bronchial epithelium of human airway bifurcations employing Monte Carlo methods. Hot spots of alpha particle hits were observed at the branching points of bronchial airway bifurcations, suggesting that multiple alpha particle hits may occur primarily at carinal ridges. Random alpha particle intersections of bronchial cells during a given exposure period, selected from a Poisson distribution, were simulated by an initiation-promotion model, based on experimentally observed cellular transformation and survival functions. To consider potential bystander effects, which have been observed in cellular in vitro studies, alpha particle interactions were also simulated for larger sensitive target volumes in bronchial epithelium, consisting of a collection of cells. Lung cancer risk simulations indicated that cancer induction for continuous exposures is related to the cycle time of an irradiated cell, thus exhibiting a distinct dose-rate effect. While the dominant role of single hits leads to a linear dose-response relationship at low radon exposure levels, predicted lung cancer risk for a collection of interacting cells exhibits a linear-quadratic response, suggesting that bystander effects, if operating at all under in vivo irradiations, may be restricted to a small number of adjacent cells. (author)
Mobile Robot Motion Using Cellular Automaton Model to Avoid Transient Obstacles
Directory of Open Access Journals (Sweden)
Kohei Arai
2013-10-01
Full Text Available The obstacle avoidance is currently treated by methods that fall into two broad categories: global and local approach. This paper considers the obstacles whose velocity and direction cannot be easily predicted. Such obstacle is called transient obstacle. To avoid such kind of obstacle, we introduce a local path planning method for a robotics by using cellular automaton approach. The cellular automaton was combined with Dijkstra shortest path algorithm as global path planning to obtain a path for mobile robot to be able to avoid transient obstacle along the path. Using the proposed method, a scene in a typical corridor has been created. Moreover, this paper also evaluated two kinds of obstacle avoidance motion. First, the robot uses the “stop and go” method, which is the robot decreases its speed while encounter a transient obstacle. The second one is detour method, in which the robot makes a detour motion to avoid a transient obstacle. To coupe the drawbacks of local path planning, this paper also propose the enhancement of detour method. The simulation results show that in dynamic environment with transient obstacles, the “stop and go” method produces minimal collision with shortest-distance path. While, using the detour method generates minimal collision with time-minimal navigation path.
Directory of Open Access Journals (Sweden)
L. Liu
2014-09-01
Full Text Available Flash floods have occurred frequently and severely in the urban areas of South China. An effective process-oriented urban flood inundation model becomes an urgent demand for urban storm water and emergency management. This study develops an effective and flexible cellular automaton (CA model to simulate storm water runoff and the flood inundation process during extreme storm events. The process of infiltration, inlets discharge and flow dynamic can be simulated only with little pre-processing on commonly available basic urban geographic data. In this model, a set of gravitational diverging rules are implemented in a cellular automation (CA model to govern the water flow in a 3 x 3 cell template of a raster layer. The model is calibrated by one storm event and validated by another in a small urban catchment in Guangzhou of Southern China. The depth of accumulated water at the catchment outlet is interpreted from street monitoring sensors and verified by on-site survey. A good level of agreement between the simulated process and the reality is reached for both storm events. The model reproduces the changing extent and depth of flooded areas at the catchment outlet with an accuracy of 4 cm in water depth. Comparisons with a physically-based 2-D model (FloodMap results show that the model have the capability of simulating flow dynamics. The high computational efficiency of CA model can satisfy the demand of city emergency management. The encouraging results of the simulations demonstrate that the CA-based approach is capable of effectively representing the key processes associated with a storm event and reproducing the process of water accumulation at the catchment outlet for making process-considered city emergency management decisions.
Energy Technology Data Exchange (ETDEWEB)
Meireles, Sincler P. de; Santos, Adriano M.; Grynberg, Suely Epsztein, E-mail: spm@cdtn.b, E-mail: amsantos@cdtn.b, E-mail: seg@cdtn.b [Centro de Desenvolvimento da Tecnologia Nuclear (CDTN/CNEN-MG), Belo Horizonte, MG (Brazil); Nunes, Maria Eugenia S., E-mail: mariaeugenia@iceb.ufop.b [Universidade Federal de Ouro Preto (UFOP), MG (Brazil)
2011-07-01
During recent years, there has been a shift from an approach focused entirely on DNA as the main target of ionizing radiation to a vision that considers complex signaling pathways in cells and among cells within tissues. Several newly recognized responses were classified as the so-called non-target responses in which the biological effects are not directly related to the amount of energy deposited in the DNA of cells that were traversed by radiation. In 1992 the bystander effect was described referring to a series of responses such as death, chromosomal instability or other abnormalities that occur in non-irradiated cells that came into contact with irradiated cells or medium from irradiated cells. In this work, we have developed a mathematical model via cellular automata, to quantify cell death induced by the bystander effect. The model is based on experiments with irradiated cells conditioned medium which suggests that irradiated cells secrete molecules in the medium that are capable of damaging other cells. The computational model consists of two-dimensional cellular automata which is able to simulate the transmission of bystander signals via extrinsic route and via Gap junctions. The model has been validated by experimental results in the literature. The time evolution of the effect and the dose-response curves were obtained in good accordance to them. Simulations were conducted for different values of bystander and irradiated cell densities with constant dose. From this work, we have obtained a relationship between cell density and effect. (author)
International Nuclear Information System (INIS)
During recent years, there has been a shift from an approach focused entirely on DNA as the main target of ionizing radiation to a vision that considers complex signaling pathways in cells and among cells within tissues. Several newly recognized responses were classified as the so-called non-target responses in which the biological effects are not directly related to the amount of energy deposited in the DNA of cells that were traversed by radiation. In 1992 the bystander effect was described referring to a series of responses such as death, chromosomal instability or other abnormalities that occur in non-irradiated cells that came into contact with irradiated cells or medium from irradiated cells. In this work, we have developed a mathematical model via cellular automata, to quantify cell death induced by the bystander effect. The model is based on experiments with irradiated cells conditioned medium which suggests that irradiated cells secrete molecules in the medium that are capable of damaging other cells. The computational model consists of two-dimensional cellular automata which is able to simulate the transmission of bystander signals via extrinsic route and via Gap junctions. The model has been validated by experimental results in the literature. The time evolution of the effect and the dose-response curves were obtained in good accordance to them. Simulations were conducted for different values of bystander and irradiated cell densities with constant dose. From this work, we have obtained a relationship between cell density and effect. (author)
Energy Technology Data Exchange (ETDEWEB)
Kemper, A. [Institut fuer Theoretische Physik, Universitaet zu Koeln, Cologne (Germany). E-mail: kemper@thp.uni-koeln.de; Schadschneider, A. [Institut fuer Theoretische Physik, Universitaet zu Koeln, Cologne (Germany). E-mail: as@thp.uni-koeln.de; Zittartz, J. [Institut fuer Theoretische Physik, Universitaet zu Koeln, Cologne (Germany)
2001-05-18
We apply the transfer-matrix density-matrix renormalization group (TMRG) to a stochastic model, the Domany-Kinzel cellular automaton, which exhibits a non-equilibrium phase transition in the directed percolation universality class. Estimates for the stochastic time evolution, phase boundaries and critical exponents can be obtained with high precision. This is possible using only modest numerical effort since the thermodynamic limit can be taken analytically in our approach. We also point out further advantages of the TMRG over other numerical approaches, such as classical DMRG or Monte Carlo simulations. (author). Letter-to-the-editor.
International Nuclear Information System (INIS)
We apply the transfer-matrix density-matrix renormalization group (TMRG) to a stochastic model, the Domany-Kinzel cellular automaton, which exhibits a non-equilibrium phase transition in the directed percolation universality class. Estimates for the stochastic time evolution, phase boundaries and critical exponents can be obtained with high precision. This is possible using only modest numerical effort since the thermodynamic limit can be taken analytically in our approach. We also point out further advantages of the TMRG over other numerical approaches, such as classical DMRG or Monte Carlo simulations. (author). Letter-to-the-editor
DEFF Research Database (Denmark)
Qing, Hai; Mishnaevsky, Leon
2009-01-01
A 3D hierarchical computational model of deformation and stiffness of wood, which takes into account the structures of wood at several scale levels (cellularity, multilayered nature of cell walls, composite-like structures of the wall layers) is developed. At the mesoscale, the softwood cell is...... presented as a 3D hexagon-shape-tube with multilayered walls. The layers in the softwood cell are considered as considered as composite reinforced by microfibrils (celluloses). The elastic properties of the layers are determined with Halpin–Tsai equations, and introduced into mesoscale finite element...
Stylized Facts Generated Through Cellular Automata Models. Case of Study: The Game of Life
Coronel-Brizio, H F; Rodriguez-Achach, M E; Stevens-Ramirez, G A
2007-01-01
In the present work, a geometrical method to generate a two dimensional random walk by means of a bidimensional Cellular Automaton is presented. We illustrate it by means of Conway's Game of Life with periodical borders, with a large lattice of 3000 x 3000 cells. The obtained random walk is of character anomalous, and its projection to a one dimensional random walk is analyzed, showing that it presents some statistical properties similar to the so-called stylized facts observed in financial time series. We consider that the procedure presented here is important not only because of its simplicity, but also because it could help us to understand and shed light on the stylized facts formation mechanism.
Modelling the role of nucleation on recrystallization kinetics: A cellular automata approach
Tripathy, Haraprasanna; Rai, Arun Kumar; Hajra, Raj Narayan; Raju, Subramanian; Saibaba, Saroja
2016-05-01
In present study, a two dimensional cellular automata (CA) simulation has been carried out to study the effect of nucleation mode on the kinetics of recrystallization and microstructure evolution in an austenitic stainless steel. Two different nucleation modes i.e. site saturation and continuous nucleation with interface control growth mechanism has been considered in this modified CA algorithm. The observed Avrami exponent for both nucleation modes shows a better agreement with the theoretical predicted values. The site saturated nucleation mode shows a nearly consistent value of Avrami exponent, whereas in the case of continuous nucleation the exponent shows a little variation during transformation. The simulations in the present work can be applied for the optimization of microstructure and properties in austenitic steels.
Dimastrogiovanni, Giorgio; Córdoba, Marlon; Navarro, Isabel; Jáuregui, Olga; Porte, Cinta
2015-08-01
This work investigates the suitability of the rainbow trout liver cell line (RTL-W1) as an in-vitro model to study the ability of model endocrine disrupters, namely TBT, TPT, 4-NP, BPA and DEHP, to act as metabolic disrupters by altering cellular lipids and markers of lipid metabolism. Among the tested compounds, BPA and DEHP significantly increased the intracellular accumulation of triacylglycerols (TAGs), while all the compounds -apart from TPT-, altered membrane lipids - phosphatidylcholines (PCs) and plasmalogen PCs - indicating a strong interaction of the toxicants with cell membranes and cell signaling. RTL-W1 expressed a number of genes involved in lipid metabolism that were modulated by exposure to BPA, TBT and TPT (up-regulation of FATP1 and FAS) and 4-NP and DEHP (down-regulation of FAS and LPL). Multiple and complex modes of action of these chemicals were observed in RTL-W1 cells, both in terms of expression of genes related to lipid metabolism and alteration of cellular lipids. Although further characterization is needed, this might be a useful model for the detection of chemicals leading to steatosis or other diseases associated with lipid metabolism in fish. PMID:26143618
Directory of Open Access Journals (Sweden)
H. Rezazadeh
2009-04-01
Full Text Available The concept of virtual cellular manufacturing system (VCMS is finding acceptance among researchers as an extension to grouptechnology. In fact, in order to realize benefits of cellular manufacturing system in the functional layout, the VCMS createsprovisional groups of resources (machines, parts and workers in the production planning and control system. This paperdevelops a mathematical model to design the VCMS under a dynamic environment with a more integrated approach whereproduction planning, system reconfiguration and workforce requirements decisions are incorporated. The advantages of theproposed model are as follows: considering the operations sequence, alternative process plans for part types, machine timecapacity,worker time‐capacity, cross‐training, lot splitting, maximal cell size, balanced workload for cells and workers. Anefficient linear programming embedded particle swarm optimization algorithm is used to solve the proposed model. Thealgorithm searches over the 0‐1 integer variables and for each 0‐1 integer solution visited; corresponding values of integervariables are determined by solving a linear programming sub‐problem using the simplex algorithm. Numerical examples showthat the proposed method is efficient and effective in searching for near optimal solutions.
Feng, Song; Ollivier, Julien F; Swain, Peter S; Soyer, Orkun S
2015-10-30
Systems biologists aim to decipher the structure and dynamics of signaling and regulatory networks underpinning cellular responses; synthetic biologists can use this insight to alter existing networks or engineer de novo ones. Both tasks will benefit from an understanding of which structural and dynamic features of networks can emerge from evolutionary processes, through which intermediary steps these arise, and whether they embody general design principles. As natural evolution at the level of network dynamics is difficult to study, in silico evolution of network models can provide important insights. However, current tools used for in silico evolution of network dynamics are limited to ad hoc computer simulations and models. Here we introduce BioJazz, an extendable, user-friendly tool for simulating the evolution of dynamic biochemical networks. Unlike previous tools for in silico evolution, BioJazz allows for the evolution of cellular networks with unbounded complexity by combining rule-based modeling with an encoding of networks that is akin to a genome. We show that BioJazz can be used to implement biologically realistic selective pressures and allows exploration of the space of network architectures and dynamics that implement prescribed physiological functions. BioJazz is provided as an open-source tool to facilitate its further development and use. Source code and user manuals are available at: http://oss-lab.github.io/biojazz and http://osslab.lifesci.warwick.ac.uk/BioJazz.aspx. PMID:26101250
Directory of Open Access Journals (Sweden)
Pelzer Lindsay
2011-06-01
Full Text Available Abstract Background Leukodystrophies are devastating diseases characterized by dys- and hypo-myelination. While there are a number of histological and imaging studies of these disorders, there are limited biochemical data available. We undertook targeted lipidomic analyses of Pelizaeus-Merzbacher disease (PMD fibroblasts, PMD lymphocytes, and 158JP oligodendrocytes, a murine model of PMD, to define the lipid changes in these cell models. Further targeted metabolomics analyses were conducted to obtain a preliminary evaluation of the metabolic consequences of lipid changes and gene mutations in these cell models. Results In both PMD fibroblasts and lymphocytes, and 158JP oligodendrocytes, ethanolamine plasmalogens were significantly decreased. Labeling studies with 158JP oligodendrocytes further demonstrated a decreased rate of lipid remodeling at sn-2. Targeted metabolomics analyses of these cells revealed dramatic increases in cellular levels of myo-inositol. Further uptake studies demonstrated increased rates of myo-inositol uptake by PMD lymphocytes. Conclusions Our data demonstrating PlsEtn decrements, support previous studies indicating leukodystrophy cells possess significant peroxisomal deficits. Our data for the first time also demonstrate that decrements in peroxisomal function coupled with the PLP1 gene defects of PMD, result in changes in the function of membrane myo-inositol solute carriers resulting in dramatic increases in cellular myo-inositol levels.
Directory of Open Access Journals (Sweden)
Bruno Baynat
2012-10-01
Full Text Available The last years have seen an exponentially growing interest for mobile telecommunication services. As a consequence, a great diversity of applications is expected to be supported by cellular networks. To answer this ever increasing demand, the ITU-R defined the requirements that the fourth generation (4G of mobile standards must fulfill. Today, two especially promising candidates for 4G stand out: WiMAX and LTE. However, 4G cellular networks are still far from being implemented, and the high deployment costs render over-provisioning out of question. We thus propose in this paper accurate and convenient analytical models well-suited for the complex dimensioning of these promising access networks. Our main interest is WiMAX, yet, we show how our models can be easily used to consider LTE cells since both technologies are based on OFDMA. Generic Markovian models are developed specifically for three service classes defined in the WiMAX standard: UGS, ertPS and BE, respectively corresponding to VoIP, VoIP with silence suppression and best-effort traffic. First, we consider cells carrying either UGS, ertPS or BE traffic. Three methods to combine the previous models are then proposed to assume both UGS and BE traffic in the studied cell. Finally, we provide a way to easily integrate the ertPS traffic and obtain a UGS/ertPS/BE model able to account for multiple traffic profiles in each service class while keeping an instantaneous resolution. The proposed models are compared in depth with realistic simulations that show their accuracy. Lastly, we demonstrate through different examples how our models can be used to answer dimensioning issues which would be intractable with simulations.
Study of cellular retention of HMPAO and ECD in a model simulating the blood-brain barrier
International Nuclear Information System (INIS)
The HMPAO and ECD are two technetium-labelled lipophilic agents clinically used in the imagery of cerebral perfusion. These molecules cross the membranes and are retained inside the cell after being converted to a hydrophilic form. The aim of this study is to establish the distribution of this retention at the level of blood-brain barrier (BBB) and nerve cells. The incorporation of HMPAO or ECD was studied on a model of co-culture simulating the BBB by means of a T84 single-cell layer of tight junction separated from another layer of U373 astrocyte cells. The cell quality and tight junction permeability were evaluated by the cellular retention of 111-indium chloride and by para-cellular diffusion of 14C mannitol,d-1. The values reported below were obtained at 180 minutes when the radiotracers were added near the 'T84 layer'. The cell quality is validated by the low cellular retention of the indium chloride(2.3±0.3 μg-1 for the T84 cells and 8.2±5.8 μg-1 for the U373 cells). The activity of 14C mannitol,d-1 diminishes by 23 ± 5 % in the added compartment. The retention of ECD by the U373 cells is significantly higher (20.7 ±4.5 g-1) than that of T84 cells (2.9 ± 0.2 μg-1). For HMPAO a non-significant tendency could be observed (49 ± 34 μg-1 for the U373 cells and 38 ± 25 μg-1 for the T84 cells)> The results of cellular retention of indium by HMPAO or ECD when added near 'U373 layer' are not significantly different.In conclusion, independently of the side exposed to the radiotracers, one observes an enhanced incorporation of the U373 cells. The ensemble of these results represent additional arguments in favour of a specific cellular incorporation of the radiotracers, independent of the BBB permittivity
de la Cruz, Roberto; Spill, Fabian; Alarcón, Tomás
2016-01-01
We propose a modelling framework to analyse the stochastic behaviour of heterogeneous, multi-scale cellular populations. We illustrate our methodology with a particular example in which we study a population with an oxygen-regulated proliferation rate. Our formulation is based on an age-dependent stochastic process. Cells within the population are characterised by their age. The age-dependent (oxygen-regulated) birth rate is given by a stochastic model of oxygen-dependent cell cycle progression. We then formulate an age-dependent birth-and-death process, which dictates the time evolution of the cell population. The population is under a feedback loop which controls its steady state size: cells consume oxygen which in turns fuels cell proliferation. We show that our stochastic model of cell cycle progression allows for heterogeneity within the cell population induced by stochastic effects. Such heterogeneous behaviour is reflected in variations in the proliferation rate. Within this set-up, we have established...
International Nuclear Information System (INIS)
Tritium release from the lithium ceramics as a fusion reactor breeder material is strongly affected by the composition of the sweep-gas as result of its influences with the material's surface. The typical surface processes which play important roles are adsorption, desorption and interaction between vacancy site and the constituents of the sweep-gas. Among a large number of studies and models, yet it seems to be difficult to model the overall behaviour of those processes due to its complex time-transient nature. In the present work the coarse grained atomic simulation based on the Cellular Automaton (CA) is used to model the dynamics of near-surface interaction between Li2O surface and sweep-gas that is consisting of a noble gas, hydrogen gas and water vapour. (author)
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Yao Xiao
2015-01-01
Full Text Available This paper aimed to analyze the influence of drivers’ behavior of phone use while driving on traffic flow, including both traffic efficiency and traffic safety. An improved cellular automaton model was proposed to simulate traffic flow with distracted drivers based on the Nagel-Schreckenberg model. The driving characters of drivers using a phone were first discussed and a value representing the probability to use a phone while driving was put into the CA model. Simulation results showed that traffic flow rate was significantly reduced if some drivers used a phone compared to no phone use. The flow rate and velocity decreased as the proportion of drivers using a phone increased. While, under low density, the risk of traffic decreased first and then increased as the distracted drivers increased, the distracted behavior of drivers, like using a phone, could reduce the flow rate by 5 percent according to the simulation.
Nakazato, Ken'ichiro
2014-01-01
A new cellular automaton (CA) model is presented for the self-organized criticality (SOC) in recurrent bursts of soft gamma repeaters (SGRs), which are interpreted as avalanches of reconnection in the magnetosphere of neutron stars. The nodes of a regular dodecahedron and a truncated icosahedron are adopted as spherically closed grids enclosing a neutron star. It is found that the system enters the SOC state if there are sites where the expectation value of the added perturbation is nonzero. The energy distributions of SOC avalanches in CA simulations are described by a power law with a cutoff, which is consistent with the observations of SGR 1806-20 and SGR 1900+14. The power-law index is not universal and depends on the amplitude of the perturbation. This result shows that the SOC of SGRs can be illustrated not only by the crust quake model but also by the magnetic reconnection model.
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Yuli eCao
2016-02-01
Full Text Available The mechanisms involved in traumatic brain injury (TBI have yet to be fully characterized. One mechanism that, especially in high energy trauma, could be of importance is cavitation. Cavitation can be described as a process of vaporization, bubble generation and bubble implosion as a result of a decrease and subsequent increase in pressure. Cavitation as an injury mechanism is difficult to visualize and model due to its short duration and limited spatial distribution. One strategy to analyze the cellular response of cavitation is to employ suitable in vitro models. The flyer plate is an in vitro high energy trauma model that includes cavitation as a trauma mechanism. A copper fragment is accelerated by means of a laser, hits the bottom of a cell culture well causing cavitation and shock waves inside the well and cell medium. We have found the flyer plate model to be efficient, reproducible and easy to control. In this study we have used the model to analyze the cellular response to microcavitation in SH-SY5Y neuroblastoma, Caco-2, and C6 glioma cell lines. Mitotic activity in neuroblastoma and glioma was investigated with BrdU staining, and cell numbers were calculated using automated time-lapse imaging. We found variations between cell types and between different zones surrounding the lesion with these methods. It was also shown that the injured cell cultures released S-100B in a dose dependent manner. Using gene expression microarray a number of gene families of potential interest were found to be strongly, but differently regulated in neuroblastoma and glioma at 24 hr post trauma. The data from the gene expression arrays may be used to identify new candidates for biomarkers in cavitation trauma. We conclude that our model is useful for studies of trauma in vitro and that it could be applied in future treatment studies.
Structural-mechanical model of wax crystal networks—a mesoscale cellular solid approach
International Nuclear Information System (INIS)
Mineral waxes are widely used materials in industrial applications; however, the relationship between structure and mechanical properties is poorly understood. In this work, mineral wax-oil networks were characterized as closed-cell cellular solids, and differences in their mechanical response predicted from structural data. The systems studied included straight-chain paraffin wax (SW)-oil mixtures and polyethylene wax (PW)-oil mixtures. Analysis of cryogenic-SEM images of wax-oil networks allowed for the determination of the length (l) and thickness (t) of the wax cell walls as a function of wax mass fraction (Φ). A linear relationship between t/l and Φ (t/l ∼ Φ 0.89) suggested that wax-oil networks were cellular solids of the closed-cell type. However, the scaling behavior of the elastic modulus with the volume fraction of solids did not agree with theoretical predictions, yielding the same scaling exponent, μ = 0.84, for both waxes. This scaling exponent obtained from mechanical measurements could be predicted from the scaling behavior of the effective wax cell size as a function of wax mass fraction in oil obtained by cryogenic scanning electron microscopy. Microscopy studies allowed us to propose that wax-oil networks are structured as an ensemble of close-packed spherical cells filled with oil, and that it is the links between cells that yield under simple uniaxial compression. Thus, the Young’s moduli for the links between cells in SW and PW wax systems could be estimated as E L(SW) = 2.76 × 109 Pa and E L(PW) = 1.64 × 109 Pa, respectively. The structural parameter responsible for the observed differences in the mechanical strength between the two wax-oil systems is the size of the cells. Polyethylene wax has much smaller cell sizes than the straight chain wax and thus displays a higher Young’s modulus and yield stress. (papers)
Liu, L.; Liu, Y.; Wang, X.; Yu, D.; Liu, K.; Huang, H.; Hu, G.
2015-03-01
Flash floods have occurred frequently in the urban areas of southern China. An effective process-oriented urban flood inundation model is urgently needed for urban storm-water and emergency management. This study develops an efficient and flexible cellular automaton (CA) model to simulate storm-water runoff and the flood inundation process during extreme storm events. The process of infiltration, inlets discharge and flow dynamics can be simulated with little preprocessing on commonly available basic urban geographic data. In this model, a set of gravitational diverging rules are implemented to govern the water flow in a rectangular template of three cells by three cells of a raster layer. The model is calibrated by one storm event and validated by another in a small urban catchment in Guangzhou of southern China. The depth of accumulated water at the catchment outlet is interpreted from street-monitoring closed-circuit television (CCTV) videos and verified by on-site survey. A good level of agreement between the simulated process and the reality is reached for both storm events. The model reproduces the changing extent and depth of flooded areas at the catchment outlet with an accuracy of 4 cm in water depth. Comparisons with a physically based 2-D model (FloodMap) show that the model is capable of effectively simulating flow dynamics. The high computational efficiency of the CA model can meet the needs of city emergency management.
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Fuqian Shi
2012-01-01
Full Text Available Emotional cellular (EC, proposed in our previous works, is a kind of semantic cell that contains kernel and shell and the kernel is formalized by a triple- L = , where P denotes a typical set of positive examples relative to word-L, d is a pseudodistance measure on emotional two-dimensional space: valence-arousal, and δ is a probability density function on positive real number field. The basic idea of EC model is to assume that the neighborhood radius of each semantic concept is uncertain, and this uncertainty will be measured by one-dimensional density function δ. In this paper, product form features were evaluated by using ECs and to establish the product style database, fuzzy case based reasoning (FCBR model under a defined similarity measurement based on fuzzy nearest neighbors (FNN incorporating EC was applied to extract product styles. A mathematical formalized inference system for product style was also proposed, and it also includes uncertainty measurement tool emotional cellular. A case study of style acquisition of mobile phones illustrated the effectiveness of the proposed methodology.
Xu, Xiao-Jian; Wang, Ya-Chuan; Wang, Bo; Zhang, Kai
2016-06-01
We propose a modified core-shell model to depict the size-dependent elastic properties of materials with several different cross-sections. By using the Young-Laplace equation, a modified Euler-Bernoulli equation, which has taken a power-law relation between the bulk and surface moduli into account, is derived. A finite element method of the modified Euler-Bernoulli equation is formulated, and assembled to investigate the dispersion relations of the infinite two-dimensional periodic square cellular networks. The effectiveness of the proposed core-shell model is verified by comparing with results of the experiments and the molecular dynamics simulations available in the literature. Numerical results show that surface effects play an important role on the cellular networks with small diameters, large aspect ratios and high wave frequencies. Meanwhile, the analytical expressions for the size-dependent elastic modulus may be useful for the study of the size-dependent elasticity of materials and structures at small length scales.
Reconstructing the emergence of cellular life through the synthesis of model protocells.
Mansy, S S; Szostak, J W
2009-01-01
The complexity of modern biological life has long made it difficult to understand how life could emerge spontaneously from the chemistry of the early earth. The key to resolving this mystery lies in the simplicity of the earliest living cells, together with the ability of the appropriate molecular building blocks to spontaneously self-assemble into larger structures. In our view, the two key components of a primitive cell are not only self-assembling, but also self-replicating, structures: the nucleic acid genome and the cell membrane. Here, we summarize recent experimental progress toward the synthesis of efficient self-replicating nucleic acid and membrane vesicle systems and discuss some of the issues that arise during efforts to integrate these two subsystems into a coherent whole. We have shown that spontaneous nucleic-acid-copying chemistry can take place within membrane vesicles, using externally supplied activated nucleotides as substrates. Thus, membranes need not be a barrier to the uptake of environmentally supplied nutrients. We examine some of the remaining obstacles that must be overcome to enable the synthesis of a complete self-replicating protocell, and we discuss the implications of these experiments for our understanding of the emergence of Darwinian evolution and the origin and early evolution of cellular life. PMID:19734203
Sub-cellular modeling of platelet transport in blood flow through microchannels with constriction.
Yazdani, Alireza; Karniadakis, George Em
2016-05-11
Platelet transport through arterial constrictions is one of the controlling processes influencing their adhesive functions and the formation of thrombi. We perform high-fidelity mesoscopic simulations of blood flow in microchannels with constriction, resembling arterial stenoses. The wall shear rates inside the constrictions reach levels as high as ≈8000 s(-1), similar to those encountered in moderate atherosclerotic plaques. Both red blood cells and platelets are resolved at sub-cellular resolution using the Dissipative Particle Dynamics (DPD) method. We perform a systematic study on the red blood cell and platelet transport by considering different levels of constriction, blood hematocrit and flow rates. We find that higher levels of constriction and wall shear rates lead to significantly enhanced margination of platelets, which may explain the experimental observations of enhanced post-stenosis platelet aggregation. We also observe similar margination effects for stiff particles of spherical shapes such as leukocytes. To our knowledge, such numerical simulations of dense blood through complex geometries have not been performed before, and our quantitative findings could shed new light on the associated physiological processes such as ATP release, plasma skimming, and thrombus formation. PMID:27087267
Lancaster, Gemma; Suprunenko, Yevhen F.; Jenkins, Kirsten; Stefanovska, Aneta
2016-01-01
Altered cellular energy metabolism is a hallmark of many diseases, one notable example being cancer. Here, we focus on the identification of the transition from healthy to abnormal metabolic states. To do this, we study the dynamics of energy production in a cell. Due to the thermodynamic openness of a living cell, the inability to instantaneously match fluctuating supply and demand in energy metabolism results in nonautonomous time-varying oscillatory dynamics. However, such oscillatory dynamics is often neglected and treated as stochastic. Based on experimental evidence of metabolic oscillations, we show that changes in metabolic state can be described robustly by alterations in the chronotaxicity of the corresponding metabolic oscillations, i.e. the ability of an oscillator to resist external perturbations. We also present a method for the identification of chronotaxicity, applicable to general oscillatory signals and, importantly, apply this to real experimental data. Evidence of chronotaxicity was found in glycolytic oscillations in real yeast cells, verifying that chronotaxicity could be used to study transitions between metabolic states. PMID:27483987
Development of an elementary climate model: two-layer cellular case
Schmidt, L E; Knox, R S; Schmidt, Laura E.; Knox, Robert S.
2003-01-01
A qualitative understanding of the greenhouse effect has long been available through models based on globally- and time-averaged quantities. We examine here a simple 864-cell climatological model that emphasizes vertical radiative energy transport within each cell. It reproduces yearly average temperatures obtained earlier from one of these global models and predicts a locally distributed non-radiative flux when observed temperatures are employed as input data. Vertical and lateral transport of latent heat do not appear explicitly in this model. They are apparently handled well by one non-radiative flux variable, SNR, which shows a strong latitude dependence. Only the Sahara desert and Saudi Arabian regions appear to be complex. For those interested in climatology and construction of climate models, our model provides constraints upon specifying averaged non-radiative energy transport. The model is a useful simplification for learning about radiative energy transfer into and out of Earth?s atmosphere and for ...
Tahayori, Bahman; Meffin, Hamish; Sergeev, Evgeni N.; Mareels, Iven M. Y.; Burkitt, Anthony N.; Grayden, David B.
2014-12-01
Objective. The objective of this paper is to present a concrete application of the cellular composite model for calculating the membrane potential, described in an accompanying paper. Approach. A composite model that is used to determine the membrane potential for both longitudinal and transverse modes of stimulation is demonstrated. Main results. Two extreme limits of the model, near-field and far-field for an electrode close to or distant from a neuron, respectively, are derived in this paper. Results for typical neural tissue are compared using the composite, near-field and far-field models as well as the standard isotropic volume conductor model. The self-consistency of the composite model, its spatial profile response and the extracellular potential time behaviour are presented. The magnitudes of the longitudinal and transverse components for different values of electrode-neurite separations are compared. Significance. The unique features of the composite model and its simplified versions can be used to accurately estimate the spatio-temporal response of neural tissue to extracellular electrical stimulation.
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Wenjun Zhao
Full Text Available The mechanisms underlying acute myeloid leukemia (AML treatment failure are not clear. Here, we established a mouse model of AML by syngeneic transplantation of BXH-2 derived myeloid leukemic cells and developed an efficacious Ara-C-based regimen for treatment of these mice. We proved that leukemic cell load was correlated with survival. We also demonstrated that the susceptibility of leukemia cells to Ara-C could significantly affect the survival. To examine the molecular alterations in cells with different sensitivity, genome-wide expression of the leukemic cells was profiled, revealing that overall 366 and 212 genes became upregulated or downregulated, respectively, in the resistant cells. Many of these genes are involved in the regulation of cell cycle, cellular proliferation, and apoptosis. Some of them were further validated by quantitative PCR. Interestingly, the Ara-C resistant cells retained the sensitivity to ABT-737, an inhibitor of anti-apoptosis proteins, and treatment with ABT-737 prolonged the life span of mice engrafted with resistant cells. These results suggest that leukemic load and intrinsic cellular resistance can affect the outcome of AML treated with Ara-C. Incorporation of apoptosis inhibitors, such as ABT-737, into traditional cytotoxic regimens merits consideration for the treatment of AML in a subset of patients with resistance to Ara-C. This work provided direct in vivo evidence that leukemic load and intrinsic cellular resistance can affect the outcome of AML treated with Ara-C, suggesting that incorporation of apoptosis inhibitors into traditional cytotoxic regimens merits consideration for the treatment of AML in a subset of patients with resistance to Ara-C.
Danila, Bogdan; Mocanu, Gabriela
2015-01-01
We investigate the transition to Self Organized Criticality in a two-dimensional model of a flux tube with a background flow. The magnetic induction equation, represented by a partial differential equation with a stochastic source term, is discretized and implemented on a two dimensional cellular automaton. The energy released by the automaton during one relaxation event is the magnetic energy. As a result of the simulations we obtain the time evolution of the energy release, of the system control parameter, of the event lifetime distribution and of the event size distribution, respectively, and we establish that a Self Organized Critical state is indeed reached by the system. Moreover, energetic initial impulses in the magnetohydrodynamic flow can lead to one dimensional signatures in the magnetic two dimensional system, once the Self Organized Critical regime is established. The applications of the model for the study of Gamma Ray Bursts is briefly considered, and it is shown that some astrophysical paramet...
DEFF Research Database (Denmark)
Skiadas, Ioannis V.; Ahring, Birgitte Kiær
2002-01-01
characteristics and lead to different reactor behaviour. A dynamic mathematical model has been developed for the anaerobic digestion of a glucose based synthetic wastewater in UASB reactors. Cellular automata (CA) theory has been applied to simulate the granule development process. The model takes......The advantageous performance of the UASB reactors is due to the immobilisation of the active biomass, since bacteria coagulate forming aggregates usually called granules. Changes in organic loading rate, hydraulic loading rate or influent substrate composition usually result in changes in granule...... into consideration that granule diameter and granule microbial composition are functions of the reactor operational parameters and is capable of predicting the UASB performance and the layer structure of the granules....
Tuberculose ostéoarticulaire (mal de Pott exclu): à propos de 120 cas à Abidjan
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
Olsen, Megan; Siegelmann-Danieli, Nava; Siegelmann, Hava T.
2010-01-01
Computational models in the field of cancer research have focused primarily on estimates of biological events based on laboratory generated data. We introduce a novel in-silico technology that takes us to the next level of prediction models and facilitates innovative solutions through the mathematical system. The model's building blocks are cells defined phenotypically as normal or tumor, with biological processes translated into equations describing the life protocols of the cells in a quant...
Marcos, Ernesto; Lazo, Laura; Gil, Lázaro; Izquierdo, Alienys; Suzarte, Edith; Valdés, Iris; Blanco, Aracelys; Ancizar, Julio; Alba, José Suárez; Pérez, Yusleydis de la C; Cobas, Karen; Romero, Yaremis; Guillén, Gerardo; Guzmán, María G; Hermida, Lisset
2016-08-01
Despite the many efforts made by the scientific community in the development of vaccine candidates against dengue virus (DENV), no vaccine has been licensed up to date. Although the immunopathogenesis associated to the disease is a key factor to take into account by vaccine developers, the lack of animal models that reproduce the clinical signs of the disease has hampered the vaccine progress. Non-human primates support viral replication, but they are very expensive and do not show signs of disease. Immunocompromised mice develop viremia and some signs of the disease; however, they are not valuable for vaccine testing. Nowadays, immunocompetent mice are the most used model to evaluate the immunogenicity of vaccine candidates. These animals are resistant to DENV infection; therefore, the intracranial inoculation with neuroadapted virus, which provokes viral encephalitis, represents an alternative to evaluate the protective capacity of vaccine candidates. Previous results have demonstrated the crucial role of cellular immune response in the protection induced by the virus and vaccine candidates in this mouse encephalitis model. However, in the present work we are proposing that the magnitude of the cell-mediated immunity and the inflammatory response generated by the vaccine can modulate the survival rate after viral challenge. We observed that the intracranial challenge of naïve mice with DENV-2 induces the recruitment of immune cells that contribute to the reduction of viral load, but does not increase the survival rate. On the contrary, animals treated with cyclophosphamide, an immunosuppressive drug that affects proliferating lymphocytes, had a higher viral load but a better survival rate than untreated animals. These results suggest that the immune system is playing an immunopathogenic role in this model and the survival rate may not be a suitable endpoint in the evaluation of vaccine candidates based on antigens that induce a strong cellular immune response
Astrocytic gap junctional networks suppress cellular damage in an in vitro model of ischemia
International Nuclear Information System (INIS)
Highlights: • Astrocytes exhibit characteristic changes in [Ca2+]i under OGD. • Astrocytic [Ca2+]i increase is synchronized with a neuronal anoxic depolarization. • Gap junctional couplings protect neurons as well as astrocytes during OGD. - Abstract: Astrocytes play pivotal roles in both the physiology and the pathophysiology of the brain. They communicate with each other via extracellular messengers as well as through gap junctions, which may exacerbate or protect against pathological processes in the brain. However, their roles during the acute phase of ischemia and the underlying cellular mechanisms remain largely unknown. To address this issue, we imaged changes in the intracellular calcium concentration ([Ca2+]i) in astrocytes in mouse cortical slices under oxygen/glucose deprivation (OGD) condition using two-photon microscopy. Under OGD, astrocytes showed [Ca2+]i oscillations followed by larger and sustained [Ca2+]i increases. While the pharmacological blockades of astrocytic receptors for glutamate and ATP had no effect, the inhibitions of gap junctional intercellular coupling between astrocytes significantly advanced the onset of the sustained [Ca2+]i increase after OGD exposure. Interestingly, the simultaneous recording of the neuronal membrane potential revealed that the onset of the sustained [Ca2+]i increase in astrocytes was synchronized with the appearance of neuronal anoxic depolarization. Furthermore, the blockade of gap junctional coupling resulted in a concurrent faster appearance of neuronal depolarizations, which remain synchronized with the sustained [Ca2+]i increase in astrocytes. These results indicate that astrocytes delay the appearance of the pathological responses of astrocytes and neurons through their gap junction-mediated intercellular network under OGD. Thus, astrocytic gap junctional networks provide protection against tissue damage during the acute phase of ischemia
Astrocytic gap junctional networks suppress cellular damage in an in vitro model of ischemia
Energy Technology Data Exchange (ETDEWEB)
Shinotsuka, Takanori; Yasui, Masato; Nuriya, Mutsuo, E-mail: mnuriya@z2.keio.jp
2014-02-07
Highlights: • Astrocytes exhibit characteristic changes in [Ca{sup 2+}]{sub i} under OGD. • Astrocytic [Ca{sup 2+}]{sub i} increase is synchronized with a neuronal anoxic depolarization. • Gap junctional couplings protect neurons as well as astrocytes during OGD. - Abstract: Astrocytes play pivotal roles in both the physiology and the pathophysiology of the brain. They communicate with each other via extracellular messengers as well as through gap junctions, which may exacerbate or protect against pathological processes in the brain. However, their roles during the acute phase of ischemia and the underlying cellular mechanisms remain largely unknown. To address this issue, we imaged changes in the intracellular calcium concentration ([Ca{sup 2+}]{sub i}) in astrocytes in mouse cortical slices under oxygen/glucose deprivation (OGD) condition using two-photon microscopy. Under OGD, astrocytes showed [Ca{sup 2+}]{sub i} oscillations followed by larger and sustained [Ca{sup 2+}]{sub i} increases. While the pharmacological blockades of astrocytic receptors for glutamate and ATP had no effect, the inhibitions of gap junctional intercellular coupling between astrocytes significantly advanced the onset of the sustained [Ca{sup 2+}]{sub i} increase after OGD exposure. Interestingly, the simultaneous recording of the neuronal membrane potential revealed that the onset of the sustained [Ca{sup 2+}]{sub i} increase in astrocytes was synchronized with the appearance of neuronal anoxic depolarization. Furthermore, the blockade of gap junctional coupling resulted in a concurrent faster appearance of neuronal depolarizations, which remain synchronized with the sustained [Ca{sup 2+}]{sub i} increase in astrocytes. These results indicate that astrocytes delay the appearance of the pathological responses of astrocytes and neurons through their gap junction-mediated intercellular network under OGD. Thus, astrocytic gap junctional networks provide protection against tissue damage
Tucker, G. E.; Hobley, D. E. J.; Hutton, E.; Gasparini, N. M.; Istanbulluoglu, E.; Adams, J. M.; Nudurupati, S. S.
2015-11-01
CellLab-CTS 2015 is a Python-language software library for creating two-dimensional, continuous-time stochastic (CTS) cellular automaton models. The model domain consists of a set of grid nodes, with each node assigned an integer state-code that represents its condition or composition. Adjacent pairs of nodes may undergo transitions to different states, according to a user-defined average transition rate. A model is created by writing a Python code that defines the possible states, the transitions, and the rates of those transitions. The code instantiates, initializes, and runs one of four object classes that represent different types of CTS model. CellLab-CTS provides the option of using either square or hexagonal grid cells. The software provides the ability to treat particular grid-node states as moving particles, and to track their position over time. Grid nodes may also be assigned user-defined properties, which the user can update after each transition through the use of a callback function. As a component of the Landlab modeling framework, CellLab-CTS models take advantage of a suite of Landlab's tools and capabilities, such as support for standardized input and output.
Directory of Open Access Journals (Sweden)
Boyin Liu
Full Text Available Different toxicity tests for carbon nanotubes (CNT have been developed to assess their impact on human health and on aquatic and terrestrial animal and plant life. We present a new model, the fruit fly Drosophila embryo offering the opportunity for rapid, inexpensive and detailed analysis of CNTs toxicity during embryonic development. We show that injected DiI labelled multi-walled carbon nanotubes (MWCNTs become incorporated into cells in early Drosophila embryos, allowing the study of the consequences of cellular uptake of CNTs on cell communication, tissue and organ formation in living embryos. Fluorescently labelled subcellular structures showed that MWCNTs remained cytoplasmic and were excluded from the nucleus. Analysis of developing ectodermal and neural stem cells in MWCNTs injected embryos revealed normal division patterns and differentiation capacity. However, an increase in cell death of ectodermal but not of neural stem cells was observed, indicating stem cell-specific vulnerability to MWCNT exposure. The ease of CNT embryo injections, the possibility of detailed morphological and genomic analysis and the low costs make Drosophila embryos a system of choice to assess potential developmental and cellular effects of CNTs and test their use in future CNT based new therapies including drug delivery.