Cellular potts models multiscale extensions and biological applications
Scianna, Marco
2013-01-01
A flexible, cell-level, and lattice-based technique, the cellular Potts model accurately describes the phenomenological mechanisms involved in many biological processes. Cellular Potts Models: Multiscale Extensions and Biological Applications gives an interdisciplinary, accessible treatment of these models, from the original methodologies to the latest developments. The book first explains the biophysical bases, main merits, and limitations of the cellular Potts model. It then proposes several innovative extensions, focusing on ways to integrate and interface the basic cellular Potts model at the mesoscopic scale with approaches that accurately model microscopic dynamics. These extensions are designed to create a nested and hybrid environment, where the evolution of a biological system is realistically driven by the constant interplay and flux of information between the different levels of description. Through several biological examples, the authors demonstrate a qualitative and quantitative agreement with t...
A hybrid parallel framework for the cellular Potts model simulations
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}).
Multi-scale modeling in morphogenesis: a critical analysis of the cellular Potts model.
Anja Voss-Böhme
Full Text Available Cellular Potts models (CPMs are used as a modeling framework to elucidate mechanisms of biological development. They allow a spatial resolution below the cellular scale and are applied particularly when problems are studied where multiple spatial and temporal scales are involved. Despite the increasing usage of CPMs in theoretical biology, this model class has received little attention from mathematical theory. To narrow this gap, the CPMs are subjected to a theoretical study here. It is asked to which extent the updating rules establish an appropriate dynamical model of intercellular interactions and what the principal behavior at different time scales characterizes. It is shown that the longtime behavior of a CPM is degenerate in the sense that the cells consecutively die out, independent of the specific interdependence structure that characterizes the model. While CPMs are naturally defined on finite, spatially bounded lattices, possible extensions to spatially unbounded systems are explored to assess to which extent spatio-temporal limit procedures can be applied to describe the emergent behavior at the tissue scale. To elucidate the mechanistic structure of CPMs, the model class is integrated into a general multiscale framework. It is shown that the central role of the surface fluctuations, which subsume several cellular and intercellular factors, entails substantial limitations for a CPM's exploitation both as a mechanistic and as a phenomenological model.
A curious relationship between Potts glass models
Yamaguchi, Chiaki
2015-08-01
A Potts glass model proposed by Nishimori and Stephen [H. Nishimori, M.J. Stephen, Phys. Rev. B 27, 5644 (1983)] is analyzed by means of the replica mean field theory. This model is a discrete model, has a gauge symmetry, and is called the Potts gauge glass model. By comparing the present results with the results of the conventional Potts glass model, we find the coincidences and differences between the models. We find a coincidence that the property for the Potts glass phase in this model is coincident with that in the conventional model at the mean field level. We find a difference that, unlike in the case of the conventional p-state Potts glass model, this system for large p does not become ferromagnetic at low temperature under a concentration of ferromagnetic interaction. The present results support the act of numerically investigating the present model for study of the Potts glass phase in finite dimensions.
Scianna, Marco; Preziosi, Luigi
2014-03-01
Cell migration is fundamental in a wide variety of physiological and pathological phenomena, among other in cancer invasion and development. In particular, the migratory/invasive capability of single metastatic cells is fundamental in determining the malignancy of a solid tumor. Specific cell migration phenotypes result for instance from the reciprocal interplay between the biophysical and biochemical properties of both the malignant cells themselves and of the surrounding environment. In particular, the extracellular matrices (ECMs) forming connective tissues can provide both loosely organized zones and densely packed barriers, which may impact cell invasion mode and efficiency. The critical processes involved in cell movement within confined spaces are (i) the proteolytic activity of matrix metalloproteinases (MMPs) and (ii) the deformation of the entire cell body, and in particular of the nucleus. We here present an extended cellular Potts model (CPM) to simulate a bio-engineered matrix system, which tests the active motile behavior of a single cancer cell into narrow channels of different widths. As distinct features of our approach, the cell is modeled as a compartmentalized discrete element, differentiated in the nucleus and in the cytosolic region, while a directional shape-dependent movement is explicitly driven by the evolution of its polarity vector. As outcomes, we find that, in a large track, the tumor cell is not able to maintain a directional movement. On the contrary, a structure of subcellular width behaves as a contact guidance sustaining cell persistent locomotion. In particular, a MMP-deprived cell is able to repolarize and follow the micropattern geometry, while a full MMP activity leads to a secondary track expansion by degrading the matrix structure. Finally, we confirm that cell movement within a subnuclear structure can be achieved either by pericellular proteolysis or by a significant deformation of cell nucleus.
Interface sharpness in the Potts model
Ruiz, J.
1989-01-01
A simple proof is given for the existence of a sharp interface between two ordered phases for the three-dimensional 2 double-prime-state Potts model (n integer). The results show that the roughening temperature of the three-dimensional Potts model is greater than the transition temperature of the two-dimensional Potts model. For a large arbitrary spin integer, it is expected that this roughening temperature is equal to the transition temperature (of the 3D model), i.e., that the interface between two ordered phases is harp up to the transition temperature, at which it is wetted by a film of the disordered phase. It is also expected that for a large arbitrary spin integer, the a-f interface (between an ordered and the disordered phase) is sharp at the transition temperature
Star-Triangle Relation of the Chiral Potts Model Revisited
Horibe, M.; Shigemoto, K.
2001-01-01
We give the simple proof of the star-triangle relation of the chiral Potts model. We also give the constructive way to understand the star-triangle relation of the chiral Potts model, which may give the hint to give the new integrable models.
Exchange algebra and exotic supersymmetry in the Chiral Potts model
Bernard, D.; Pasquier, V.
1989-01-01
We obtain an exchange algebra for the Chiral Potts model, the elements of which are linear in the parameters defining the rapidity curve. This enables us to connect the Chiral Potts model to a U q (GL(2)) algebra. On the other hand, looking at the model from the S-matrix point of view relates it to a Z N generalisation of the supersymmetric algebra
Ferromagnetic Potts models with multisite interaction
Schreiber, Nir; Cohen, Reuven; Haber, Simi
2018-03-01
We study the q -state Potts model with four-site interaction on a square lattice. Based on the asymptotic behavior of lattice animals, it is argued that when q ≤4 the system exhibits a second-order phase transition and when q >4 the transition is first order. The q =4 model is borderline. We find 1 /lnq to be an upper bound on Tc, the exact critical temperature. Using a low-temperature expansion, we show that 1 /(θ lnq ) , where θ >1 is a q -dependent geometrical term, is an improved upper bound on Tc. In fact, our findings support Tc=1 /(θ lnq ) . This expression is used to estimate the finite correlation length in first-order transition systems. These results can be extended to other lattices. Our theoretical predictions are confirmed numerically by an extensive study of the four-site interaction model using the Wang-Landau entropic sampling method for q =3 ,4 ,5 . In particular, the q =4 model shows an ambiguous finite-size pseudocritical behavior.
Non compact continuum limit of two coupled Potts models
Vernier, Éric; Jacobsen, Jesper Lykke; Saleur, Hubert
2014-01-01
We study two Q-state Potts models coupled by the product of their energy operators, in the regime 2 3 (2) vertex model. It corresponds to a selfdual system of two antiferromagnetic Potts models, coupled ferromagnetically. We derive the Bethe ansatz equations and study them numerically for two arbitrary twist angles. The continuum limit is shown to involve two compact bosons and one non compact boson, with discrete states emerging from the continuum at appropriate twists. The non compact boson entails strong logarithmic corrections to the finite-size behaviour of the scaling levels, an understanding of which allows us to correct an earlier proposal for some of the critical exponents. In particular, we infer the full set of magnetic scaling dimensions (watermelon operators) of the Potts model. (paper)
ZNxZN generalization of the chiral Potts model
Bazhanov, V.V.; Kashaev, R.M.; Mangazeev, V.V.
1990-01-01
It is shown that the R-matrix which interwines two 3-by-N 2 state cyclic L-operators can be considered as a Boltzmann weight of four-spin box for a lattice model with two-spin interaction juct as the R-matrix of the checkerboard chiral Potts model. The rapidity variables lie on the same algebraiz curve as in the chiral Potts model. Factorization properties of the L-operator and its connection to the SOS models, are also discussed. 13 refs.; 11 figs
Two-Dimensional Wetting Transition Modeling with the Potts Model
Lopes, Daisiane M.; Mombach, José C. M.
2017-12-01
A droplet of a liquid deposited on a surface structured in pillars may have two states of wetting: (1) Cassie-Baxter (CB), the liquid remains on top of the pillars, also known as heterogeneous wetting, or (2) Wenzel, the liquid fills completely the cavities of the surface, also known as homogeneous wetting. Studies show that between these two states, there is an energy barrier that, when overcome, results in the transition of states. The transition can be achieved by changes in geometry parameters of the surface, by vibrations of the surface or by evaporation of the liquid. In this paper, we present a comparison of two-dimensional simulations of the Cassie-Wenzel transition on pillar-structured surfaces using the cellular Potts model (CPM) with studies performed by Shahraz et al. In our work, we determine a transition diagram by varying the surface parameters such as the interpillar distance ( G) and the pillar height ( H). Our results were compared to those obtained by Shahraz et al. obtaining good agreement.
High-temperature series expansions for random Potts models
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.
Monte Carlo investigation of the one-dimensional Potts model
Karma, A.S.; Nolan, M.J.
1983-01-01
Monte Carlo results are presented for a variety of one-dimensional dynamical q-state Potts models. Our calculations confirm the expected universal value z = 2 for the dynamic scaling exponent. Our results also indicate that an increase in q at fixed correlation length drives the dynamics into the scaling regime
The Potts model and flows. 1. The pair correlation function
Essam, J.W.; Tsallis, C.
1985-01-01
It is shown that the partition function for the lambda-state Potts model with pair-interactions is related to the expected number of integer mod-lambda flows in a percolation model. The relation is generalised to the pair correlation function. The resulting high temperature expansion coefficients are shown to be the flow polynomials of graph theory. An observation of Tsallis and Levy concerning the equivalent transmissivity of a cluster is also proved. (Author) [pt
Mixing of the Glauber dynamics for the ferromagnetic Potts model
Bordewich, Magnus; Greenhill, Catherine; Patel, Viresh
2013-01-01
We present several results on the mixing time of the Glauber dynamics for sampling from the Gibbs distribution in the ferromagnetic Potts model. At a fixed temperature and interaction strength, we study the interplay between the maximum degree ($\\Delta$) of the underlying graph and the number of colours or spins ($q$) in determining whether the dynamics mixes rapidly or not. We find a lower bound $L$ on the number of colours such that Glauber dynamics is rapidly mixing if at least $L$ colours...
Complex zeros of the partition function of the Q-state Potts model
Ghulghazaryan, R.G.
2002-01-01
Using the dynamical systems theory, the Yang-Lee and Potts zeros of the one-dimensional Q-state Potts model are investigated for Q>0. It is shown that in the one-dimensional case the phase transition points on the complex plane may be found from the condition of existence of neutral fixed points. Densities of the Yang-Lee and Potts zeros and corresponding critical exponents are found. The Yang-Lee and Potts zeros are classified depending on the parameters of the model
Critical manifold of the kagome-lattice Potts model
Jacobsen, Jesper Lykke; Scullard, Christian R
2012-01-01
Any two-dimensional infinite regular lattice G can be produced by tiling the plane with a finite subgraph B⊆G; we call B a basis of G. We introduce a two-parameter graph polynomial P B (q, v) that depends on B and its embedding in G. The algebraic curve P B (q, v) = 0 is shown to provide an approximation to the critical manifold of the q-state Potts model, with coupling v = e K − 1, defined on G. This curve predicts the phase diagram not only in the physical ferromagnetic regime (v > 0), but also in the antiferromagnetic (v B (q, v) = 0 provides the exact critical manifold in the limit of infinite B. Furthermore, for some lattices G—or for the Ising model (q = 2) on any G—the polynomial P B (q, v) factorizes for any choice of B: the zero set of the recurrent factor then provides the exact critical manifold. In this sense, the computation of P B (q, v) can be used to detect exact solvability of the Potts model on G. We illustrate the method for two choices of G: the square lattice, where the Potts model has been exactly solved, and the kagome lattice, where it has not. For the square lattice we correctly reproduce the known phase diagram, including the antiferromagnetic transition and the singularities in the Berker–Kadanoff phase at certain Beraha numbers. For the kagome lattice, taking the smallest basis with six edges we recover a well-known (but now refuted) conjecture of F Y Wu. Larger bases provide successive improvements on this formula, giving a natural extension of Wu’s approach. We perform large-scale numerical computations for comparison and find excellent agreement with the polynomial predictions. For v > 0 the accuracy of the predicted critical coupling v c is of the order 10 −4 or 10 −5 for the six-edge basis, and improves to 10 −6 or 10 −7 for the largest basis studied (with 36 edges). This article is part of ‘Lattice models and integrability’, a special issue of Journal of Physics A: Mathematical and Theoretical in honour of
Effects of Connectivity Disorder on the Potts Model
Janke, W.; Weigel, M.
2003-01-01
The relevance of quenched, uncorrelated disorder coupling to the local energy density, its paradigm being the random-bond model, is judged by the Harris criterion. A generalization of the underlying argument to the case of spatially correlated disorder, exemplified by quasi-crystals, has been given by Luck. We address the question, whether a relevance criterion of this type is applicable to the case of spin models coupled to different kinds of random graphs. The geometrical fluctuation exponent appearing in Luck's criterion is precisely determined for the case of two-dimensional Poissonian Voronoi-Delaunay random lattices and planar, ''flat'' φ 3 Feynman diagrams. While previous work for the latter graphs is in accord with the determined relevance threshold, a preliminary analysis of the result of a Monte Carlo simulation of the three-states Pott model on Poissonian Voronoi Lattices presented here does not meet the expectation from the relevance criterion. (author)
Double Potts chain and exact results for some two-dimensional models
Yurishchev, M.A.
2000-11-01
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)
Partition function zeros of the one-dimensional Potts model: the recursive method
Ghulghazaryan, R G; Ananikian, N S
2003-01-01
The Yang-Lee, Fisher and Potts zeros of the one-dimensional Q-state Potts model are studied using the theory of dynamical systems. An exact recurrence relation for the partition function is derived. It is shown that zeros of the partition function may be associated with neutral fixed points of the recurrence relation. Further, a general equation for zeros of the partition function is found and a classification of the Yang-Lee, Fisher and Potts zeros is given. It is shown that the Fisher zeros in a nonzero magnetic field are located on several lines in the complex temperature plane and that the number of these lines depends on the value of the magnetic field. Analytical expressions for the densities of the Yang-Lee, Fisher and Potts zeros are derived. It is shown that densities of all types of zeros of the partition function are singular at the edge singularity points with the same critical exponent
Nonintersecting string model and graphical approach: equivalence with a Potts model
Perk, J.H.H.; Wu, F.Y.
1986-01-01
Using a graphical method the authors establish the exact equivalence of the partition function of a q-state nonintersecting string (NIS) model on an arbitrary planar, even-valenced lattice with that of a q 2 -state Potts model on a relaxed lattice. The NIS model considered in this paper is one in which the vertex weights are expressible as sums of those of basic vertex types, and the resulting Potts model generally has multispin interactions. For the square and Kagome lattices this leads to the equivalence of a staggered NIS model with Potts models with anisotropic pair interactions, indicating that these NIS models have a first-order transition for q greater than 2. For the triangular lattice the NIS model turns out to be the five-vertex model of Wu and Lin and it relates to a Potts model with two- and three-site interactions. The most general model the authors discuss is an oriented NIS model which contains the six-vertex model and the NIS models of Stroganov and Schultz as special cases
Ising and Potts models: binding disorder-and dimension effects
Curado, E.M.F.
1983-01-01
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) [pt
Optimal region of latching activity in an adaptive Potts model for networks of neurons
Abdollah-nia, Mohammad-Farshad; Saeedghalati, Mohammadkarim; Abbassian, Abdolhossein
2012-01-01
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
Potts Model in One-Dimension on Directed Small-World Networks
Aquino, Édio O.; Lima, F. W. S.; Araújo, Ascânio D.; Costa Filho, Raimundo N.
2018-06-01
The critical properties of the Potts model with q=3 and 8 states in one-dimension on directed small-world networks are investigated. This disordered system is simulated by updating it with the Monte Carlo heat bath algorithm. The Potts model on these directed small-world networks presents in fact a second-order phase transition with a new set of critical exponents for q=3 considering a rewiring probability p=0.1. For q=8 the system exhibits only a first-order phase transition independent of p.
Random matrix theory and higher genus integrability: the quantum chiral Potts model
Angles d'Auriac, J.Ch.; Maillard, J.M.; Viallet, C.M.
2002-01-01
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)
Potts Model with Invisible Colors : Random-Cluster Representation and Pirogov–Sinai Analysis
Enter, Aernout C.D. van; Iacobelli, Giulio; Taati, Siamak
We study a recently introduced variant of the ferromagnetic Potts model consisting of a ferromagnetic interaction among q “visible” colors along with the presence of r non-interacting “invisible” colors. We introduce a random-cluster representation for the model, for which we prove the existence of
Parallel family trees for transfer matrices in the Potts model
Navarro, Cristobal A.; Canfora, Fabrizio; Hitschfeld, Nancy; Navarro, Gonzalo
2015-02-01
The computational cost of transfer matrix methods for the Potts model is related to the question in how many ways can two layers of a lattice be connected? Answering the question leads to the generation of a combinatorial set of lattice configurations. This set defines the configuration space of the problem, and the smaller it is, the faster the transfer matrix can be computed. The configuration space of generic (q , v) transfer matrix methods for strips is in the order of the Catalan numbers, which grows asymptotically as O(4m) where m is the width of the strip. Other transfer matrix methods with a smaller configuration space indeed exist but they make assumptions on the temperature, number of spin states, or restrict the structure of the lattice. In this paper we propose a parallel algorithm that uses a sub-Catalan configuration space of O(3m) to build the generic (q , v) transfer matrix in a compressed form. The improvement is achieved by grouping the original set of Catalan configurations into a forest of family trees, in such a way that the solution to the problem is now computed by solving the root node of each family. As a result, the algorithm becomes exponentially faster than the Catalan approach while still highly parallel. The resulting matrix is stored in a compressed form using O(3m ×4m) of space, making numerical evaluation and decompression to be faster than evaluating the matrix in its O(4m ×4m) uncompressed form. Experimental results for different sizes of strip lattices show that the parallel family trees (PFT) strategy indeed runs exponentially faster than the Catalan Parallel Method (CPM), especially when dealing with dense transfer matrices. In terms of parallel performance, we report strong-scaling speedups of up to 5.7 × when running on an 8-core shared memory machine and 28 × for a 32-core cluster. The best balance of speedup and efficiency for the multi-core machine was achieved when using p = 4 processors, while for the cluster
Reducing a cortical network to a Potts model yields storage capacity estimates
Naim, Michelangelo; Boboeva, Vezha; Kang, Chol Jun; Treves, Alessandro
2018-04-01
An autoassociative network of Potts units, coupled via tensor connections, has been proposed and analysed as an effective model of an extensive cortical network with distinct short- and long-range synaptic connections, but it has not been clarified in what sense it can be regarded as an effective model. We draw here the correspondence between the two, which indicates the need to introduce a local feedback term in the reduced model, i.e. in the Potts network. An effective model allows the study of phase transitions. As an example, we study the storage capacity of the Potts network with this additional term, the local feedback w, which contributes to drive the activity of the network towards one of the stored patterns. The storage capacity calculation, performed using replica tools, is limited to fully connected networks, for which a Hamiltonian can be defined. To extend the results to the case of intermediate partial connectivity, we also derive the self-consistent signal-to-noise analysis for the Potts network; and finally we discuss the implications for semantic memory in humans.
Square-lattice random Potts model: criticality and pitchfork bifurcation
Costa, U.M.S.; Tsallis, C.
1983-01-01
Within a real space renormalization group framework based on self-dual clusters, the criticality of the quenched bond-mixed q-state Potts ferromagnet on square lattice is discussed. On qualitative grounds it is exhibited that the crossover from the pure fixed point to the random one occurs, while q increases, through a pitchfork bifurcation; the relationship with Harris criterion is analyzed. On quantitative grounds high precision numerical values are presented for the critical temperatures corresponding to various concentrations of the coupling constants J 1 and J 2 , and various ratios J 1 /J 2 . The pure, random and crossover critical exponents are discussed as well. (Author) [pt
Self-duality for coupled Potts models on the triangular lattice
Richard, Jean-Francois; Jacobsen, Jesper Lykke; Picco, Marco
2004-01-01
We present self-dual manifolds for coupled Potts models on the triangular lattice. We exploit two different techniques: duality followed by decimation, and mapping to a related loop model. The latter technique is found to be superior, and it allows us to include three-spin couplings. Starting from three coupled models, such couplings are necessary for generating self-dual solutions. A numerical study of the case of two coupled models leads to the identification of novel critical points
Variational approach for the N-state spin and gauge Potts model
Masperi, L.; Omero, C.
1981-05-01
A hamiltonian variational treatment is applied both to the spin Potts model and to its gauge version for any number of states N and spatial dimensions d>=2. Regarding the former we reproduce correct critical coupling and latent heat for not too low N and d. For the latter, our approach turns the gauge theory into an equivalent d-dimensional classical spin model, which evaluated for d+1=4 gives results in agreement with 1/N expansions. (author)
Critical dynamics of the Potts model: short-time Monte Carlo simulations
Silva, Roberto da; Drugowich de Felicio, J.R.
2004-01-01
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
Multiscale multifractal DCCA and complexity behaviors of return intervals for Potts price model
Wang, Jie; Wang, Jun; Stanley, H. Eugene
2018-02-01
To investigate the characteristics of extreme events in financial markets and the corresponding return intervals among these events, we use a Potts dynamic system to construct a random financial time series model of the attitudes of market traders. We use multiscale multifractal detrended cross-correlation analysis (MM-DCCA) and Lempel-Ziv complexity (LZC) perform numerical research of the return intervals for two significant China's stock market indices and for the proposed model. The new MM-DCCA method is based on the Hurst surface and provides more interpretable cross-correlations of the dynamic mechanism between different return interval series. We scale the LZC method with different exponents to illustrate the complexity of return intervals in different scales. Empirical studies indicate that the proposed return intervals from the Potts system and the real stock market indices hold similar statistical properties.
Uniqueness of Gibbs measure for Potts model with countable set of spin values
Ganikhodjaev, N.N.; Rozikov, U.A.
2004-11-01
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 {a i =1,2,...}, where a is an element of (0,1). (author)
Entropy-driven phase transition in low-temperature antiferromagnetic Potts models
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
Kinetic Monte Carlo Potts Model for Simulating a High Burnup Structure in UO2
Oh, Jae-Yong; Koo, Yang-Hyun; Lee, Byung-Ho
2008-01-01
A Potts model, based on the kinetic Monte Carlo method, was originally developed for magnetic domain evolutions, but it was also proposed as a model for a grain growth in polycrystals due to similarities between Potts domain structures and grain structures. It has modeled various microstructural phenomena such as grain growths, a recrystallization, a sintering, and so on. A high burnup structure (HBS) is observed in the periphery of a high burnup UO 2 fuel. Although its formation mechanism is not clearly understood yet, its characteristics are well recognized: The HBS microstructure consists of very small grains and large bubbles instead of original as-sintered grains. A threshold burnup for the HBS is observed at a local burnup 60-80 Gwd/tM, and the threshold temperature is 1000-1200 .deg. C. Concerning a energy stability, the HBS can be created if the system energy of the HBS is lower than that of the original structure in an irradiated UO 2 . In this paper, a Potts model was implemented for simulating the HBS by calculating system energies, and the simulation results were compared with the HBS characteristics mentioned above
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.
An explicit formula for the interface tension of the 2D Potts model
Borgs, Christian; Janke, Wolfhard
1992-11-01
We consider the exact correlation length calculations for the two-dimensional Potts model at the transition point β_t by Klümper, Schadschneider and Zittartz, and by Buffenoir and Wallon. We argue that the correlation length calculated by the latter authors is the correlation length in the disordered phase and then combine their result with duality and the assumption of complete wetting to give an explicit formula for the order-disorder interface tension σ_od of this model. The result is used to clarify a controversy stemming from different numerical simulations of σ_od.
C-periodicity and the physical mass in the 3-state Potts model
Gavai, R.V.; Polley, L.
1993-07-01
The standard infinite-volume definition of connected correlation function and particle mass in the 3-state Potts model can be implemented in Monte Carlo simulations by using C-periodic spatial boundary conditions. This avoids both the breaking of translation invariance (cold wall b.c.) and the phase-dependent and thus possible biased evaluation of data (periodic b.c.). The numerical feasibility of the standard definitions is demonstrated by sample computations on a 24 x 24 x 48 lattice. (author). 11 refs, 5 figs, 1 tab
The Potts models and flows. III, standard and subgraph break-collapse methods
Magalhaes, A.C.N. de; Essam, J.W.
1987-01-01
An algorithm is developed for the exact calculation of the many spin correlation functions of Potts model clusters which is more efficient than the standard break-collapse method traditionally used in real space renormalization group calculations. The improved performance is based on a relationship which, at any stage of the calculation, allows the replacement of certain subgraphs by single effective edges. Our method avoids, as in the standard one, the time consuming summation over spin states and can be very useful in series expansions and real space renormalisation group calculations on crystal lattices. (Author) [pt
Renormalization group study of the one-dimensional quantum Potts model
Solyom, J.; Pfeuty, P.
1981-01-01
The phase transition of the classical two-dimensional Potts model, in particular the order of the transition as the number of components q increases, is studied by constructing renormalization group transformations on the equivalent one-dimensional quatum problem. It is shown that the block transformation with two sites per cell indicates the existence of a critical qsub(c) separating the small q and large q regions with different critical behaviours. The physically accessible fixed point for q>qsub(c) is a discontinuity fixed point where the specific heat exponent α=1 and therefore the transition is of first order. (author)
Antonov, N V; Kapustin, A S
2012-01-01
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)
Simulation of High Burnup Structure in UO2 Using Potts Model
Oh, Jae Yong; Koo, Yang Hyun; Lee, Byung Ho
2009-01-01
The evolution of a high burnup structure (HBS) in a light water reactor (LWR) UO 2 fuel was simulated using the Potts model. A simulation system for the Potts model was defined as a two-dimensional triangular lattice, for which the stored energy was calculated from both the irradiation damage of the UO 2 matrix and the formation of a grain boundary in the newly recrystallized small HBS grains. In the simulation, the evolution probability of the HBS is calculated by the system energy difference between before and after the Monte Carlo simulation step. The simulated local threshold burnup for the HBS formation was 62 MWd/kgU, consistent with the observed threshold burnup range of 60-80 MWd/kgU. The simulation revealed that the HBS was heterogeneously nucleated on the intergranular bubbles in the proximity of the threshold burnup and then additionally on the intragranular bubbles for a burnup above 86 MWd/kgU. In addition, the simulation carried out under a condition of no bubbles indicated that the bubbles played an important role in lowering the threshold burnup for the HBS formation, thereby enabling the HBS to be observed in the burnup range of conventional high burnup fuels
The storage capacity of Potts models for semantic memory retrieval
Kropff, Emilio; Treves, Alessandro
2005-08-01
We introduce and analyse a minimal network model of semantic memory in the human brain. The model is a global associative memory structured as a collection of N local modules, each coding a feature, which can take S possible values, with a global sparseness a (the average fraction of features describing a concept). We show that, under optimal conditions, the number cM of modules connected on average to a module can range widely between very sparse connectivity (high dilution, c_{M}/N\\to 0 ) and full connectivity (c_{M}\\to N ), maintaining a global network storage capacity (the maximum number pc of stored and retrievable concepts) that scales like pc~cMS2/a, with logarithmic corrections consistent with the constraint that each synapse may store up to a fraction of a bit.
Yang-Lee zeros for a Potts model of helix-coil transition with nontrivial topology
Ananikian, N.; Ananikyan, L.; Artuso, R.; Sargsyan, K.
2007-07-01
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)
'Duality twisted'boundary conditions in n-state Potts Models
Schuetz, G.
1992-11-01
We discuss a new class of toroidal boundary conditions for one-dimensional quantum Hamiltonian with S n symmetry which are related to two-dimensional n-state Potts models in the extreme anisotropic Hamiltonian limit. At their self-dual point (a point were a second-order phase transition occurs for n=2,3,4) the duality transformation is shown to be an additional symmetry giving rise to a new class of 'duality twisted' toroidal boundary conditions. This corresponding Hamiltonians are given in terms of generators of the periodic Temprely-Lieb algebra with an odd number of generators. We discuss as an example the critical Ising model. Here the complete spectrum for the new boundary conditions can be obtained from a projection mechanism in the spin-1/2 XXZ Heisenberg chain. (author)
The spectrum of massive excitations of 3d 3-state Potts model and universality
Falcone, R.; Fiore, R.; Gravina, M.; Papa, A.
2007-01-01
We consider the mass spectrum of the 3d 3-state Potts model in the broken phase (a) near the second order Ising critical point in the temperature-magnetic field plane and (b) near the weakly first order transition point at zero magnetic field. In the case (a), we compare the mass spectrum with the prediction from universality of mass ratios in the 3d Ising class; in the case (b), we determine a mass ratio to be compared with the corresponding one in the spectrum of screening masses of the (3+1)d SU(3) pure gauge theory at finite temperature in the deconfined phase near the transition. The agreement in the comparison in the case (a) would represent a non-trivial test of validity of the conjecture of spectrum universality. A positive answer to the comparison in the case (b) would suggest the possibility to extend this conjecture to weakly first order phase transitions
Low-temperature expansions and correlation functions of the Z3-chiral Potts model
Han, N.S.; Honecker, A.
1993-04-01
Using perturbative methods we derive new results for the spectrum and correlation functions of the general Z 3 -chiral Potts quantum chain in the massive low-temperature phase. Explicit calculations of the ground state energy and the first excitations in the zero momentum sector give excellent approximations and confirm the general statement that the spectrum in the low-temperature phase of general Z n -spin quantum chains is identical to one in the high-temperature phase where the role of charge and boundary conditions are interchanged. Using a perturbative expansion of the ground state for the Z 3 model we are able to gain some insight in correlation functions. We argue that they might be oscillating and give estimates for the oscillation length as well as the correlation length. (orig.)
Applications of neural networks to the studies of phase transitions of two-dimensional Potts models
Li, C.-D.; Tan, D.-R.; Jiang, F.-J.
2018-04-01
We study the phase transitions of two-dimensional (2D) Q-states Potts models on the square lattice, using the first principles Monte Carlo (MC) simulations as well as the techniques of neural networks (NN). We demonstrate that the ideas from NN can be adopted to study these considered phase transitions efficiently. In particular, even with a simple NN constructed in this investigation, we are able to obtain the relevant information of the nature of these phase transitions, namely whether they are first order or second order. Our results strengthen the potential applicability of machine learning in studying various states of matters. Subtlety of applying NN techniques to investigate many-body systems is briefly discussed as well.
Random-field Potts model for the polar domains of lead magnesium niobate and lead scandium tantalate
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.
Cubic rare-earth compounds: variants of the three-state Potts model
Kim, D.; Levy, P.M.; Uffer, L.F.
1975-01-01
In appropriate cubic fields, rare-earth ions have sixfold degenerate ground states. When the angular momentum of the rare earth is large, the six levels are characterized by states that are directed along the cube edges. Within these states the angular momentum operators J/sub x/, J/sub y/, and J/sub z/ have particularly simple matrix representations. The projection of an isotropic pair coupling between the rare earths onto these sixfold degenerate states leads to an interaction Hamiltonian H = -I Σ/sub (ij)/ sigma/sub i/sigma/sub j/delta/sub l/sub i/sub l/sub j//, where sigma takes on the values +-1 and l the values x, y, and z. This interaction is a variant of the three-state Potts model. Magnetic and quadrupolar anisotropy field terms are added to the Hamiltonian and the symmetry properties of the phase diagram associated with this model are determined. For nonzero quadrupolar anisotropy fields, the model is shown to have the thermodynamic behavior of an Ising model. However, for zero fields a new symmetry appears and in the mean-field approximation the model has tricritical-like exponents. This simple model is able to account for the large specific-heat critical exponent α' = 1 / 2 which has been observed for holmium antimonide in zero external fields. To the extent that the mean-field approximation is an accurate guide, we predict there are many cubic rare-earth compounds which exhibit tricritical-like behavior in zero field. In addition, for pure quadrupole coupling between rare earths in the sixfold degenerate states, the interaction Hamiltonian is exactly the three-state Potts model. In the mean-field approximation this system has a first-order phase transition. However, a small quadrupolar anisotropy field is sufficient to drive the system to a wing critical point. The specific heat has a critical exponent of α = 2 / 3 or 1 depending on the path taken to approach this critical point. (auth)
Oh, Jae-Yong, E-mail: tylor@kaeri.re.kr [Korea Atomic Energy Research Institute, Daedeok-daero 1045, Yuseong, Daejeon 305-353 (Korea, Republic of); Koo, Yang-Hyun; Lee, Byung-Ho; Tahk, Young-Wook [Korea Atomic Energy Research Institute, Daedeok-daero 1045, Yuseong, Daejeon 305-353 (Korea, Republic of)
2011-07-15
This paper evaluated the effects of porosity on the effective thermal conductivity of UO{sub 2} fuel by combining the Potts model and the finite difference method (FDM). Two types of microstructures representing irradiated UO{sub 2} microstructures were simulated by the Potts model in the three dimensional cubic system. One represented very small intragranular bubbles and a few intergranular bubbles under a low temperature condition. The other represented large intergranular bubbles under a high temperature or annealing condition. For the simulated microstructures, the effective thermal conductivities were determined by FDM calculation of the temperature distributions under steady state condition. They were compared with an experimental equation and the effect of bubble morphology was investigated by fitting a porosity shape factor in the Maxwell-Eucken equation. The simulation results showed a good agreement with an experimental equation and demonstrated the capability of the Potts model to provide information on microstructure for calculating the effective thermal conductivity of UO{sub 2} fuel.
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.
Operator content of the critical Potts model in d dimensions and logarithmic correlations
Vasseur, Romain; Jacobsen, Jesper Lykke
2014-01-01
Using the symmetric group S Q symmetry of the Q-state Potts model, we classify the (scalar) operator content of its underlying field theory in arbitrary dimension. In addition to the usual identity, energy and magnetization operators, we find fields that generalize the N-cluster operators well-known in two dimensions, together with their subleading counterparts. We give the explicit form of all these operators – up to non-universal constants – both on the lattice and in the continuum limit for the Landau theory. We compute exactly their two- and three-point correlation functions on an arbitrary graph in terms of simple probabilities, and give the general form of these correlation functions in the continuum limit at the critical point. Specializing to integer values of the parameter Q, we argue that the analytic continuation of the S Q symmetry yields logarithmic correlations at the critical point in arbitrary dimension, thus implying a mixing of some scaling fields by the scale transformation generator. All these logarithmic correlation functions are given a clear geometrical meaning, which can be checked in numerical simulations. Several physical examples are discussed, including bond percolation, spanning trees and forests, resistor networks and the Ising model. We also briefly address the generalization of our approach to the O(n) model
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/.
Finite-size behaviour of generalized susceptibilities in the whole phase plane of the Potts model
Pan, Xue; Zhang, Yanhua; Chen, Lizhu; Xu, Mingmei; Wu, Yuanfang
2018-01-01
We study the sign distribution of generalized magnetic susceptibilities in the temperature-external magnetic field plane using the three-dimensional three-state Potts model. We find that the sign of odd-order susceptibility is opposite in the symmetric (disorder) and broken (order) phases, but that of the even-order one remains positive when it is far away from the phase boundary. When the critical point is approached from the crossover side, negative fourth-order magnetic susceptibility is observable. It is also demonstrated that non-monotonic behavior occurs in the temperature dependence of the generalized susceptibilities of the energy. The finite-size scaling behavior of the specific heat in this model is mainly controlled by the critical exponent of the magnetic susceptibility in the three-dimensional Ising universality class. Supported by Fund Project of National Natural Science Foundation of China (11647093, 11405088, 11521064), Fund Project of Sichuan Provincial Department of Education (16ZB0339), Fund Project of Chengdu Technological University (2016RC004) and the Major State Basic Research Development Program of China (2014CB845402)
The covariance matrix of the Potts model: A random cluster analysis
Borgs, C.; Chayes, J.T.
1996-01-01
We consider the covariance matrix, G mn = q 2 x ,m); δ(σ y ,n)>, of the d-dimensional q-states Potts model, rewriting it in the random cluster representation of Fortuin and Kasteleyn. In many of the q ordered phases, we identify the eigenvalues of this matrix both in terms of representations of the unbroken symmetry group of the model and in terms of random cluster connectivities and covariances, thereby attributing algebraic significance to these stochastic geometric quantities. We also show that the correlation length and the correlation length corresponding to the decay rate of one on the eigenvalues in the same as the inverse decay rate of the diameter of finite clusters. For dimension of d=2, we show that this correlation length and the correlation length of two-point function with free boundary conditions at the corresponding dual temperature are equal up to a factor of two. For systems with first-order transitions, this relation helps to resolve certain inconsistencies between recent exact and numerical work on correlation lengths at the self-dual point β o . For systems with second order transitions, this relation implies the equality of the correlation length exponents from above below threshold, as well as an amplitude ratio of two. In the course of proving the above results, we establish several properties of independent interest, including left continuity of the inverse correlation length with free boundary conditions and upper semicontinuity of the decay rate for finite clusters in all dimensions, and left continuity of the two-dimensional free boundary condition percolation probability at β o . We also introduce DLR equations for the random cluster model and use them to establish ergodicity of the free measure. In order to prove these results, we introduce a new class of events which we call decoupling events and two inequalities for these events
Jacobsen, J L; Saleur, H
2008-02-29
We determine exactly the probability distribution of the number N_(c) of valence bonds connecting a subsystem of length L>1 to the rest of the system in the ground state of the XXX antiferromagnetic spin chain. This provides, in particular, the asymptotic behavior of the valence-bond entanglement entropy S_(VB)=N_(c)ln2=4ln2/pi(2)lnL disproving a recent conjecture that this should be related with the von Neumann entropy, and thus equal to 1/3lnL. Our results generalize to the Q-state Potts model.
Degenerate ground states and multiple bifurcations in a two-dimensional q-state quantum Potts model.
Dai, Yan-Wei; Cho, Sam Young; Batchelor, Murray T; Zhou, Huan-Qiang
2014-06-01
We numerically investigate the two-dimensional q-state quantum Potts model on the infinite square lattice by using the infinite projected entangled-pair state (iPEPS) algorithm. We show that the quantum fidelity, defined as an overlap measurement between an arbitrary reference state and the iPEPS ground state of the system, can detect q-fold degenerate ground states for the Z_{q} broken-symmetry phase. Accordingly, a multiple bifurcation of the quantum ground-state fidelity is shown to occur as the transverse magnetic field varies from the symmetry phase to the broken-symmetry phase, which means that a multiple-bifurcation point corresponds to a critical point. A (dis)continuous behavior of quantum fidelity at phase transition points characterizes a (dis)continuous phase transition. Similar to the characteristic behavior of the quantum fidelity, the magnetizations, as order parameters, obtained from the degenerate ground states exhibit multiple bifurcation at critical points. Each order parameter is also explicitly demonstrated to transform under the Z_{q} subgroup of the symmetry group of the Hamiltonian. We find that the q-state quantum Potts model on the square lattice undergoes a discontinuous (first-order) phase transition for q=3 and q=4 and a continuous phase transition for q=2 (the two-dimensional quantum transverse Ising model).
Excited state TBA and renormalized TCSA in the scaling Potts model
Lencsés, M.; Takács, G.
2014-09-01
We consider the field theory describing the scaling limit of the Potts quantum spin chain using a combination of two approaches. The first is the renormalized truncated conformal space approach (TCSA), while the second one is a new thermodynamic Bethe Ansatz (TBA) system for the excited state spectrum in finite volume. For the TCSA we investigate and clarify several aspects of the renormalization procedure and counter term construction. The TBA system is first verified by comparing its ultraviolet limit to conformal field theory and the infrared limit to exact S matrix predictions. We then show that the TBA and the renormalized TCSA match each other to a very high precision for a large range of the volume parameter, providing both a further verification of the TBA system and a demonstration of the efficiency of the TCSA renormalization procedure. We also discuss the lessons learned from our results concerning recent developments regarding the low-energy scattering of quasi-particles in the quantum Potts spin chain.
On P-Adic Quasi Gibbs Measures for Q + 1-State Potts Model on the Cayley Tree
Mukhamedov, Farrukh
2010-06-01
In the present paper we introduce a new class of p-adic measures, associated with q +1-state Potts model, called p-adic quasi Gibbs measure, which is totally different from the p-adic Gibbs measure. We establish the existence p-adic quasi Gibbs measures for the model on a Cayley tree. If q is divisible by p, then we prove the occurrence of a strong phase transition. If q and p are relatively prime, then there is a quasi phase transition. These results are totally different from the results of [F.M.Mukhamedov, U.A. Rozikov, Indag. Math. N.S. 15(2005) 85-100], since q is divisible by p, which means that q + 1 is not divided by p, so according to a main result of the mentioned paper, there is a unique and bounded p-adic Gibbs measure (different from p-adic quasi Gibbs measure). (author)
Monte Carlo simulation of the three-state vector Potts model on a three-dimensional random lattice
Jianbo Zhang; Heping Ying
1991-09-01
We have performed a numerical simulation of the three-state vector Potts model on a three-dimensional random lattice. The averages of energy density, magnetization, specific heat and susceptibility of the system in the N 3 (N=8,10,12) lattices were calculated. The results show that a first order nature of the Z(3) symmetry breaking transition appears, as characterized by a thermal hysterisis in the energy density as well as an abrupt drop of magnetization being sharper and discontinuous with increasing of volume in the cross-over region. The results obtained on the random lattice were consistent with those obtained on the three-dimensional cubic lattice. (author). 12 refs, 4 figs
Matthäus, Franziska; Pahle, Jürgen
2017-01-01
This contributed volume comprises research articles and reviews on topics connected to the mathematical modeling of cellular systems. These contributions cover signaling pathways, stochastic effects, cell motility and mechanics, pattern formation processes, as well as multi-scale approaches. All authors attended the workshop on "Modeling Cellular Systems" which took place in Heidelberg in October 2014. The target audience primarily comprises researchers and experts in the field, but the book may also be beneficial for graduate students.
Multi-particle structure in the Zn-chiral Potts models
Gehlen, G. von; Honecker, A.
1992-10-01
We calculate the lowest translationally invariant levels of the Z 3 - and Z 4 -symmetrical chiral Potts quantum chains, using numerical diagonalization of the hamiltonian for N≤12 and N≤10 sites, respectively, and extrapolating N→∞. In the high-temperature massive phase we find that the pattern of the low-lying zero momentum levels can be explained assuming the existence of n-1 particles carrying Z n -charges Q=1, ..., n-1 (mass m Q ), and their scattering states. In the superintegrable case the masses of the n-1 particles become proportional to their respective charges: m Q =Qm 1 . Exponential convergence in N is observed for the single particle gaps, while power convergence is seen for the scattering levels. We also verify that qualitatively the same pattern appears for the self-dual and integrable cases. For general Z n we show that the energy-momentum relations of the particles show a parity non-conservation asymmetry which for very high temperatures is exclusive due to the presence of a macroscopic momentum P m =(1-2Q/n)Φ, where Φ is the chiral angle and Q is the Z n -charge of the respective particle. (orig.)
On the critical frontiers of Potts ferromagnets
Magalhaes, A.C.N. de; Tsallis, C.
1981-01-01
A conjecture concerning the critical frontiers of q- state Potts ferromagnets on d- dimensional lattices (d > 1) which generalize a recent one stated for planar lattices is formulated. The present conjecture is verified within satisfactory accuracy (exactly in some cases) for all the lattices or arrays whose critical points are known. Its use leads to the prediction of: a) a considerable amount of new approximate critical points (26 on non-planar regular lattices, some others on Husimi trees and cacti); b) approximate critical frontiers for some 3- dimensional lattices; c) the possibly asymptotically exact critical point on regular lattices in the limit d→infinite for all q>=1; d) the possibly exact critical frontier for the pure Potts model on fully anisotropic Bethe lattices; e) the possibly exact critical frontier for the general quenched random-bond Potts ferromagnet (any P(J)) on isotropic Bethe lattices. (Author) [pt
Praveen, E., E-mail: svmstaya@gmail.com; Satyanarayana, S. V. M., E-mail: svmstaya@gmail.com [Department of Physics, Pondicherry University, Puducherry-605014 (India)
2014-04-24
Traditional definition of phase transition involves an infinitely large system in thermodynamic limit. Finite systems such as biological proteins exhibit cooperative behavior similar to phase transitions. We employ recently discovered analysis of inflection points of microcanonical entropy to estimate the transition temperature of the phase transition in q state Potts model on a finite two dimensional square lattice for q=3 (second order) and q=8 (first order). The difference of energy density of states (DOS) Δ ln g(E) = ln g(E+ ΔE) −ln g(E) exhibits a point of inflexion at a value corresponding to inverse transition temperature. This feature is common to systems exhibiting both first as well as second order transitions. While the difference of DOS registers a monotonic variation around the point of inflexion for systems exhibiting second order transition, it has an S-shape with a minimum and maximum around the point of inflexion for the case of first order transition.
Praveen, E.; Satyanarayana, S. V. M.
2014-01-01
Traditional definition of phase transition involves an infinitely large system in thermodynamic limit. Finite systems such as biological proteins exhibit cooperative behavior similar to phase transitions. We employ recently discovered analysis of inflection points of microcanonical entropy to estimate the transition temperature of the phase transition in q state Potts model on a finite two dimensional square lattice for q=3 (second order) and q=8 (first order). The difference of energy density of states (DOS) Δ ln g(E) = ln g(E+ ΔE) −ln g(E) exhibits a point of inflexion at a value corresponding to inverse transition temperature. This feature is common to systems exhibiting both first as well as second order transitions. While the difference of DOS registers a monotonic variation around the point of inflexion for systems exhibiting second order transition, it has an S-shape with a minimum and maximum around the point of inflexion for the case of first order transition
Anon.
1982-01-01
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
On the τ(2)-model in the chiral Potts model and cyclic representation of the quantum group Uq(sl2)
Roan Shishyr
2009-01-01
We identify the precise relationship between the five-parameter τ (2) -family in the N-state chiral Potts model and XXZ chains with U q (sl 2 )-cyclic representation. By studying the Yang-Baxter relation of the six-vertex model, we discover a one-parameter family of L-operators in terms of the quantum group U q (sl 2 ). When N is odd, the N-state τ (2) -model can be regarded as the XXZ chain of U q (sl 2 ) cyclic representations with q N =1. The symmetry algebra of the τ (2) -model is described by the quantum affine algebra U q (sl 2 -hat) via the canonical representation. In general, for an arbitrary N, we show that the XXZ chain with a U q (sl 2 )-cyclic representation for q 2N = 1 is equivalent to two copies of the same N-state τ (2) -model. (fast track communication)
Bayesian Image Segmentations by Potts Prior and Loopy Belief Propagation
Tanaka, Kazuyuki; Kataoka, Shun; Yasuda, Muneki; Waizumi, Yuji; Hsu, Chiou-Ting
2014-12-01
This paper presents a Bayesian image segmentation model based on Potts prior and loopy belief propagation. The proposed Bayesian model involves several terms, including the pairwise interactions of Potts models, and the average vectors and covariant matrices of Gauss distributions in color image modeling. These terms are often referred to as hyperparameters in statistical machine learning theory. In order to determine these hyperparameters, we propose a new scheme for hyperparameter estimation based on conditional maximization of entropy in the Potts prior. The algorithm is given based on loopy belief propagation. In addition, we compare our conditional maximum entropy framework with the conventional maximum likelihood framework, and also clarify how the first order phase transitions in loopy belief propagations for Potts models influence our hyperparameter estimation procedures.
Hierarchy of the low-lying excitations for the (2+1-dimensional q=3 Potts model in the ordered phase
Yoshihiro Nishiyama
2017-03-01
Full Text Available The (2+1-dimensional q=3 Potts model was simulated with the exact diagonalization method. In the ordered phase, the elementary excitations (magnons are attractive, forming a series of bound states in the low-energy spectrum. We investigate the low-lying spectrum through a dynamical susceptibility, which is readily tractable with the exact diagonalization method via the continued-fraction expansion. As a result, we estimate the series of (scaled mass gaps, m2,3,4/m1 (m1: single-magnon mass, in proximity to the transition point.
Cosserat modeling of cellular solids
Onck, P.R.
Cellular solids inherit their macroscopic mechanical properties directly from the cellular microstructure. However, the characteristic material length scale is often not small compared to macroscopic dimensions, which limits the applicability of classical continuum-type constitutive models. Cosserat
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)
Andrade, Pedro H.A. de; Cabral, Manuela O.M.; Lima, Fernando R. De A.
2015-01-01
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)
Bedini, Andrea; Jacobsen, Jesper Lykke
2010-01-01
Combining tree decomposition and transfer matrix techniques provides a very general algorithm for computing exact partition functions of statistical models defined on arbitrary graphs. The algorithm is particularly efficient in the case of planar graphs. We illustrate it by computing the Potts model partition functions and chromatic polynomials (the number of proper vertex colourings using Q colours) for large samples of random planar graphs with up to N = 100 vertices. In the latter case, our algorithm yields a sub-exponential average running time of ∼ exp(1.516√N), a substantial improvement over the exponential running time ∼exp (0.245N) provided by the hitherto best-known algorithm. We study the statistics of chromatic roots of random planar graphs in some detail, comparing the findings with results for finite pieces of a regular lattice.
Ahmad, Mohd Ali Khameini; Liao, Lingmin; Saburov, Mansoor
2018-06-01
We study the set of p-adic Gibbs measures of the q-state Potts model on the Cayley tree of order three. We prove the vastness of the set of the periodic p-adic Gibbs measures for such model by showing the chaotic behavior of the corresponding Potts-Bethe mapping over Q_p for the prime numbers p≡1 (mod 3). In fact, for 0< |θ -1|_p< |q|_p^2 < 1 where θ =\\exp _p(J) and J is a coupling constant, there exists a subsystem that is isometrically conjugate to the full shift on three symbols. Meanwhile, for 0< |q|_p^2 ≤ |θ -1|_p< |q|_p < 1, there exists a subsystem that is isometrically conjugate to a subshift of finite type on r symbols where r ≥ 4. However, these subshifts on r symbols are all topologically conjugate to the full shift on three symbols. The p-adic Gibbs measures of the same model for the prime numbers p=2,3 and the corresponding Potts-Bethe mapping are also discussed. On the other hand, for 0< |θ -1|_p< |q|_p < 1, we remark that the Potts-Bethe mapping is not chaotic when p=3 and p≡ 2 (mod 3) and we could not conclude the vastness of the set of the periodic p-adic Gibbs measures. In a forthcoming paper with the same title, we will treat the case 0< |q|_p ≤ |θ -1|_p < 1 for all prime numbers p.
Bauer, Bela; Troyer, Matthias; Gull, Emanuel; Trebst, Simon; Huse, David A
2010-01-01
The numerical simulation of strongly first-order phase transitions has remained a notoriously difficult problem even for classical systems due to the exponentially suppressed (thermal) equilibration in the vicinity of such a transition. In the absence of efficient update techniques, a common approach for improving equilibration in Monte Carlo simulations is broadening the sampled statistical ensemble beyond the bimodal distribution of the canonical ensemble. Here we show how a recently developed feedback algorithm can systematically optimize such broad-histogram ensembles and significantly speed up equilibration in comparison with other extended ensemble techniques such as flat-histogram, multicanonical and Wang–Landau sampling. We simulate, as a prototypical example of a strong first-order transition, the two-dimensional Potts model with up to Q = 250 different states in large systems. The optimized histogram develops a distinct multi-peak structure, thereby resolving entropic barriers and their associated phase transitions in the phase coexistence region—such as droplet nucleation and annihilation, and droplet–strip transitions for systems with periodic boundary conditions. We characterize the efficiency of the optimized histogram sampling by measuring round-trip times τ(N, Q) across the phase transition for samples comprised of N spins. While we find power-law scaling of τ versus N for small Q∼ 2 , we observe a crossover to exponential scaling for larger Q. These results demonstrate that despite the ensemble optimization, broad-histogram simulations cannot fully eliminate the supercritical slowing down at strongly first-order transitions
The potts chain in a random field: an exact solution
Riera, R.; Chaves, C.M.G.F.; Santos, Raimundo R. dos.
1984-01-01
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) [pt
Nonlinear complexity behaviors of agent-based 3D Potts financial dynamics with random environments
Xing, Yani; Wang, Jun
2018-02-01
A new microscopic 3D Potts interaction financial price model is established in this work, to investigate the nonlinear complexity behaviors of stock markets. 3D Potts model, which extends the 2D Potts model to three-dimensional, is a cubic lattice model to explain the interaction behavior among the agents. In order to explore the complexity of real financial markets and the 3D Potts financial model, a new random coarse-grained Lempel-Ziv complexity is proposed to certain series, such as the price returns, the price volatilities, and the random time d-returns. Then the composite multiscale entropy (CMSE) method is applied to the intrinsic mode functions (IMFs) and the corresponding shuffled data to study the complexity behaviors. The empirical results indicate that the 3D financial model is feasible.
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.
Bauer, Bela; Gull, Emanuel; Trebst, Simon; Troyer, Matthias; Huse, David A.
2010-01-01
The numerical simulation of strongly first-order phase transitions has remained a notoriously difficult problem even for classical systems due to the exponentially suppressed (thermal) equilibration in the vicinity of such a transition. In the absence of efficient update techniques, a common approach for improving equilibration in Monte Carlo simulations is broadening the sampled statistical ensemble beyond the bimodal distribution of the canonical ensemble. Here we show how a recently developed feedback algorithm can systematically optimize such broad-histogram ensembles and significantly speed up equilibration in comparison with other extended ensemble techniques such as flat-histogram, multicanonical and Wang-Landau sampling. We simulate, as a prototypical example of a strong first-order transition, the two-dimensional Potts model with up to Q = 250 different states in large systems. The optimized histogram develops a distinct multi-peak structure, thereby resolving entropic barriers and their associated phase transitions in the phase coexistence region—such as droplet nucleation and annihilation, and droplet-strip transitions for systems with periodic boundary conditions. We characterize the efficiency of the optimized histogram sampling by measuring round-trip times τ(N, Q) across the phase transition for samples comprised of N spins. While we find power-law scaling of τ versus N for small Q \\lesssim 50 and N \\lesssim 40^2 , we observe a crossover to exponential scaling for larger Q. These results demonstrate that despite the ensemble optimization, broad-histogram simulations cannot fully eliminate the supercritical slowing down at strongly first-order transitions.
Pott's Spine with Bilateral Psoas Abscesses
Masavkar, Sanjeevani; Shanbag, Preeti; Inamdar, Prithi
2012-01-01
A high degree of suspicion and appropriate imaging studies are required for the early diagnosis of Pott's spine. We describe a 4-year-old boy with Pott's disease of the lumbar spine with bilateral psoas abscesses. The child responded to conservative treatment with antituberculous treatment and ultrasonographically guided percutaneous drainage of the abscesses.
Computerized tomography in atypical Pott's disease
Cabrera, M.N.B.; Wang, E.H.M.
1993-01-01
Classical Pott's disease is described as a two-vertebrae disease with the destruction of the intervening invertebral disc. Computerized tomography has been used in the differential diagnosis of spine infections and neoplasms. We reviewed CT scans of patients seen at the Philippine General Hospital over a two-year period with atypical presentations of atypical tuberculous spondylitis. We used the computerized tomography findings described as characteristic of classical Pott's disease as criteria in evaluating the CT scans of patients diagnosed to have Atypical Pott's Disease. Although the number of patients prevented sensitivity and specificity studies to be done, our results strongly suggest that the same CT criteria used to diagnose Classical Pott's Disease may also be used to diagnose Pott's disease in its atypical form. (Author.). 13 refs
Influence of lattice defects on criticality of Potts ferromagnet
Souza Costa, U.M. de.
1985-01-01
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)
Strange attractor in the Potts spin glass on hierarchical lattices
Lima, Washington de [Universidade Federal de Pernambuco, Centro Acadêmico do Agreste, Pernambuco (Brazil); Camelo-Neto, G. [Universidade Federal de Alagoas, Núcleo de Ciências Exatas, Laboratório de Física Teórica e Computacional, CEP 57309-005 Arapiraca, Alagoas (Brazil); Coutinho, S., E-mail: sergio@ufpe.br [Universidade Federal de Pernambuco, Departamento de Física, Laboratório de Física Teórica e Computacional, Cidade Universitária, CEP 50670-901 Recife, Pernambuco (Brazil)
2013-11-29
The spin-glass q-state Potts model on d-dimensional diamond hierarchical lattices is investigated by an exact real space renormalization group scheme. Above a critical dimension d{sub l}(q) for q>2, the coupling constants probability distribution flows to a low-temperature strange attractor or to the high-temperature paramagnetic fixed point, according to the temperature is below or above the critical temperature T{sub c}(q,d). The strange attractor was investigated considering four initial different distributions for q=3 and d=5 presenting strong robustness in shape and temperature interval suggesting a condensed phase with algebraic decay.
Potts disease: Diagnosis with magnetic resonance imaging
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.
Potts disease: Diagnosis with magnetic resonance imaging
Pursey, Jacqueline; Stewart, Sharon
2010-01-01
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.
A cellular automata model for ant trails
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 ...
Overview of cellular automaton models for corrosion
Perez-Brokate, Cristian Felipe; De Lamare, Jacques; Dung di Caprio; Feron, Damien; Chausse, Annie
2014-01-01
A review of corrosion process modeling using cellular automata methods is presented. This relatively new and growing approach takes into account the stochastic nature of the phenomena and uses physico-chemical rules to make predictions at a mesoscopic scale. Milestone models are analyzed and perspectives are established. (authors)
Cellular modeling of fault-tolerant multicomputers
Morgan, G
1987-01-01
Work described was concerned with a novel method for investigation of fault tolerance in large regular networks of computers. Motivation was to provide a technique useful in rapid evaluation of highly reliable systems that exploit the low cost and ease of volume production of simple microcomputer components. First, a system model and simulator based upon cellular automata are developed. This model is characterized by its simplicity and ease of modification when adapting to new types of network. Second, in order to test and verify the predictive capabilities of the cellular system, a more-detailed simulation is performed based upon an existing computational model, that of the Transputer. An example application is used to exercise various systems designed using the cellular model. Using this simulator, experimental results are obtained both for existing well-understood configurations and for more novel types also developed here. In all cases it was found that the cellular model and simulator successfully predicted the ranking in reliability improvement of the systems studied.
Fuzzy cellular automata models in immunology
Ahmed, E.
1996-01-01
The self-nonself character of antigens is considered to be fuzzy. The Chowdhury et al. cellular automata model is generalized accordingly. New steady states are found. The first corresponds to a below-normal help and suppression and is proposed to be related to autoimmune diseases. The second corresponds to a below-normal B-cell level
Dilute Potts chain in a magnetic field
Chaves, C.M.; Riera, R.
1983-03-01
The Potts lattice gas in presence of a uniform magnetic field is solved exactly in one dimension. For negative values of the exchange parameter, the magnetization curve exhibits two or three steps, depending on the concentration of vacancies. These steps arise as a result of the competition between the exchange interaction and the magnetic field, being associated to different structural distribution of vacancies and to the magnetic ordering of one or both sublattices. (Author) [pt
Discrete dynamic modeling of cellular signaling networks.
Albert, Réka; Wang, Rui-Sheng
2009-01-01
Understanding signal transduction in cellular systems is a central issue in systems biology. Numerous experiments from different laboratories generate an abundance of individual components and causal interactions mediating environmental and developmental signals. However, for many signal transduction systems there is insufficient information on the overall structure and the molecular mechanisms involved in the signaling network. Moreover, lack of kinetic and temporal information makes it difficult to construct quantitative models of signal transduction pathways. Discrete dynamic modeling, combined with network analysis, provides an effective way to integrate fragmentary knowledge of regulatory interactions into a predictive mathematical model which is able to describe the time evolution of the system without the requirement for kinetic parameters. This chapter introduces the fundamental concepts of discrete dynamic modeling, particularly focusing on Boolean dynamic models. We describe this method step-by-step in the context of cellular signaling networks. Several variants of Boolean dynamic models including threshold Boolean networks and piecewise linear systems are also covered, followed by two examples of successful application of discrete dynamic modeling in cell biology.
A Mathematical Model for Cisplatin Cellular Pharmacodynamics
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 and statistical mechanical models
Rujan, P.
1987-01-01
The authors elaborate on the analogy between the transfer matrix of usual lattice models and the master equation describing the time development of cellular automata. Transient and stationary properties of probabilistic automata are linked to surface and bulk properties, respectively, of restricted statistical mechanical systems. It is demonstrated that methods of statistical physics can be successfully used to describe the dynamic and the stationary behavior of such automata. Some exact results are derived, including duality transformations, exact mappings, disorder, and linear solutions. Many examples are worked out in detail to demonstrate how to use statistical physics in order to construct cellular automata with desired properties. This approach is considered to be a first step toward the design of fully parallel, probabilistic systems whose computational abilities rely on the cooperative behavior of their components
A cellular automata model of bone formation.
Van Scoy, Gabrielle K; George, Estee L; Opoku Asantewaa, Flora; Kerns, Lucy; Saunders, Marnie M; Prieto-Langarica, Alicia
2017-04-01
Bone remodeling is an elegantly orchestrated process by which osteocytes, osteoblasts and osteoclasts function as a syncytium to maintain or modify bone. On the microscopic level, bone consists of cells that create, destroy and monitor the bone matrix. These cells interact in a coordinated manner to maintain a tightly regulated homeostasis. It is this regulation that is responsible for the observed increase in bone gain in the dominant arm of a tennis player and the observed increase in bone loss associated with spaceflight and osteoporosis. The manner in which these cells interact to bring about a change in bone quality and quantity has yet to be fully elucidated. But efforts to understand the multicellular complexity can ultimately lead to eradication of metabolic bone diseases such as osteoporosis and improved implant longevity. Experimentally validated mathematical models that simulate functional activity and offer eventual predictive capabilities offer tremendous potential in understanding multicellular bone remodeling. Here we undertake the initial challenge to develop a mathematical model of bone formation validated with in vitro data obtained from osteoblastic bone cells induced to mineralize and quantified at 26 days of culture. A cellular automata model was constructed to simulate the in vitro characterization. Permutation tests were performed to compare the distribution of the mineralization in the cultures and the distribution of the mineralization in the mathematical models. The results of the permutation test show the distribution of mineralization from the characterization and mathematical model come from the same probability distribution, therefore validating the cellular automata model. Copyright © 2017 Elsevier Inc. All rights reserved.
Potts glass reflection of the decoding threshold for qudit quantum error correcting codes
Jiang, Yi; Kovalev, Alexey A.; Pryadko, Leonid P.
We map the maximum likelihood decoding threshold for qudit quantum error correcting codes to the multicritical point in generalized Potts gauge glass models, extending the map constructed previously for qubit codes. An n-qudit quantum LDPC code, where a qudit can be involved in up to m stabilizer generators, corresponds to a ℤd Potts model with n interaction terms which can couple up to m spins each. We analyze general properties of the phase diagram of the constructed model, give several bounds on the location of the transitions, bounds on the energy density of extended defects (non-local analogs of domain walls), and discuss the correlation functions which can be used to distinguish different phases in the original and the dual models. This research was supported in part by the Grants: NSF PHY-1415600 (AAK), NSF PHY-1416578 (LPP), and ARO W911NF-14-1-0272 (LPP).
A generalized cellular automata approach to modeling first order ...
system, consisting of space, time and state, structured with simple local rules without ... Sensitivity analysis of a stochastic cellular automata model. 413 ..... Baetens J M and De Baets B 2011 Design and parameterization of a stochastic cellular.
Retropharyngeal cold abscess without Pott's spine | Singh | South ...
Retropharyngeal cold abscess without Pott's spine. ... pyogenic osteomyelitis, tube‚rculosis of the spine, or external injuries caused by endoscopes ... in an adult woman without tuberculosis of the cervical spine who was managed surgically by ...
Modeling cellular effects of coal pollutants
Anon.
1981-01-01
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
Surface effects in the Potts ferromagnet
Tsallis, C.; Sarmento, E.F.
1984-01-01
Within a real space renormalisation group framework, the phase diagram of a semi-infinite cubic-lattice q-state Potts ferromagnet is studied, in which the free surface coupling constant J sub(S) = (1+Δ)J sub(B) might be different from the bulk one J sub(B). The starting value Δ sub(c) (q) is calculated above which surface order is possible even if bulk order is absent. Our results can be alternatively seen as approximate for the simple cubic lattice (as a matter of fact, the Ising value Δ sub(c) (2) obtained approaches the series result better than any other theory known consequently Δ sub(c) (q) is expected to be quite satisfactory even for q not= 2) or as exact for a well defined diamond-like hierarchical lattice. In the q →0 limit, Δ sub(c) diverges as 1/√q. (Author) [pt
Pott's disease: a case of Mycobacterium xenopi infection of the spine.
Alfreijat, Majd; Ononiwu, Chiagozie; Sexton, Carlton
2012-01-01
Pott's disease is an infection of the spine with Mycobacterium tuberculosis that causes destruction of the spine elements resulting in progressive kyphosis. We are describing a rare case of Pott's disease where Mycobacterium xenopi was the inculpated organism.
Extended Cellular Automata Models of Particles and Space-Time
Beedle, Michael
2005-04-01
Models of particles and space-time are explored through simulations and theoretical models that use Extended Cellular Automata models. The expanded Cellular Automata Models consist go beyond simple scalar binary cell-fields, into discrete multi-level group representations like S0(2), SU(2), SU(3), SPIN(3,1). The propagation and evolution of these expanded cellular automatas are then compared to quantum field theories based on the "harmonic paradigm" i.e. built by an infinite number of harmonic oscillators, and with gravitational models.
Cellular-automata supercomputers for fluid-dynamics modeling
Margolus, N.; Toffoli, T.; Vichniac, G.
1986-01-01
We report recent developments in the modeling of fluid dynamics, and give experimental results (including dynamical exponents) obtained using cellular automata machines. Because of their locality and uniformity, cellular automata lend themselves to an extremely efficient physical realization; with a suitable architecture, an amount of hardware resources comparable to that of a home computer can achieve (in the simulation of cellular automata) the performance of a conventional supercomputer
Katira, Parag; Bonnecaze, Roger T; Zaman, Muhammad H
2013-01-01
Malignant transformation, though primarily driven by genetic mutations in cells, is also accompanied by specific changes in cellular and extra-cellular mechanical properties such as stiffness and adhesivity. As the transformed cells grow into tumors, they interact with their surroundings via physical contacts and the application of forces. These forces can lead to changes in the mechanical regulation of cell fate based on the mechanical properties of the cells and their surrounding environment. A comprehensive understanding of cancer progression requires the study of how specific changes in mechanical properties influences collective cell behavior during tumor growth and metastasis. Here we review some key results from computational models describing the effect of changes in cellular and extra-cellular mechanical properties and identify mechanistic pathways for cancer progression that can be targeted for the prediction, treatment, and prevention of cancer.
Dynamic behavior of cellular materials and cellular structures: Experiments and modeling
Gao, Ziyang
Cellular solids, including cellular materials and cellular structures (CMS), have attracted people's great interests because of their low densities and novel physical, mechanical, thermal, electrical and acoustic properties. They offer potential for lightweight structures, energy absorption, thermal management, etc. Therefore, the studies of cellular solids have become one of the hottest research fields nowadays. From energy absorption point of view, any plastically deformed structures can be divided into two types (called type I and type II), and the basic cells of the CMS may take the configurations of these two types of structures. Accordingly, separated discussions are presented in this thesis. First, a modified 1-D model is proposed and numerically solved for a typical type II structure. Good agreement is achieved with the previous experimental data, hence is used to simulate the dynamic behavior of a type II chain. Resulted from different load speeds, interesting collapse modes are observed, and the parameters which govern the cell's post-collapse behavior are identified through a comprehensive non-dimensional analysis on general cellular chains. Secondly, the MHS specimens are chosen as an example of type I foam materials because of their good uniformity of the cell geometry. An extensive experimental study was carried out, where more attention was paid to their responses to dynamic loadings. Great enhancement of the stress-strain curve was observed in dynamic cases, and the energy absorption capacity is found to be several times higher than that of the commercial metal foams. Based on the experimental study, finite elemental simulations and theoretical modeling are also conducted, achieving good agreements and demonstrating the validities of those models. It is believed that the experimental, numerical and analytical results obtained in the present study will certainly deepen the understanding of the unsolved fundamental issues on the mechanical behavior of
Modeling and Analysis of Cellular CDMA Forward Channel
Tighe, Jan
2001-01-01
In this thesis, we develop the forward channel model for a DS-CDMA cellular system operating in a slow-flat Rayleigh fading and log normal shadowing environment, which incorporates the extended Hata...
A generalized cellular automata approach to modeling first order ...
... inhibitors deforming the allosteric site or inhibitors changing the structure of active ... Cell-based models with discrete state variables, such as Cellular Automata ... capture the essential features of a discrete real system, consisting of space, ...
PASSENGER TRAFFIC MOVEMENT MODELLING BY THE CELLULAR-AUTOMAT APPROACH
T. Mikhaylovskaya
2009-01-01
Full Text Available The mathematical model of passenger traffic movement developed on the basis of the cellular-automat approach is considered. The program realization of the cellular-automat model of pedastrians streams movement in pedestrian subways at presence of obstacles, at subway structure narrowing is presented. The optimum distances between the obstacles and the angle of subway structure narrowing providing pedastrians stream safe movement and traffic congestion occurance are determined.
Risser, L.; Vincent, T.; Ciuciu, P.; Risser, L.; Idier, J.; Risser, L.; Forbes, F.
2011-01-01
In this paper, we propose a fast numerical scheme to estimate Partition Functions (PF) of symmetric Potts fields. Our strategy is first validated on 2D two-color Potts fields and then on 3D two- and three-color Potts fields. It is then applied to the joint detection-estimation of brain activity from functional Magnetic Resonance Imaging (fMRI) data, where the goal is to automatically recover activated, deactivated and inactivated brain regions and to estimate region dependent hemodynamic filters. For any brain region, a specific 3D Potts field indeed embodies the spatial correlation over the hidden states of the voxels by modeling whether they are activated, deactivated or inactive. To make spatial regularization adaptive, the PFs of the Potts fields over all brain regions are computed prior to the brain activity estimation. Our approach is first based upon a classical path-sampling method to approximate a small subset of reference PFs corresponding to pre-specified regions. Then, we propose an extrapolation method that allows us to approximate the PFs associated to the Potts fields defined over the remaining brain regions. In comparison with preexisting methods either based on a path sampling strategy or mean-field approximations, our contribution strongly alleviates the computational cost and makes spatially adaptive regularization of whole brain fMRI datasets feasible. It is also robust against grid inhomogeneities and efficient irrespective of the topological configurations of the brain regions. (authors)
Giovanni Dalmasso
Full Text Available Mitochondria are semi-autonomous organelles that supply energy for cellular biochemistry through oxidative phosphorylation. Within a cell, hundreds of mobile mitochondria undergo fusion and fission events to form a dynamic network. These morphological and mobility dynamics are essential for maintaining mitochondrial functional homeostasis, and alterations both impact and reflect cellular stress states. Mitochondrial homeostasis is further dependent on production (biogenesis and the removal of damaged mitochondria by selective autophagy (mitophagy. While mitochondrial function, dynamics, biogenesis and mitophagy are highly-integrated processes, it is not fully understood how systemic control in the cell is established to maintain homeostasis, or respond to bioenergetic demands. Here we used agent-based modeling (ABM to integrate molecular and imaging knowledge sets, and simulate population dynamics of mitochondria and their response to environmental energy demand. Using high-dimensional parameter searches we integrated experimentally-measured rates of mitochondrial biogenesis and mitophagy, and using sensitivity analysis we identified parameter influences on population homeostasis. By studying the dynamics of cellular subpopulations with distinct mitochondrial masses, our approach uncovered system properties of mitochondrial populations: (1 mitochondrial fusion and fission activities rapidly establish mitochondrial sub-population homeostasis, and total cellular levels of mitochondria alter fusion and fission activities and subpopulation distributions; (2 restricting the directionality of mitochondrial mobility does not alter morphology subpopulation distributions, but increases network transmission dynamics; and (3 maintaining mitochondrial mass homeostasis and responding to bioenergetic stress requires the integration of mitochondrial dynamics with the cellular bioenergetic state. Finally, (4 our model suggests sources of, and stress conditions
Computational model of cellular metabolic dynamics
Li, Yanjun; Solomon, Thomas; Haus, Jacob M
2010-01-01
of the 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......: intracellular metabolite concentrations and patterns of glucose disposal. Model variations were simulated to investigate three alternative mechanisms to explain insulin enhancements: Model 1 (M.1), simple mass action; M.2, insulin-mediated activation of key metabolic enzymes (i.e., hexokinase, glycogen synthase......, by application of mechanism M.3, the model predicts metabolite concentration changes and glucose partitioning patterns consistent with experimental data. The reaction rate fluxes quantified by this detailed model of insulin/glucose metabolism provide information that can be used to evaluate the development...
Equilibrium state of the mean-field Potts glass
Janiš, Václav; Klíč, Antonín
2011-01-01
Roč. 23, č. 2 (2011), s. 1-5 ISSN 0953-8984 Institutional research plan: CEZ:AV0Z10100520 Keywords : Potts glass * replica-symmetry breaking * asymptotic expansion Subject RIV: BE - Theoretical Physics Impact factor: 2.546, year: 2011 http://iopscience.iop.org/0953-8984/23/2/022204/
Exact results on the one-dimensional Potts lattice gas
Riera, R.; Chaves, C.M.G.F.
1982-12-01
An exact calculation of the Potts Lattice Gas in one dimension is presented. Close to T=O 0 K, the uniform susceptibility presents an essencial singularity, when the excharge parameter is positive, and a power law behaviour with critical exponent γ=1, when this parameter is negative. (Author) [pt
Dynamical quantum phase transitions in the quantum Potts chain
Karrasch, C.; Schuricht, D.|info:eu-repo/dai/nl/369284690
2017-01-01
We analyze the dynamics of the return amplitude following a sudden quench in the three-state quantum Potts chain. For quenches crossing the quantum critical point from the paramagnetic to the ferromagnetic phase, the corresponding rate function is non-analytic at critical times and behaves linearly
Exact results on the one-dimensional Potts lattice gas
Riera, R.; Chaves, C.M.G.F.
1983-01-01
An exact calculation of the Potts Lattice Gas in one dimension is presented. Close to T=O 0 K, the uniform susceptibility presents an essential singularity, when the exchange parameter is positive, and a power law behaviour with critical exponent γ=1, when this parameter is negative. (Author) [pt
A cellular automata model for ant trails
In this study, the unidirectional ant traffic flow with U-turn in an ant trail was inves- tigated using ... the literature, it was considered in the model that (i) ant colony consists of two kinds of ants, good- ... ponents without a central controller [8].
Fire and Heat Spreading Model Based on Cellular Automata Theory
Samartsev, A. A.; Rezchikov, A. F.; Kushnikov, V. A.; Ivashchenko, V. A.; Bogomolov, A. S.; Filimonyuk, L. Yu; Dolinina, O. N.; Kushnikov, O. V.; Shulga, T. E.; Tverdokhlebov, V. A.; Fominykh, D. S.
2018-05-01
The distinctive feature of the proposed fire and heat spreading model in premises is the reduction of the computational complexity due to the use of the theory of cellular automata with probability rules of behavior. The possibilities and prospects of using this model in practice are noted. The proposed model has a simple mechanism of integration with agent-based evacuation models. The joint use of these models could improve floor plans and reduce the time of evacuation from premises during fires.
Modeling integrated cellular machinery using hybrid Petri-Boolean networks.
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
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
Bezzi, M.
2001-01-01
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
Xu, Kaixuan, E-mail: kaixuanxubjtu@yeah.net; Wang, Jun
2017-02-26
In this paper, recently introduced permutation entropy and sample entropy are further developed to the fractional cases, weighted fractional permutation entropy (WFPE) and fractional sample entropy (FSE). The fractional order generalization of information entropy is utilized in the above two complexity approaches, to detect the statistical characteristics of fractional order information in complex systems. The effectiveness analysis of proposed methods on the synthetic data and the real-world data reveals that tuning the fractional order allows a high sensitivity and more accurate characterization to the signal evolution, which is useful in describing the dynamics of complex systems. Moreover, the numerical research on nonlinear complexity behaviors is compared between the returns series of Potts financial model and the actual stock markets. And the empirical results confirm the feasibility of the proposed model. - Highlights: • Two new entropy approaches for estimation of nonlinear complexity are proposed for the financial market. • Effectiveness analysis of proposed methods is presented and their respective features are studied. • Empirical research of proposed analysis on seven world financial market indices. • Numerical simulation of Potts financial dynamics is preformed for nonlinear complexity behaviors.
Xu, Kaixuan; Wang, Jun
2017-01-01
In this paper, recently introduced permutation entropy and sample entropy are further developed to the fractional cases, weighted fractional permutation entropy (WFPE) and fractional sample entropy (FSE). The fractional order generalization of information entropy is utilized in the above two complexity approaches, to detect the statistical characteristics of fractional order information in complex systems. The effectiveness analysis of proposed methods on the synthetic data and the real-world data reveals that tuning the fractional order allows a high sensitivity and more accurate characterization to the signal evolution, which is useful in describing the dynamics of complex systems. Moreover, the numerical research on nonlinear complexity behaviors is compared between the returns series of Potts financial model and the actual stock markets. And the empirical results confirm the feasibility of the proposed model. - Highlights: • Two new entropy approaches for estimation of nonlinear complexity are proposed for the financial market. • Effectiveness analysis of proposed methods is presented and their respective features are studied. • Empirical research of proposed analysis on seven world financial market indices. • Numerical simulation of Potts financial dynamics is preformed for nonlinear complexity behaviors.
Empirical study on entropy models of cellular manufacturing systems
Zhifeng Zhang; Renbin Xiao
2009-01-01
From the theoretical point of view,the states of manufacturing resources can be monitored and assessed through the amount of information needed to describe their technological structure and operational state.The amount of information needed to describe cellular manufacturing systems is investigated by two measures:the structural entropy and the operational entropy.Based on the Shannon entropy,the models of the structural entropy and the operational entropy of cellular manufacturing systems are developed,and the cognizance of the states of manufacturing resources is also illustrated.Scheduling is introduced to measure the entropy models of cellular manufacturing systems,and the feasible concepts of maximum schedule horizon and schedule adherence are advanced to quantitatively evaluate the effectiveness of schedules.Finally,an example is used to demonstrate the validity of the proposed methodology.
Station Model for Rail Transit System Using Cellular Automata
Xun Jing; Ning Bin; Li Keping
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. (general)
The adaptive cruise control vehicles in the cellular automata model
Jiang Rui; Wu Qingsong
2006-01-01
This Letter presented a cellular automata model where the adaptive cruise control vehicles are modelled. In this model, the constant time headway policy is adopted. The fundamental diagram is presented. The simulation results are in good agreement with the analytical ones. The mixture of ACC vehicles with manually driven vehicles is investigated. It is shown that with the introduction of ACC vehicles, the jam can be suppressed
Modeling cellular networks in fading environments with dominant specular components
Alammouri, Ahmad; Elsawy, Hesham; Salem, Ahmed Sultan; Di Renzo, Marco; Alouini, Mohamed-Slim
2016-01-01
to the Nakagami-m fading in some special cases. However, neither the Rayleigh nor the Nakagami-m accounts for dominant specular components (DSCs) which may appear in realistic fading channels. In this paper, we present a tractable model for cellular networks
Radio Channel Modelling for UAV Communication over Cellular Networks
Amorim, Rafhael Medeiros de; Nguyen, Huan Cong; Mogensen, Preben Elgaard
2017-01-01
The main goal of this paper is to obtain models for path loss exponents and shadowing for the radio channel between airborne Unmanned Aerial Vehicles (UAVs) and cellular networks. In this pursuit, field measurements were conducted in live LTE networks at the 800 MHz frequency band, using a commer...
Complex Automata: Multi-scale Modeling with Coupled Cellular Automata
Hoekstra, A.G.; Caiazzo, A.; Lorenz, E.; Falcone, J.-L.; Chopard, B.; Hoekstra, A.G.; Kroc, J.; Sloot, P.M.A.
2010-01-01
Cellular Automata (CA) are generally acknowledged to be a powerful way to describe and model natural phenomena [1-3]. There are even tempting claims that nature itself is one big (quantum) information processing system, e.g. [4], and that CA may actually be nature’s way to do this processing [5-7].
Radiative corrections to the quark masses in the ferromagnetic Ising and Potts field theories
Sergei B. Rutkevich
2017-10-01
Full Text Available We consider the Ising Field Theory (IFT, and the 3-state Potts Field Theory (PFT, which describe the scaling limits of the two-dimensional lattice q-state Potts model with q=2, and q=3, respectively. At zero magnetic field h=0, both field theories are integrable away from the critical point, have q degenerate vacua in the ferromagnetic phase, and q(q−1 particles of the same mass – the kinks interpolating between two different vacua. Application of a weak magnetic field induces confinement of kinks into bound states – the “mesons” (for q=2,3 consisting predominantly of two kinks, and “baryons” (for q=3, which are essentially the three-kink excitations. The kinks in the confinement regime are also called “the quarks”. We review and refine the Form Factor Perturbation Theory (FFPT, adapting it to the analysis of the confinement problem in the limit of small h, and apply it to calculate the corrections to the kink (quark masses induced by the multi-kink fluctuations caused by the weak magnetic field. It is shown that the subleading third-order ∼h3 correction to the kink mass vanishes in the IFT. The leading second order ∼h2 correction to the kink mass in the 3-state PFT is estimated by truncation the infinite form factor expansion at the first term representing contribution of the two-kink fluctuations into the kink self-energy.
Radiative corrections to the quark masses in the ferromagnetic Ising and Potts field theories
Rutkevich, Sergei B.
2017-10-01
We consider the Ising Field Theory (IFT), and the 3-state Potts Field Theory (PFT), which describe the scaling limits of the two-dimensional lattice q-state Potts model with q = 2, and q = 3, respectively. At zero magnetic field h = 0, both field theories are integrable away from the critical point, have q degenerate vacua in the ferromagnetic phase, and q (q - 1) particles of the same mass - the kinks interpolating between two different vacua. Application of a weak magnetic field induces confinement of kinks into bound states - the "mesons" (for q = 2 , 3) consisting predominantly of two kinks, and "baryons" (for q = 3), which are essentially the three-kink excitations. The kinks in the confinement regime are also called "the quarks". We review and refine the Form Factor Perturbation Theory (FFPT), adapting it to the analysis of the confinement problem in the limit of small h, and apply it to calculate the corrections to the kink (quark) masses induced by the multi-kink fluctuations caused by the weak magnetic field. It is shown that the subleading third-order ∼h3 correction to the kink mass vanishes in the IFT. The leading second order ∼h2 correction to the kink mass in the 3-state PFT is estimated by truncation the infinite form factor expansion at the first term representing contribution of the two-kink fluctuations into the kink self-energy.
Simple method to calculate percolation, Ising and Potts clusters
Tsallis, C.
1981-01-01
A procedure ('break-collapse method') is introduced which considerably simplifies the calculation of two - or multirooted clusters like those commonly appearing in real space renormalization group (RG) treatments of bond-percolation, and pure and random Ising and Potts problems. The method is illustrated through two applications for the q-state Potts ferromagnet. The first of them concerns a RG calculation of the critical exponent ν for the isotropic square lattice: numerical consistence is obtained (particularly for q→0) with den Nijs conjecture. The second application is a compact reformulation of the standard star-triangle and duality transformations which provide the exact critical temperature for the anisotropic triangular and honeycomb lattices. (Author) [pt
[Pott's puffy tumor: a rare complication of frontal sinusitis].
Aínsa Laguna, D; Pons Morales, S; Muñoz Tormo-Figueres, A; Vega Senra, M I; Otero Reigada, M C
2014-05-01
Pott's puffy tumor is a rare complication of frontal sinusitis characterized by swelling and edema in the brow due to a subperiosteal abscess associated with frontal osteomyelitis. Added complications are cellulitis by extension to the orbit and intracranial infection by posterior extension, with high risk of meningitis, intracranial abscess, and venous sinus thrombosis. Early diagnosis and aggressive medical or surgical treatment are essential for optimal recovery of affected patients. In the antibiotic age it is extremely rare, with very few cases described in the recent literature. A case is presented of a Pott inflammatory tumor in a 7 year-old boy, as a complication of acute pansinusitis who presented with front preseptal swelling and intracranial involvement with thrombosis of ophthalmic and superior orbital veins and frontal epidural abscess extending to the subarachnoid space. Copyright © 2013 Asociación Española de Pediatría. Published by Elsevier Espana. All rights reserved.
Anisotropic square lattice Potts ferromagnet: renormalization group treatment
Oliveira, P.M.C. de; Tsallis, C.
1981-01-01
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 - [pt
Pott's Puffy Tumor Arising from Frontal Sinusitis
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.
A Markov Process Inspired Cellular Automata Model of Road Traffic
Wang, Fa; Li, Li; Hu, Jianming; Ji, Yan; Yao, Danya; Zhang, Yi; Jin, Xuexiang; Su, Yuelong; Wei, Zheng
2008-01-01
To provide a more accurate description of the driving behaviors in vehicle queues, a namely Markov-Gap cellular automata model is proposed in this paper. It views the variation of the gap between two consequent vehicles as a Markov process whose stationary distribution corresponds to the observed distribution of practical gaps. The multiformity of this Markov process provides the model enough flexibility to describe various driving behaviors. Two examples are given to show how to specialize i...
Modeling cellular networks in fading environments with dominant specular components
AlAmmouri, Ahmad
2016-07-26
Stochastic geometry (SG) has been widely accepted as a fundamental tool for modeling and analyzing cellular networks. However, the fading models used with SG analysis are mainly confined to the simplistic Rayleigh fading, which is extended to the Nakagami-m fading in some special cases. However, neither the Rayleigh nor the Nakagami-m accounts for dominant specular components (DSCs) which may appear in realistic fading channels. In this paper, we present a tractable model for cellular networks with generalized two-ray (GTR) fading channel. The GTR fading explicitly accounts for two DSCs in addition to the diffuse components and offers high flexibility to capture diverse fading channels that appear in realistic outdoor/indoor wireless communication scenarios. It also encompasses the famous Rayleigh and Rician fading as special cases. To this end, the prominent effect of DSCs is highlighted in terms of average spectral efficiency. © 2016 IEEE.
Car Deceleration Considering Its Own Velocity in Cellular Automata Model
Li Keping
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 the field measure than that of NaSch model.
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.
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.
Computer Modeling of the Earliest Cellular Structures and Functions
Pohorille, Andrew; Chipot, Christophe; Schweighofer, Karl
2000-01-01
In the absence of extinct or extant record of protocells (the earliest ancestors of contemporary cells). the most direct way to test our understanding 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 proto-cellular 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 membranestructures at water-membrane interfaces and insert into membranes, (b) how these peptides aggregate to form membrane-spanning structures (eg. channels), and (c) by what mechanisms such aggregates perform essential proto-cellular 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 item in the system are solved iteratively. The problems of interest required simulations on multi-nanosecond time scales, which corresponded to 10(exp 6)-10(exp 8) time steps.
Survival into seventh decade after a potts palliation for tetralogy of Fallot
Oosterhof, Thomas; Jacobs, Monique; Cramer, Maarten-Jan; Mulder, Barbara J. M.
2007-01-01
In this case report we present a 62-year-old patient with unrepaired tetralogy of Fallot who underwent a Potts shunt for palliation. Survival into late adulthood of patients with unoperated tetralogy of Fallot is rare. This patient is currently in New York Heart Association (NYHA) class II. A Potts
Pott's disease: a case of Mycobacterium xenopi infection of the spine
Majd Alfreijat
2013-01-01
Full Text Available Pott's disease is an infection of the spine with Mycobacterium tuberculosis that causes destruction of the spine elements resulting in progressive kyphosis. We are describing a rare case of Pott's disease where Mycobacterium xenopi was the inculpated organism.
Unified Stochastic Geometry Model for MIMO Cellular Networks with Retransmissions
Afify, Laila H.
2016-10-11
This paper presents a unified mathematical paradigm, based on stochastic geometry, for downlink cellular networks with multiple-input-multiple-output (MIMO) base stations (BSs). The developed paradigm accounts for signal retransmission upon decoding errors, in which the temporal correlation among the signal-to-interference-plus-noise-ratio (SINR) of the original and retransmitted signals is captured. In addition to modeling the effect of retransmission on the network performance, the developed mathematical model presents twofold analysis unification for MIMO cellular networks literature. First, it integrates the tangible decoding error probability and the abstracted (i.e., modulation scheme and receiver type agnostic) outage probability analysis, which are largely disjoint in the literature. Second, it unifies the analysis for different MIMO configurations. The unified MIMO analysis is achieved by abstracting unnecessary information conveyed within the interfering signals by Gaussian signaling approximation along with an equivalent SISO representation for the per-data stream SINR in MIMO cellular networks. We show that the proposed unification simplifies the analysis without sacrificing the model accuracy. To this end, we discuss the diversity-multiplexing tradeoff imposed by different MIMO schemes and shed light on the diversity loss due to the temporal correlation among the SINRs of the original and retransmitted signals. Finally, several design insights are highlighted.
Unified Stochastic Geometry Model for MIMO Cellular Networks with Retransmissions
Afify, Laila H.; Elsawy, Hesham; Al-Naffouri, Tareq Y.; Alouini, Mohamed-Slim
2016-01-01
This paper presents a unified mathematical paradigm, based on stochastic geometry, for downlink cellular networks with multiple-input-multiple-output (MIMO) base stations (BSs). The developed paradigm accounts for signal retransmission upon decoding errors, in which the temporal correlation among the signal-to-interference-plus-noise-ratio (SINR) of the original and retransmitted signals is captured. In addition to modeling the effect of retransmission on the network performance, the developed mathematical model presents twofold analysis unification for MIMO cellular networks literature. First, it integrates the tangible decoding error probability and the abstracted (i.e., modulation scheme and receiver type agnostic) outage probability analysis, which are largely disjoint in the literature. Second, it unifies the analysis for different MIMO configurations. The unified MIMO analysis is achieved by abstracting unnecessary information conveyed within the interfering signals by Gaussian signaling approximation along with an equivalent SISO representation for the per-data stream SINR in MIMO cellular networks. We show that the proposed unification simplifies the analysis without sacrificing the model accuracy. To this end, we discuss the diversity-multiplexing tradeoff imposed by different MIMO schemes and shed light on the diversity loss due to the temporal correlation among the SINRs of the original and retransmitted signals. Finally, several design insights are highlighted.
Potts ferromagnet correlation length in hypercubic lattices: Renormalization - group approach
Curado, E.M.F.; Hauser, P.R.
1984-01-01
Through a real space renormalization group approach, the q-state Potts ferromagnet correlation length on hierarchical lattices is calculated. These hierarchical lattices are build in order to simulate hypercubic lattices. The high-and-low temperature correlation length asymptotic behaviours tend (in the Ising case) to the Bravais lattice correlation length ones when the size of the hierarchical lattice cells tends to infinity. It is conjectured that the asymptotic behaviours several values of q and d (dimensionality) so obtained are correct. Numerical results are obtained for the full temperature range of the correlation length. (Author) [pt
A Fluid Model for Performance Analysis in Cellular Networks
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.
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.
Integrating Cellular Metabolism into a Multiscale Whole-Body Model
Krauss, Markus; Schaller, Stephan; Borchers, Steffen; Findeisen, Rolf; Lippert, Jörg; Kuepfer, Lars
2012-01-01
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. PMID:23133351
A Cellular Automata Model of Infection Control on Medical Implants
Prieto-Langarica, Alicia; Kojouharov, Hristo; Chen-Charpentier, Benito; Tang, Liping
2011-01-01
S. epidermidis infections on medically implanted devices are a common problem in modern medicine due to the abundance of the bacteria. Once inside the body, S. epidermidis gather in communities called biofilms and can become extremely hard to eradicate, causing the patient serious complications. We simulate the complex S. epidermidis-Neutrophils interactions in order to determine the optimum conditions for the immune system to be able to contain the infection and avoid implant rejection. Our cellular automata model can also be used as a tool for determining the optimal amount of antibiotics for combating biofilm formation on medical implants. PMID:23543851
[Reparative and neoplastic spheroid cellular structures and their mathematical model].
Kogan, E A; Namiot, V A; Demura, T A; Faĭzullina, N M; Sukhikh, G T
2014-01-01
Spheroid cell structures in the cell cultures have been described and are used for studying cell-cell and cell- matrix interactions. At the same time, spheroid cell structure participation in the repair and development of cancer in vivo remains unexplored. The aim of this study was to investigate the cellular composition of spherical structures and their functional significance in the repair of squamous epithelium in human papilloma virus-associated cervical pathology--chronic cervicitis and cervical intraepithelial neoplasia 1-3 degree, and also construct a mathematical model to explain the development and behavior of such spheroid cell structure.
Simulation of root forms using cellular automata model
Winarno, Nanang; Prima, Eka Cahya; Afifah, Ratih Mega Ayu
2016-01-01
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
Sordaria macrospora, a model organism to study fungal cellular development.
Engh, Ines; Nowrousian, Minou; Kück, Ulrich
2010-12-01
During the development of multicellular eukaryotes, the processes of cellular growth and organogenesis are tightly coordinated. Since the 1940s, filamentous fungi have served as genetic model organisms to decipher basic mechanisms underlying eukaryotic cell differentiation. Here, we focus on Sordaria macrospora, a homothallic ascomycete and important model organism for developmental biology. During its sexual life cycle, S. macrospora forms three-dimensional fruiting bodies, a complex process involving the formation of different cell types. S. macrospora can be used for genetic, biochemical and cellular experimental approaches since diverse tools, including fluorescence microscopy, a marker recycling system and gene libraries, are available. Moreover, the genome of S. macrospora has been sequenced and allows functional genomics analyses. Over the past years, our group has generated and analysed a number of developmental mutants which has greatly enhanced our fundamental understanding about fungal morphogenesis. In addition, our recent research activities have established a link between developmental proteins and conserved signalling cascades, ultimately leading to a regulatory network controlling differentiation processes in a eukaryotic model organism. This review summarizes the results of our recent findings, thus advancing current knowledge of the general principles and paradigms underpinning eukaryotic cell differentiation and development. Copyright © 2010 Elsevier GmbH. All rights reserved.
Simulation of root forms using cellular automata model
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.
Cellular automaton model of coupled mass transport and chemical reactions
Karapiperis, T.
1994-01-01
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
Acanthamoeba and Dictyostelium as Cellular Models for Legionella Infection
Swart, A. Leoni; Harrison, Christopher F.; Eichinger, Ludwig; Steinert, Michael; Hilbi, Hubert
2018-01-01
Environmental bacteria of the genus Legionella naturally parasitize free-living amoebae. Upon inhalation of bacteria-laden aerosols, the opportunistic pathogens grow intracellularly in alveolar macrophages and can cause a life-threatening pneumonia termed Legionnaires' disease. Intracellular replication in amoebae and macrophages takes place in a unique membrane-bound compartment, the Legionella-containing vacuole (LCV). LCV formation requires the bacterial Icm/Dot type IV secretion system, which translocates literally hundreds of “effector” proteins into host cells, where they modulate crucial cellular processes for the pathogen's benefit. The mechanism of LCV formation appears to be evolutionarily conserved, and therefore, amoebae are not only ecologically significant niches for Legionella spp., but also useful cellular models for eukaryotic phagocytes. In particular, Acanthamoeba castellanii and Dictyostelium discoideum emerged over the last years as versatile and powerful models. Using genetic, biochemical and cell biological approaches, molecular interactions between amoebae and Legionella pneumophila have recently been investigated in detail with a focus on the role of phosphoinositide lipids, small and large GTPases, autophagy components and the retromer complex, as well as on bacterial effectors targeting these host factors. PMID:29552544
Acanthamoeba and Dictyostelium as Cellular Models for Legionella Infection
A. Leoni Swart
2018-03-01
Full Text Available Environmental bacteria of the genus Legionella naturally parasitize free-living amoebae. Upon inhalation of bacteria-laden aerosols, the opportunistic pathogens grow intracellularly in alveolar macrophages and can cause a life-threatening pneumonia termed Legionnaires' disease. Intracellular replication in amoebae and macrophages takes place in a unique membrane-bound compartment, the Legionella-containing vacuole (LCV. LCV formation requires the bacterial Icm/Dot type IV secretion system, which translocates literally hundreds of “effector” proteins into host cells, where they modulate crucial cellular processes for the pathogen's benefit. The mechanism of LCV formation appears to be evolutionarily conserved, and therefore, amoebae are not only ecologically significant niches for Legionella spp., but also useful cellular models for eukaryotic phagocytes. In particular, Acanthamoeba castellanii and Dictyostelium discoideum emerged over the last years as versatile and powerful models. Using genetic, biochemical and cell biological approaches, molecular interactions between amoebae and Legionella pneumophila have recently been investigated in detail with a focus on the role of phosphoinositide lipids, small and large GTPases, autophagy components and the retromer complex, as well as on bacterial effectors targeting these host factors.
Calibrating cellular automaton models for pedestrians walking through corners
Dias, Charitha; Lovreglio, Ruggiero
2018-05-01
Cellular Automata (CA) based pedestrian simulation models have gained remarkable popularity as they are simpler and easier to implement compared to other microscopic modeling approaches. However, incorporating traditional floor field representations in CA models to simulate pedestrian corner navigation behavior could result in unrealistic behaviors. Even though several previous studies have attempted to enhance CA models to realistically simulate pedestrian maneuvers around bends, such modifications have not been calibrated or validated against empirical data. In this study, two static floor field (SFF) representations, namely 'discrete representation' and 'continuous representation', are calibrated for CA-models to represent pedestrians' walking behavior around 90° bends. Trajectory data collected through a controlled experiment are used to calibrate these model representations. Calibration results indicate that although both floor field representations can represent pedestrians' corner navigation behavior, the 'continuous' representation fits the data better. Output of this study could be beneficial for enhancing the reliability of existing CA-based models by representing pedestrians' corner navigation behaviors more realistically.
A dynamic cellular vertex model of growing epithelial tissues
Lin, Shao-Zhen; Li, Bo; Feng, Xi-Qiao
2017-04-01
Intercellular interactions play a significant role in a wide range of biological functions and processes at both the cellular and tissue scales, for example, embryogenesis, organogenesis, and cancer invasion. In this paper, a dynamic cellular vertex model is presented to study the morphomechanics of a growing epithelial monolayer. The regulating role of stresses in soft tissue growth is revealed. It is found that the cells originating from the same parent cell in the monolayer can orchestrate into clustering patterns as the tissue grows. Collective cell migration exhibits a feature of spatial correlation across multiple cells. Dynamic intercellular interactions can engender a variety of distinct tissue behaviors in a social context. Uniform cell proliferation may render high and heterogeneous residual compressive stresses, while stress-regulated proliferation can effectively release the stresses, reducing the stress heterogeneity in the tissue. The results highlight the critical role of mechanical factors in the growth and morphogenesis of epithelial tissues and help understand the development and invasion of epithelial tumors.
Cellular automaton model for hydrogen transport dynamics through metallic surface
Shimura, K.; Yamaguchi, K.; Terai, T.; Yamawaki, M.
2002-01-01
Hydrogen re-emission and re-combination at the surface of first wall materials are a crucial issue for the understanding of the fuel recycling and for the tritium inventory in plasma facing materials. It is know to be difficult to model the transient behaviour of those processes due to their complex time-transient nature. However, cellular automata (CA) are powerful tools to model such complex systems because of their nature of discreteness in both dependent and independent variables. Then the system can be represented by the fully local interactions between cells. For that reason, complex physical and chemical systems can be described by fairly simple manner. In this study, the kinetics of desorption of adsorbed hydrogen from an ideal metallic surface is modelled in CA. Thermal desorption is simulated with this model and the comparison with the theory of rate processes is performed to identify the validity of this model. The overall results show that this model is reasonable to express the desorption kinetics
A Computational Model of Cellular Response to Modulated Radiation Fields
McMahon, Stephen J., E-mail: stephen.mcmahon@qub.ac.uk [Centre for Cancer Research and Cell Biology, Queen' s University Belfast, Belfast, Northern Ireland (United Kingdom); Butterworth, Karl T. [Centre for Cancer Research and Cell Biology, Queen' s University Belfast, Belfast, Northern Ireland (United Kingdom); McGarry, Conor K. [Centre for Cancer Research and Cell Biology, Queen' s University Belfast, Belfast, Northern Ireland (United Kingdom); Radiotherapy Physics, Northern Ireland Cancer Centre, Belfast Health and Social Care Trust, Northern Ireland (United Kingdom); Trainor, Colman [Centre for Cancer Research and Cell Biology, Queen' s University Belfast, Belfast, Northern Ireland (United Kingdom); O' Sullivan, Joe M. [Centre for Cancer Research and Cell Biology, Queen' s University Belfast, Belfast, Northern Ireland (United Kingdom); Clinical Oncology, Northern Ireland Cancer Centre, Belfast Health and Social Care Trust, Belfast, Northern Ireland (United Kingdom); Hounsell, Alan R. [Centre for Cancer Research and Cell Biology, Queen' s University Belfast, Belfast, Northern Ireland (United Kingdom); Radiotherapy Physics, Northern Ireland Cancer Centre, Belfast Health and Social Care Trust, Northern Ireland (United Kingdom); Prise, Kevin M. [Centre for Cancer Research and Cell Biology, Queen' s University Belfast, Belfast, Northern Ireland (United Kingdom)
2012-09-01
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 Computational Model of Cellular Response to Modulated Radiation Fields
McMahon, Stephen J.; Butterworth, Karl T.; McGarry, Conor K.; Trainor, Colman; O’Sullivan, Joe M.; Hounsell, Alan R.; Prise, Kevin M.
2012-01-01
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.
Pathloss Measurements and Modeling for UAVs Connected to Cellular Networks
Amorim, Rafhael Medeiros de; Mogensen, Preben Elgaard; Sørensen, Troels Bundgaard
2017-01-01
. The measurements were conducted in an operating LTE network (850 MHz), using a commercial cell phone, placed inside the frame of the UAV. Trials were conducted for UAV flying at 5 different heights measured above ground level (20, 40, 60, 80 and 100m) and a pathloss regression line was obtained from results. Then......This paper assess field measurements, as part of the investigation of the suitability of cellular networks for providing connectivity to UAVs (unmanned aerial vehicles). Evaluation is done by means of field measurements obtained in a rural environment in Denmark with an airbone UAV......, downlink (DL) SINR levels obtained during flight measurements are also presented. An important result obtained from the measurents reveal that there is a height-related DL SINR degradation. Three main sources of uncertainty on the pathloss model that could be responsible for the SINR degradation are also...
Two-dimensional Potts antiferromagnets with a phase transition at arbitrarily large q
Huang, Y.; Chen, K.; Deng, Y.; Jacobsen, J. L.; Kotecký, R.; Salas, J.; Sokal, Alan D.; Swart, Jan M.
2013-01-01
Roč. 87, Č. 1 (2013), 12136-1-12136-5 ISSN 1539-3755 R&D Projects: GA ČR GAP201/12/2613 Institutional support: RVO:67985556 Keywords : Monte Carlo simulation * two-dimensional lattices * q-state Potts Subject RIV: BE - Theoretical Physics Impact factor: 2.326, year: 2013 http://library.utia.cas.cz/separaty/2013/SI/swart-two-dimensional potts antiferromagnets with a phase transition at arbitrarily large q.pdf
Cellular automaton model of mass transport with chemical reactions
Karapiperis, T.; Blankleider, B.
1993-10-01
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
Multiscale modeling of porous ceramics using movable cellular automaton method
Smolin, Alexey Yu.; Smolin, Igor Yu.; Smolina, Irina Yu.
2017-10-01
The paper presents a multiscale model for porous ceramics based on movable cellular automaton method, which is a particle method in novel computational mechanics of solid. The initial scale of the proposed approach corresponds to the characteristic size of the smallest pores in the ceramics. At this scale, we model uniaxial compression of several representative samples with an explicit account of pores of the same size but with the unique position in space. As a result, we get the average values of Young's modulus and strength, as well as the parameters of the Weibull distribution of these properties at the current scale level. These data allow us to describe the material behavior at the next scale level were only the larger pores are considered explicitly, while the influence of small pores is included via effective properties determined earliar. If the pore size distribution function of the material has N maxima we need to perform computations for N-1 levels in order to get the properties step by step from the lowest scale up to the macroscale. The proposed approach was applied to modeling zirconia ceramics with bimodal pore size distribution. The obtained results show correct behavior of the model sample at the macroscale.
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
Cellular Automata for Modeling the field-scale erosion
Diaz Suarez, Jorge; Bagarotti Marin, Angel; Ruiz Perez, Maria Elena
2008-01-01
Full text: The Cellular Automaton (CA) is a system used discrete dynamic modeling of many physical systems. Their fundamental properties are the interaction at the local level, homogeneity and parallelism. It has been used as a secondary for the simulation of large systems where the use of equations in partial derivatives is complex and costly from the computational point of view. On the other hand, the high complexity of spatial interaction in the processes involved in the erosion-transport-deposition of sediments at field level, considerably limiting the use of base models physics. The objective of this study is to model the main processes involved in erosion water supply of soils through the use of the CAMELot system, based on an extension of the original paradigm of the CA. The CAMELot system has been used in the simulation of systems of large spatial extent, where the laws of local interaction between automata have a deep physical sense. This system guarantees both the input of the necessary specifications and simulation in parallel, as the visualization and the general management of the system. They are exposed to each of the submodels used in it and the overall dynamics of the system is analyzed. (author)
Cellular Model of Atherogenesis Based on Pluripotent Vascular Wall Pericytes.
Ivanova, Ekaterina A; Orekhov, Alexander N
2016-01-01
Pericytes are pluripotent cells that can be found in the vascular wall of both microvessels and large arteries and veins. They have distinct morphology with long branching processes and form numerous contacts with each other and with endothelial cells, organizing the vascular wall cells into a three-dimensional network. Accumulating evidence demonstrates that pericytes may play a key role in the pathogenesis of vascular disorders, including atherosclerosis. Macrovascular pericytes are able to accumulate lipids and contribute to growth and vascularization of the atherosclerotic plaque. Moreover, they participate in the local inflammatory process and thrombosis, which can lead to fatal consequences. At the same time, pericytes can represent a useful model for studying the atherosclerotic process and for the development of novel therapeutic approaches. In particular, they are suitable for testing various substances' potential for decreasing lipid accumulation induced by the incubation of cells with atherogenic low-density lipoprotein. In this review we will discuss the application of cellular models for studying atherosclerosis and provide several examples of successful application of these models to drug research.
A Computational model for compressed sensing RNAi cellular screening
Tan Hua
2012-12-01
Full Text Available Abstract Background RNA interference (RNAi becomes an increasingly important and effective genetic tool to study the function of target genes by suppressing specific genes of interest. This system approach helps identify signaling pathways and cellular phase types by tracking intensity and/or morphological changes of cells. The traditional RNAi screening scheme, in which one siRNA is designed to knockdown one specific mRNA target, needs a large library of siRNAs and turns out to be time-consuming and expensive. Results In this paper, we propose a conceptual model, called compressed sensing RNAi (csRNAi, which employs a unique combination of group of small interfering RNAs (siRNAs to knockdown a much larger size of genes. This strategy is based on the fact that one gene can be partially bound with several small interfering RNAs (siRNAs and conversely, one siRNA can bind to a few genes with distinct binding affinity. This model constructs a multi-to-multi correspondence between siRNAs and their targets, with siRNAs much fewer than mRNA targets, compared with the conventional scheme. Mathematically this problem involves an underdetermined system of equations (linear or nonlinear, which is ill-posed in general. However, the recently developed compressed sensing (CS theory can solve this problem. We present a mathematical model to describe the csRNAi system based on both CS theory and biological concerns. To build this model, we first search nucleotide motifs in a target gene set. Then we propose a machine learning based method to find the effective siRNAs with novel features, such as image features and speech features to describe an siRNA sequence. Numerical simulations show that we can reduce the siRNA library to one third of that in the conventional scheme. In addition, the features to describe siRNAs outperform the existing ones substantially. Conclusions This csRNAi system is very promising in saving both time and cost for large-scale RNAi
From equilibrium spin models to probabilistic cellular automata
Georges, A.; Le Doussal, P.
1989-01-01
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
Cellular automata model for traffic flow with safe driving conditions
Lárraga María Elena; Alvarez-Icaza Luis
2014-01-01
In this paper, a recently introduced cellular automata (CA) model is used for a statistical analysis of the inner microscopic structure of synchronized traffic flow. The analysis focuses on the formation and dissolution of clusters or platoons of vehicles, as the mechanism that causes the presence of this synchronized traffic state with a high flow. This platoon formation is one of the most interesting phenomena observed in traffic flows and plays an important role both in manual and automated highway systems (AHS). Simulation results, obtained from a single-lane system under periodic boundary conditions indicate that in the density region where the synchronized state is observed, most vehicles travel together in platoons with approximately the same speed and small spatial distances. The examination of velocity variations and individual vehicle gaps shows that the flow corresponding to the synchronized state is stable, safe and highly correlated. Moreover, results indicate that the observed platoon formation in real traffic is reproduced in simulations by the relation between vehicle headway and velocity that is embedded in the dynamics definition of the CA model. (general)
A Computational Model of Cellular Engraftment on Lung Scaffolds
Joshua J. Pothen
2016-10-01
Full Text Available The possibility that stem cells might be used to regenerate tissue is now being investigated for a variety of organs, but these investigations are still essentially exploratory and have few predictive tools available to guide experimentation. We propose, in this study, that the field of lung tissue regeneration might be better served by predictive tools that treat stem cells as agents that obey certain rules of behavior governed by both their phenotype and their environment. Sufficient knowledge of these rules of behavior would then, in principle, allow lung tissue development to be simulated computationally. Toward this end, we developed a simple agent-based computational model to simulate geographic patterns of cells seeded onto a lung scaffold. Comparison of the simulated patterns to those observed experimentally supports the hypothesis that mesenchymal stem cells proliferate preferentially toward the scaffold boundary, whereas alveolar epithelial cells do not. This demonstrates that a computational model of this type has the potential to assist in the discovery of rules of cellular behavior
A Computational Model of Cellular Engraftment on Lung Scaffolds.
Pothen, Joshua J; Rajendran, Vignesh; Wagner, Darcy; Weiss, Daniel J; Smith, Bradford J; Ma, Baoshun; Bates, Jason H T
2016-01-01
The possibility that stem cells might be used to regenerate tissue is now being investigated for a variety of organs, but these investigations are still essentially exploratory and have few predictive tools available to guide experimentation. We propose, in this study, that the field of lung tissue regeneration might be better served by predictive tools that treat stem cells as agents that obey certain rules of behavior governed by both their phenotype and their environment. Sufficient knowledge of these rules of behavior would then, in principle, allow lung tissue development to be simulated computationally. Toward this end, we developed a simple agent-based computational model to simulate geographic patterns of cells seeded onto a lung scaffold. Comparison of the simulated patterns to those observed experimentally supports the hypothesis that mesenchymal stem cells proliferate preferentially toward the scaffold boundary, whereas alveolar epithelial cells do not. This demonstrates that a computational model of this type has the potential to assist in the discovery of rules of cellular behavior.
Ishimoto, Yukitaka; Morishita, Yoshihiro
2014-11-01
In order to describe two-dimensionally packed cells in epithelial tissues both mathematically and physically, there have been developed several sorts of geometrical models, such as the vertex model, the finite element model, the cell-centered model, and the cellular Potts model. So far, in any case, pressures have not neatly been dealt with and the curvatures of the cell boundaries have been even omitted through their approximations. We focus on these quantities and formulate them in the vertex model. Thus, a model with the curvatures is constructed, and its algorithm for simulation is provided. The possible extensions and applications of this model are also discussed.
A survey on the modeling and applications of cellular automata theory
Gong, Yimin
2017-09-01
The Cellular Automata Theory is a discrete model which is now widely used in scientific researches and simulations. The model is comprised of some cells which changes according to a specific rule over time. This paper provides a survey of the Modeling and Applications of Cellular Automata Theory, which focus on the program realization of Cellular Automata Theory and the application of Cellular Automata in each field, such as road traffic, land use, and cutting machines. Each application is further explained, and several related main models are briefly introduced. This research aims to help decision-makers formulate appropriate development plans.
Simulasi Tumbukan Partikel Gas Ideal Dengan Model Cellular Automata Dua Dimensi
Abdul Basid, Annisa Mujriati
2010-01-01
Telah dilakukan simulasi tumbukan partikel gas ideal dengan menggunakan model cellular automata dua dimensi untuk memvisualisasikan tumbukan partikel gas ideal. Tumbukan partikel disimulasikan dengan menggunakan model cellular automata dua dimensi. Di dalam cellular automata, pergerakan partikel diatur dengan suatu aturan yaitu aturan delapan tetangga yang merupakan aturan acak. Hasil program simulasi tumbukan partikel gas ideal dengan model cellular automata dua dimensi mengguna...
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
An improved cellular automaton method to model multispecies biofilms.
Tang, Youneng; Valocchi, Albert J
2013-10-01
Biomass-spreading rules used in previous cellular automaton methods to simulate multispecies biofilm introduced extensive mixing between different biomass species or resulted in spatially discontinuous biomass concentration and distribution; this caused results based on the cellular automaton methods to deviate from experimental results and those from the more computationally intensive continuous method. To overcome the problems, we propose new biomass-spreading rules in this work: Excess biomass spreads by pushing a line of grid cells that are on the shortest path from the source grid cell to the destination grid cell, and the fractions of different biomass species in the grid cells on the path change due to the spreading. To evaluate the new rules, three two-dimensional simulation examples are used to compare the biomass distribution computed using the continuous method and three cellular automaton methods, one based on the new rules and the other two based on rules presented in two previous studies. The relationship between the biomass species is syntrophic in one example and competitive in the other two examples. Simulation results generated using the cellular automaton method based on the new rules agree much better with the continuous method than do results using the other two cellular automaton methods. The new biomass-spreading rules are no more complex to implement than the existing rules. Copyright © 2013 Elsevier Ltd. All rights reserved.
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. Copyright 2009 The Faculty of Homeopathy. Published by Elsevier Ltd. All rights reserved.
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.
O'Clock, George D
2016-08-01
Cellular engineering involves modification and control of cell properties, and requires an understanding of fundamentals and mechanisms of action for cellular derived product development. One of the keys to success in cellular engineering involves the quality and validity of results obtained from cell chemical signaling pathway assays. The accuracy of the assay data cannot be verified or assured if the effect of positive feedback, nonlinearities, and interrelationships between cell chemical signaling pathway elements are not understood, modeled, and simulated. Nonlinearities and positive feedback in the cell chemical signaling pathway can produce significant aberrations in assay data collection. Simulating the pathway can reveal potential instability problems that will affect assay results. A simulation, using an electrical analog for the coupled differential equations representing each segment of the pathway, provides an excellent tool for assay validation purposes. With this approach, voltages represent pathway enzyme concentrations and operational amplifier feedback resistance and input resistance values determine pathway gain and rate constants. The understanding provided by pathway modeling and simulation is strategically important in order to establish experimental controls for assay protocol structure, time frames specified between assays, and assay concentration variation limits; to ensure accuracy and reproducibility of results.
Anisotropic cubic lattice potts ferromagnet: renormalisation group treatment
Tsallis, C.; Schwaccheim, G.; Silva, L.R. da; Rio Grande do Norte Univ., Natal
1983-01-01
Within a real space renormalisation group framework, the criticality of the fully anisotropic (arbitrary J sub(x), J sub(y) and J sub(z)) q-state Potts ferromagnet in simple cubic lattice is discussed. Several already known exact results for the d=1 and d=2 particular cases are recovered. Furthermore it is obtained: (i) the q-dependence of the d=3 correlation length critical exponent ν 3 (in particular, if q→0, ν 3 (q) approximatelly ν 3 (0)+ν 3 '(0)q) where the present approximate values are ν 3 (0) or approx.= 1.105 and ν 3 '(0) or approx.=-0.66; (ii) the q-dependence d=2 d=3 crossover critical exponent phi 23 (in particular, phi 23 varies as 1/√q if q Q→0); (iii) through a convenient numerical extrapolation, a quite accurate proposal for the critical temperatures corresponding to arbitrary ratios J sub(y)/ J sub(x) and J sub(z) / J sub(x) and values of q. (Author) [pt
Theoretical modeling of cellular and dendritic solidification microstructures
Song, Younggil
the invasion process starts with a group of cells, the leader cell can detach itself from the group and grow continuously as a misoriented solitary cell in the other grain with a different misorientation. We use PF simulations to investigate the GB morphology and dynamics of a solitary cell. Solidification experiments on earth are typically performed in a thin-sample geometry to avoid fluid convection. Thus, we consider various influences on cellular and dendritic array patterns in thin samples. First, we explore the influence of crystal orientation. When a grain in a thin-sample geometry is misoriented with respect to the temperature gradient, primary cells and dendrites drift laterally in both experiments and simulations. At the same time, grain boundaries are systematically formed at the edges of the misoriented grain. The misoriented primary branches move away from the divergent grain boundary. At this boundary, cells/dendrites are generated continuously, and their spacings are larger than the dynamically selected spacings. Primary branches run into the other convergent GB, which leads to their elimination. Thus, at a stationary state, a spacing distribution is uniform with the spacing selected at the divergent GB until it decreases near the convergent GB. We perform simulations to illustrate the global evolutions of a primary spacing. In addition, we suggest a simple geometrical model and a nonlinear advection equation for the dynamics of the primary spacing evolution, which can predict the slow evolution of a primary spacing in a quasi-2D array. Experimental observations point out that the primary spacing selection could be affected by the sample thickness; however, the detailed description for the link between the primary spacing selection and a sample thickness is still missing. Here, we use PF simulations to investigate the primary cellular and dendritic spacing selection mechanisms under the influence of a sample thickness. A thin-sample geometry can limit
A Model of How Different Biology Experts Explain Molecular and Cellular Mechanisms
Trujillo, Caleb M.; Anderson, Trevor R.; Pelaez, Nancy J.
2015-01-01
Constructing explanations is an essential skill for all science learners. The goal of this project was to model the key components of expert explanation of molecular and cellular mechanisms. As such, we asked: What is an appropriate model of the components of explanation used by biology experts to explain molecular and cellular mechanisms? Do…
Variational cellular model of the molecular and crystal electronic structure
Ferreira, L.G.; Leite, J.R.
1977-12-01
A variational version of the cellular method is developed to calculate the electronic structure of molecules and crystals. Due to the simplicity of the secular equation, the method is easy to be implemented. Preliminary calculations on the hydrogen molecular ion suggest that it is also accurate and of fast convergence [pt
q-state Potts-glass neural network based on pseudoinverse rule
Xiong Daxing; Zhao Hong
2010-01-01
We study the q-state Potts-glass neural network with the pseudoinverse (PI) rule. Its performance is investigated and compared with that of the counterpart network with the Hebbian rule instead. We find that there exists a critical point of q, i.e., q cr =14, below which the storage capacity and the retrieval quality can be greatly improved by introducing the PI rule. We show that the dynamics of the neural networks constructed with the two learning rules respectively are quite different; but however, regardless of the learning rules, in the q-state Potts-glass neural networks with q≥3 there is a common novel dynamical phase in which the spurious memories are completely suppressed. This property has never been noticed in the symmetric feedback neural networks. Free from the spurious memories implies that the multistate Potts-glass neural networks would not be trapped in the metastable states, which is a favorable property for their applications.
Modeling chemical systems using cellular automata a textbook and laboratory manual
Kier, Lemont B; Cheng, Chao-Kun
2005-01-01
There are few publications on Cellular Automata and certainly no direct competition Insight into a new modeling paradigm Novel approach to the use of in silico modeling to replace or supplement costly labs.
Load-aware modeling for uplink cellular networks in a multi-channel environment
Alammouri, Ahmad; Elsawy, Hesham; Alouini, Mohamed-Slim
2014-01-01
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
Cellular automaton modeling of biological pattern formation characterization, examples, and analysis
Deutsch, Andreas
2017-01-01
This text explores the use of cellular automata in modeling pattern formation in biological systems. It describes several mathematical modeling approaches utilizing cellular automata that can be used to study the dynamics of interacting cell systems both in simulation and in practice. New in this edition are chapters covering cell migration, tissue development, and cancer dynamics, as well as updated references and new research topic suggestions that reflect the rapid development of the field. The book begins with an introduction to pattern-forming principles in biology and the various mathematical modeling techniques that can be used to analyze them. Cellular automaton models are then discussed in detail for different types of cellular processes and interactions, including random movement, cell migration, adhesive cell interaction, alignment and cellular swarming, growth processes, pigment cell pattern formation, tissue development, tumor growth and invasion, and Turing-type patterns and excitable media. In ...
A local cellular model for growth on quasicrystals
Chidyagwai, Prince; Reiter, Clifford A.
2005-01-01
The growth of real valued cellular automata using a deterministic algorithm on 2-dimensional quasicrystalline structures is investigated. Quasicrystals are intermediate between the rigid organization of crystals and disorganized random structures. Since the quasicrystalline structures may be highly symmetric or not, we are able to obtain highly organized and relatively random growth patterns. This deterministic growth produces dendrite, sector, stellar, regular polygons, round, and random DLA-like structures
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
Multi-scale modeling with cellular automata: The complex automata approach
Hoekstra, A.G.; Falcone, J.-L.; Caiazzo, A.; Chopard, B.
2008-01-01
Cellular Automata are commonly used to describe complex natural phenomena. In many cases it is required to capture the multi-scale nature of these phenomena. A single Cellular Automata model may not be able to efficiently simulate a wide range of spatial and temporal scales. It is our goal to
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
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.
Cellular modelling of river catchments and reaches: Advantages, limitations and prospects
Coulthard, T. J.; Hicks, D. M.; Van De Wiel, M. J.
2007-10-01
The last decade has witnessed the development of a series of cellular models that simulate the processes operating within river channels and drive their geomorphic evolution. Their proliferation can be partly attributed to the relative simplicity of cellular models and their ability to address some of the shortcomings of other numerical models. By using relaxed interpretations of the equations determining fluid flow, cellular models allow rapid solutions of water depths and velocities. These can then be used to drive (usually) conventional sediment transport relations to determine erosion and deposition and alter the channel form. The key advance of using these physically based yet simplified approaches is that they allow us to apply models to a range of spatial scales (1-100 km 2) and time periods (1-100 years) that are especially relevant to contemporary management and fluvial studies. However, these approaches are not without their limitations and technical problems. This paper reviews the findings of nearly 10 years of research into modelling fluvial systems with cellular techniques, principally focusing on improvements in routing water and how fluvial erosion and deposition (including lateral erosion) are represented. These ideas are illustrated using sample simulations of the River Teifi, Wales. A detailed case study is then presented, demonstrating how cellular models can explore the interactions between vegetation and the morphological dynamics of the braided Waitaki River, New Zealand. Finally, difficulties associated with model validation and the problems, prospects and future issues important to the further development and application of these cellular fluvial models are outlined.
Cellular Shape Memory Alloy Structures: Experiments & Modeling (Part 1)
2012-08-01
High -‐ temperature SMAs 24 Braze Joint between two wrought pieces of a Ni24.5Pd25Ti50.5 HTSMA (HTSMA from...process can be used to join other metal alloys and high -‐ temperature SMAs 25 Cellular Shape Memory...20 30 40 50 60 910 3 4 8 5 2 T (°C) Shape memory & superelasticity 1 0 e (%) (GPa) 6 7 A NiTi wire
Stochastic Model of Vesicular Sorting in Cellular Organelles
Vagne, Quentin; Sens, Pierre
2018-02-01
The proper sorting of membrane components by regulated exchange between cellular organelles is crucial to intracellular 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 lead to fast sorting but result in a broad size distribution of sorted compartments dominated by small entities. High ratio values result in two well-defined sorted compartments but sorting is exponentially slow. Our results suggest 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 organization of intracellular compartments.
Mean-field solution of the Potts glass near the transition temperature to the ordered phase
Janiš, Václav; Klíč, Antonín
2011-01-01
Roč. 84, č. 6 (2011), "064446-1"-"064446-10" ISSN 1098-0121 Institutional research plan: CEZ:AV0Z10100520 Keywords : Potts glass * hierarchic solutions with replicated spins * continuous replica-symmetry breaking Subject RIV: BE - Theoretical Physics Impact factor: 3.691, year: 2011
Elsawy, Hesham; Hossain, Ekram
2014-01-01
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
Cellular-automation fluids: A model for flow in porous media
Rothman, D.H.
1987-01-01
Because the intrinsic inhomogeneity of porous media makes the application of proper boundary conditions difficult, fluid flow through microgeometric models has typically been achieved with idealized arrays of geometrically simple pores, throats, and cracks. The author proposes here an attractive alternative, capable of freely and accurately modeling fluid flow in grossly irregular geometries. This new method numerically solves the Navier-Stokes equations using the cellular-automation fluid model introduced by Frisch, Hasslacher, and Pomeau. The cellular-automation fluid is extraordinarily simple - particles of unit mass traveling with unit velocity reside on a triangular lattice and obey elementary collisions rules - but capable of modeling much of the rich complexity of real fluid flow. The author shows how cellular-automation fluids are applied to the study of porous media. In particular, he discusses issues of scale on the cellular-automation lattice and present the results of 2-D simulations, including numerical estimation of permeability and verification of Darcy's law
Geometric Modeling of Cellular Materials for Additive Manufacturing in Biomedical Field: A Review
Gianpaolo Savio
2018-01-01
Full Text Available Advances in additive manufacturing technologies facilitate the fabrication of cellular materials that have tailored functional characteristics. The application of solid freeform fabrication techniques is especially exploited in designing scaffolds for tissue engineering. In this review, firstly, a classification of cellular materials from a geometric point of view is proposed; then, the main approaches on geometric modeling of cellular materials are discussed. Finally, an investigation on porous scaffolds fabricated by additive manufacturing technologies is pointed out. Perspectives in geometric modeling of scaffolds for tissue engineering are also proposed.
Geometric Modeling of Cellular Materials for Additive Manufacturing in Biomedical Field: A Review.
Savio, Gianpaolo; Rosso, Stefano; Meneghello, Roberto; Concheri, Gianmaria
2018-01-01
Advances in additive manufacturing technologies facilitate the fabrication of cellular materials that have tailored functional characteristics. The application of solid freeform fabrication techniques is especially exploited in designing scaffolds for tissue engineering. In this review, firstly, a classification of cellular materials from a geometric point of view is proposed; then, the main approaches on geometric modeling of cellular materials are discussed. Finally, an investigation on porous scaffolds fabricated by additive manufacturing technologies is pointed out. Perspectives in geometric modeling of scaffolds for tissue engineering are also proposed.
Geometric Modeling of Cellular Materials for Additive Manufacturing in Biomedical Field: A Review
Rosso, Stefano; Meneghello, Roberto; Concheri, Gianmaria
2018-01-01
Advances in additive manufacturing technologies facilitate the fabrication of cellular materials that have tailored functional characteristics. The application of solid freeform fabrication techniques is especially exploited in designing scaffolds for tissue engineering. In this review, firstly, a classification of cellular materials from a geometric point of view is proposed; then, the main approaches on geometric modeling of cellular materials are discussed. Finally, an investigation on porous scaffolds fabricated by additive manufacturing technologies is pointed out. Perspectives in geometric modeling of scaffolds for tissue engineering are also proposed. PMID:29487626
Simulation Modeling by Classification of Problems: A Case of Cellular Manufacturing
Afiqah, K N; Mahayuddin, Z R
2016-01-01
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. (paper)
Soleimani, Hamid; Drakakis, Emmanuel M
2017-06-01
Recent studies have demonstrated that calcium is a widespread intracellular ion that controls a wide range of temporal dynamics in the mammalian body. The simulation and validation of such studies using experimental data would benefit from a fast large scale simulation and modelling tool. This paper presents a compact and fully reconfigurable cellular calcium model capable of mimicking Hopf bifurcation phenomenon and various nonlinear responses of the biological calcium dynamics. The proposed cellular model is synthesized on a digital platform for a single unit and a network model. Hardware synthesis, physical implementation on FPGA, and theoretical analysis confirm that the proposed cellular model can mimic the biological calcium behaviors with considerably low hardware overhead. The approach has the potential to speed up large-scale simulations of slow intracellular dynamics by sharing more cellular units in real-time. To this end, various networks constructed by pipelining 10 k to 40 k cellular calcium units are compared with an equivalent simulation run on a standard PC workstation. Results show that the cellular hardware model is, on average, 83 times faster than the CPU version.
Cellular automata model for use with real freeway data
2002-01-01
The exponential rate of increase in freeway traffic is expanding the need for accurate and : realistic methods to model and predict traffic flow. Traffic modeling and simulation facilitates an : examination of both microscopic and macroscopic views o...
Simulating Urban Growth Using a Random Forest-Cellular Automata (RF-CA Model
Courage Kamusoko
2015-04-01
Full Text Available Sustainable urban planning and management require reliable land change models, which can be used to improve decision making. The objective of this study was to test a random forest-cellular automata (RF-CA model, which combines random forest (RF and cellular automata (CA models. The Kappa simulation (KSimulation, figure of merit, and components of agreement and disagreement statistics were used to validate the RF-CA model. Furthermore, the RF-CA model was compared with support vector machine cellular automata (SVM-CA and logistic regression cellular automata (LR-CA models. Results show that the RF-CA model outperformed the SVM-CA and LR-CA models. The RF-CA model had a Kappa simulation (KSimulation accuracy of 0.51 (with a figure of merit statistic of 47%, while SVM-CA and LR-CA models had a KSimulation accuracy of 0.39 and −0.22 (with figure of merit statistics of 39% and 6%, respectively. Generally, the RF-CA model was relatively accurate at allocating “non-built-up to built-up” changes as reflected by the correct “non-built-up to built-up” components of agreement of 15%. The performance of the RF-CA model was attributed to the relatively accurate RF transition potential maps. Therefore, this study highlights the potential of the RF-CA model for simulating urban growth.
Propagation Path Loss Models for 5G Urban Micro- and Macro-Cellular Scenarios
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....
Liu, Qiang; Wan, Xiaoxia; Xie, Dehong
2014-06-01
The study presented here optimizes several steps in the spectral printer modeling workflow based on a cellular Yule-Nielsen spectral Neugebauer (CYNSN) model. First, a printer subdividing method was developed that reduces the number of sub-models while maintaining the maximum device gamut. Second, the forward spectral prediction accuracy of the CYNSN model for each subspace of the printer was improved using back propagation artificial neural network (BPANN) estimated n values. Third, a sequential gamut judging method, which clearly reduced the complexity of the optimal sub-model and cell searching process during printer backward modeling, was proposed. After that, we further modified the use of the modeling color metric and comprehensively improved the spectral and perceptual accuracy of the spectral printer model. The experimental results show that the proposed optimization approaches provide obvious improvements in aspects of the modeling accuracy or efficiency for each of the corresponding steps, and an overall improvement of the optimized spectral printer modeling workflow was also demonstrated.
Individual Subjective Initiative Merge Model Based on Cellular Automaton
Yin-Jie Xu
2013-01-01
Full Text Available The merge control models proposed for work zones are classified into two types (Hard Control Merge (HCM model and Soft Control Merge (SCM model according to their own control intensity and are compared with a new model, called Individual Subjective Initiative Merge (ISIM model, which is based on the linear lane-changing probability strategy in the merging area. The attention of this paper is paid to the positive impact of the individual subjective initiative for the whole traffic system. Three models (ISIM, HCM, and SCM are established and compared with each other by two order parameters, that is, system output and average vehicle travel time. Finally, numerical results show that both ISIM and SCM perform better than HCM. Compared with SCM, the output of ISIM is 20 vehicles per hour higher under the symmetric input condition and is more stable under the asymmetric input condition. Meanwhile, the average travel time of ISIM is 2000 time steps less under the oversaturated input condition.
Gharbieh, Mohammad; Elsawy, Hesham; Bader, Ahmed; Alouini, Mohamed-Slim
2017-01-01
The Internet of Things (IoT) is large-scale by nature, which is manifested by the massive number of connected devices as well as their vast spatial existence. Cellular networks, which provide ubiquitous, reliable, and efficient wireless access, will play fundamental rule in delivering the first-mile access for the data tsunami to be generated by the IoT. However, cellular networks may have scalability problems to provide uplink connectivity to massive numbers of connected things. To characterize the scalability of cellular uplink in the context of IoT networks, this paper develops a traffic-aware spatiotemporal mathematical model for IoT devices supported by cellular uplink connectivity. The developed model is based on stochastic geometry and queueing theory to account for the traffic requirement per IoT device, the different transmission strategies, and the mutual interference between the IoT devices. To this end, the developed model is utilized to characterize the extent to which cellular networks can accommodate IoT traffic as well as to assess and compare three different transmission strategies that incorporate a combination of transmission persistency, backoff, and power-ramping. The analysis and the results clearly illustrate the scalability problem imposed by IoT on cellular network and offer insights into effective scenarios for each transmission strategy.
Gharbieh, Mohammad
2017-05-02
The Internet of Things (IoT) is large-scale by nature, which is manifested by the massive number of connected devices as well as their vast spatial existence. Cellular networks, which provide ubiquitous, reliable, and efficient wireless access, will play fundamental rule in delivering the first-mile access for the data tsunami to be generated by the IoT. However, cellular networks may have scalability problems to provide uplink connectivity to massive numbers of connected things. To characterize the scalability of cellular uplink in the context of IoT networks, this paper develops a traffic-aware spatiotemporal mathematical model for IoT devices supported by cellular uplink connectivity. The developed model is based on stochastic geometry and queueing theory to account for the traffic requirement per IoT device, the different transmission strategies, and the mutual interference between the IoT devices. To this end, the developed model is utilized to characterize the extent to which cellular networks can accommodate IoT traffic as well as to assess and compare three different transmission strategies that incorporate a combination of transmission persistency, backoff, and power-ramping. The analysis and the results clearly illustrate the scalability problem imposed by IoT on cellular network and offer insights into effective scenarios for each transmission strategy.
Boundary effects on car accidents in a cellular automaton model
Yang Xianqing; Ma Yuqiang; Zhao Yuemin
2004-01-01
In this paper we numerically study the probability P ac of occurrence of car accidents in the Nagel-Schreckenberg (NS) model with open boundary condition. In the deterministic NS model, numerical results show that there exists a critical value of extinction rate β above which no car accidents occur, and below which the probability P ac is independent of the speed limit v max and the injection rate α, but only determined by the extinction rate β. In the non-deterministic NS model, the probability P ac is a non-monotonic function of β in the region of low β value, while it is independent of β in the region of high β value. The stochastic braking not only reduces the occurrence of car accidents, but splits degenerate effects of v max on the probability P ac . Theoretical analyses give an agreement with numerical results in the deterministic NS model and in the non-deterministic NS model with v max = 1 in the case of low β value region. Qualitative differences between open and periodic systems in the relations of P ac to the bulk density ρ imply that various correlations may exist between the two systems
Point process models for localization and interdependence of punctate cellular structures.
Li, Ying; Majarian, Timothy D; Naik, Armaghan W; Johnson, Gregory R; Murphy, Robert F
2016-07-01
Accurate representations of cellular organization for multiple eukaryotic cell types are required for creating predictive models of dynamic cellular function. To this end, we have previously developed the CellOrganizer platform, an open source system for generative modeling of cellular components from microscopy images. CellOrganizer models capture the inherent heterogeneity in the spatial distribution, size, and quantity of different components among a cell population. Furthermore, CellOrganizer can generate quantitatively realistic synthetic images that reflect the underlying cell population. A current focus of the project is to model the complex, interdependent nature of organelle localization. We built upon previous work on developing multiple non-parametric models of organelles or structures that show punctate patterns. The previous models described the relationships between the subcellular localization of puncta and the positions of cell and nuclear membranes and microtubules. We extend these models to consider the relationship to the endoplasmic reticulum (ER), and to consider the relationship between the positions of different puncta of the same type. Our results do not suggest that the punctate patterns we examined are dependent on ER position or inter- and intra-class proximity. With these results, we built classifiers to update previous assignments of proteins to one of 11 patterns in three distinct cell lines. Our generative models demonstrate the ability to construct statistically accurate representations of puncta localization from simple cellular markers in distinct cell types, capturing the complex phenomena of cellular structure interaction with little human input. This protocol represents a novel approach to vesicular protein annotation, a field that is often neglected in high-throughput microscopy. These results suggest that spatial point process models provide useful insight with respect to the spatial dependence between cellular structures.
Le mal de Pott: à propos de 82 cas
Badr Fedoul
2011-03-01
Full Text Available Nous rapportant dans cette étude, les résultats de l’expérience du service de neurochirurgie du CHU Hassan II de Fès dans la prise en charge du mal de pott dans la région de Fès. Il s’agit d’une étude rétrospective de quatre-vingt-deux cas; étalée sur une période de cinq ans (janvier 2002 au décembre 2006. L’objectif de ce travail était d’illustrer les différents aspects épidémiologiques, diagnostiques et thérapeutiques de la localisation vertébrale de la tuberculose dans notre pratique. L'âge moyen de nos patients était de 43,1 ans, avec une légère prédominance féminine (53,82%. La durée d'évolution de la maladie était longue (dix mois en moyenne; ceci est expliquée par la symptomatologie initiale insidieuse faite de rachialgies (98,78% et une admission des patients au stade de complications neurologiques (41,46%. La radiographie standard était réalisée chez tous nos patients, et complétée par la TDM dans 86.58% des cas ce qui a permis de déceler la prédominance de l'atteinte dorsale et lombaire. L'IRM est l'examen de choix, elle était demandée chez tous les malades déficitaires (37,8%.Tous nos patients ont bénéficié d'un traitement antibacillaire associé à une immobilisation du foyer pottique. Une décompression par voie antérieure était réalisée chez 29 patients (35,36 %; alors que la laminectomie n'était pratiquée que chez 5 patients (6.09 %, tandis que l'évacuation de l'abcès de psoas était réalisée chez 25 patients (30,48 %. Le diagnostic de certitude histologique était posé dans 51 cas (62,19%. Les meilleurs résultats étaient obtenus chez les malades opérés par voie antérieure, 26 cas (89,65% de récupération totale et 3 cas (10,34% partielle. L'évolution vers la consolidation et la fusion vertébrale était la règle chez tous nos malades et ceci au bout de 4 à 18 mois après le traitement.
Generic framework for mining cellular automata models on protein-folding simulations.
Diaz, N; Tischer, I
2016-05-13
Cellular automata model identification is an important way of building simplified simulation models. In this study, we describe a generic architectural framework to ease the development process of new metaheuristic-based algorithms for cellular automata model identification in protein-folding trajectories. Our framework was developed by a methodology based on design patterns that allow an improved experience for new algorithms development. The usefulness of the proposed framework is demonstrated by the implementation of four algorithms, able to obtain extremely precise cellular automata models of the protein-folding process with a protein contact map representation. Dynamic rules obtained by the proposed approach are discussed, and future use for the new tool is outlined.
Numerical cell model investigating cellular carbon fluxes in Emiliania huxleyi.
Holtz, Lena-Maria; Wolf-Gladrow, Dieter; Thoms, Silke
2015-01-07
Coccolithophores play a crucial role in the marine carbon cycle and thus it is interesting to know how they will respond to climate change. After several decades of research the interplay between intracellular processes and the marine carbonate system is still not well understood. On the basis of experimental findings given in literature, a numerical cell model is developed that describes inorganic carbon fluxes between seawater and the intracellular sites of calcite precipitation and photosynthetic carbon fixation. The implemented cell model consists of four compartments, for each of which the carbonate system is resolved individually. The four compartments are connected to each other via H(+), CO2, and HCO3(-) fluxes across the compartment-confining membranes. For CO2 accumulation around RubisCO, an energy-efficient carbon concentrating mechanism is proposed that relies on diffusive CO2 uptake. At low external CO2 concentrations and high light intensities, CO2 diffusion does not suffice to cover the carbon demand of photosynthesis and an additional uptake of external HCO3(-) becomes essential. The model is constrained by data of Emiliania huxleyi, the numerically most abundant coccolithophore species in the present-day ocean. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.
Cellular models and therapies for age-related macular degeneration
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.
Mohammad Sayemuzzaman; Manoj K. Jha
2014-01-01
State wide variant topographic features in North Carolina attract the hydro-climatologist. There is none modeling study found that predict future Land Cover Land Use (LCLU) change for whole North Carolina. In this study, satellite-derived land cover maps of year 1992, 2001 and 2006 of North Carolina were integrated within the framework of the Markov-Cellular Automata (Markov-CA) model which combines the Markov chain and Cellular Automata (CA) techniques. A Multi-Criteria Evaluation (MCE) was ...
Model of adipose tissue cellularity dynamics during food restriction.
Soula, H A; Géloën, A; Soulage, C O
2015-01-07
Adipose tissue and adipocytes play a central role in the pathogenesis of metabolic diseases related to obesity. Size of fat cells depends on the balance of synthesis and mobilization of lipids and can undergo important variations throughout the life of the organism. These variations usually occur when storing and releasing lipids according to energy demand. In particular when confronted to severe food restriction, adipocyte releases its lipid content via a process called lipolysis. We propose a mathematical model that combines cell diameter distribution and lipolytic response to show that lipid release is a surface (radius squared) limited mechanism. Since this size-dependent rate affects the cell׳s shrinkage speed, we are able to predict the cell size distribution evolution when lipolysis is the only factor at work: such as during an important food restriction. Performing recurrent surgical biopsies on rats, we measured the evolution of adipose cell size distribution for the same individual throughout the duration of the food restriction protocol. We show that our microscopic model of size dependent lipid release can predict macroscopic size distribution evolution. Copyright © 2014 Elsevier Ltd. All rights reserved.
A cellular automata intraurban model with prices and income-differentiated actors
Furtado, B.A.; Ettema, D.F.; Ruiz, R.M.; Hurkens, J.; Delden, H. van
2012-01-01
This paper presents an intraurban cellular automata model that is an extension to White and Engelen’s pioneering model. The paper’s main contribution is to distinguish between agglomerative eff ects, determined by the attraction of the neighbourhood, and disagglomerative eff ects, driven by land
Designing and implementing a regional urban modeling system using the SLEUTH cellular urban model
Jantz, Claire A.; Goetz, Scott J.; Donato, David I.; Claggett, Peter
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.
Une localisation exceptionnelle de la tuberculose vertébrale Mal de Pott sous-occipital
Yahyaoui, Sana; Majdoub, Senda; Zaghouani, Houneida; Fradj, Hosni Ben; Bakir, Dejla; Bouajina, Elyes; Kraiem, Chakib
2013-01-01
Le mal de Pott est la forme la plus commune de la tuberculose osseuse touchant essentiellement le rachis dorso-lombaire. La localisation sous-occipitale reste exceptionnelle. Le diagnostic de cette entité est le plus souvent tardif ce qui expose à des complications graves. Les radiographies standard ne sont parlantes qu’à un stade tardif de la maladie, d'où l'intérêt de l'imagerie moderne notamment la tomodensitométrie (TDM) et l'imagerie par résonance magnétique (IRM) qui permettent un diagnostic précoce. Nous rapportons un nouveau cas de tuberculose sous-occipitale. Le diagnostic était posé sur l'imagerie en coupe et confirmé histologiquement à la biopsie transorale. Sont rappelés les aspects en imagerie de cette localisation particulière du mal de Pott. PMID:23819005
Lv, Jian-Ping; Deng, Youjin; Jacobsen, Jesper Lykke; Salas, Jesús; Sokal, Alan D.
2018-04-01
We provide a criterion based on graph duality to predict whether the three-state Potts antiferromagnet on a plane quadrangulation has a zero- or finite-temperature critical point, and its universality class. The former case occurs for quadrangulations of self-dual type, and the zero-temperature critical point has central charge c =1 . The latter case occurs for quadrangulations of non-self-dual type, and the critical point belongs to the universality class of the three-state Potts ferromagnet. We have tested this criterion against high-precision computations on four lattices of each type, with very good agreement. We have also found that the Wang-Swendsen-Kotecký algorithm has no critical slowing-down in the former case, and critical slowing-down in the latter.
Bond-diluted interface between semi-infinite Potts bulks: criticality
Cavalcanti, S.B.; Tsallis, C.
1986-01-01
Within a real space renormalisation group framework, we discuss the criticality of a system constituted by two (not necessarily equal) semi-infinite ferromagnetic q-state Potts bulks separated by an interface. This interface is a bond-diluted Potts ferromagnet with a coupling constant which is in general different from those of both bulks. The phase diagram presents four physically different phases, namely the paramagnetic one, and the surface, single bulk and double bulk ferromagnetic ones. These various phases determine a multicritical surface which contains a higher order multicritical line. The critical concentration P c that is the concentration of the interface bonds which surface magnetic ordering is possible even if the bulks are disordered. An interesting feature comes out which is that P c varies continuously with J 1 /J s and J 2 /J s . The standard two-dimensional percolation concentration is recovered for J 1 =J 2 =0. (author) [pt
Kinetic theory approach to modeling of cellular repair mechanisms under genome stress.
Jinpeng Qi
Full Text Available Under acute perturbations from outer environment, a normal cell can trigger cellular self-defense mechanism in response to genome stress. To investigate the kinetics of cellular self-repair process at single cell level further, a model of DNA damage generating and repair is proposed under acute Ion Radiation (IR by using mathematical framework of kinetic theory of active particles (KTAP. Firstly, we focus on illustrating the profile of Cellular Repair System (CRS instituted by two sub-populations, each of which is made up of the active particles with different discrete states. Then, we implement the mathematical framework of cellular self-repair mechanism, and illustrate the dynamic processes of Double Strand Breaks (DSBs and Repair Protein (RP generating, DSB-protein complexes (DSBCs synthesizing, and toxins accumulating. Finally, we roughly analyze the capability of cellular self-repair mechanism, cellular activity of transferring DNA damage, and genome stability, especially the different fates of a certain cell before and after the time thresholds of IR perturbations that a cell can tolerate maximally under different IR perturbation circumstances.
Kinetic theory approach to modeling of cellular repair mechanisms under genome stress.
Qi, Jinpeng; Ding, Yongsheng; Zhu, Ying; Wu, Yizhi
2011-01-01
Under acute perturbations from outer environment, a normal cell can trigger cellular self-defense mechanism in response to genome stress. To investigate the kinetics of cellular self-repair process at single cell level further, a model of DNA damage generating and repair is proposed under acute Ion Radiation (IR) by using mathematical framework of kinetic theory of active particles (KTAP). Firstly, we focus on illustrating the profile of Cellular Repair System (CRS) instituted by two sub-populations, each of which is made up of the active particles with different discrete states. Then, we implement the mathematical framework of cellular self-repair mechanism, and illustrate the dynamic processes of Double Strand Breaks (DSBs) and Repair Protein (RP) generating, DSB-protein complexes (DSBCs) synthesizing, and toxins accumulating. Finally, we roughly analyze the capability of cellular self-repair mechanism, cellular activity of transferring DNA damage, and genome stability, especially the different fates of a certain cell before and after the time thresholds of IR perturbations that a cell can tolerate maximally under different IR perturbation circumstances.
Criticality of the Potts ferromagnet in Midgal-Kadanoff - like hierarchical lattices
Silva, L.R. da; Tsallis, C.
1987-01-01
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) [pt
Harvey Cushing, the spine surgeon: the surgical treatment of Pott disease.
Bydon, Ali; Dasenbrock, Hormuzdiyar H; Pendleton, Courtney; McGirt, Matthew J; Gokaslan, Ziya L; Quinones-Hinojosa, Alfredo
2011-08-01
Review of historical archival records. Describe Harvey Cushing's patients with spinal pathology. Harvey Cushing was a pioneer of modern surgery but his work on spine remains largely unknown. Review of the Chesney Medical Archives of the Johns Hopkins Hospital from 1896 to 1912. This is the first time that Cushing's spinal cases while he was at the Johns Hopkins Hospital, including those with Pott disease, have been described.Cushing treated three young men with psoas abscesses secondary to Pott disease during his residency: he drained the abscesses, debrided any accompanying necrotic vertebral bodies, irrigated the cavity with salt, and left the incision open to close by secondary intention. Although Cushing used Koch's "tuberculin therapy" (of intravenous administration of isolated tubercular bacilli) in one patient, he did not do so in the other two, likely because of the poor response of this first patient. Later in his tenure, Cushing performed a laminectomy on a patient with kyphosis and paraplegia secondary to Pott disease. These cases provide a view of Cushing early in his career, pointing to the extraordinary degree of independence that he had during his residency under William Steward Halsted; these cases may have been important in the surgical upbringing both of Cushing and his coresident, William Stevenson Baer, who became the first professor of Orthopedics at Johns Hopkins Hospital. At the turn of the last century, Pott disease was primarily treated by immobilization with bed rest, braces, and plaster-of-paris jackets; some surgeons also employed gradual correction of the deformity by hyperextension. Patients who failed a trial of conservative therapy (of months to years) were treated with a laminectomy. However, the limitations of these strategies led to the development of techniques that form the basis of contemporary spine surgery-instrumentation and fusion.
Renormalisation-group specific heat of the square lattice Potts ferromagnet
Martin, H.O.; Tsallis, C.
1982-01-01
The free and internal energies and specific heat of the q-state Potts ferromagnet are discussed. A real space renormalisation group approach is presented which recovers a considerable amount of exact particular results for all dimensionalities (hypercubic lattices). The square lattice case is calculated in detail by using self-dual clusters (which provide the exact critical point for all q). Comparison with Onsager results (q=2) is satisfactory; the general tendencies for q different 2 (1 [pt
Tools and Models for Integrating Multiple Cellular Networks
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].
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
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
Singh, V. K.; Jha, A. K.; Gupta, K.; Srivastav, S. K.
2017-12-01
Recent studies indicate that there is a significant improvement in the urban land use dynamics through modeling at finer spatial resolutions. Geo-computational models such as cellular automata and agent based model have given evident proof regarding the quantification of the urban growth pattern with urban boundary. In recent studies, socio- economic factors such as demography, education rate, household density, parcel price of the current year, distance to road, school, hospital, commercial centers and police station are considered to the major factors influencing the Land Use Land Cover (LULC) pattern of the city. These factors have unidirectional approach to land use pattern which makes it difficult to analyze the spatial aspects of model results both quantitatively and qualitatively. In this study, cellular automata model is combined with generic model known as Agent Based Model to evaluate the impact of socio economic factors on land use pattern. For this purpose, Dehradun an Indian city is selected as a case study. Socio economic factors were collected from field survey, Census of India, Directorate of economic census, Uttarakhand, India. A 3X3 simulating window is used to consider the impact on LULC. Cellular automata model results are examined for the identification of hot spot areas within the urban area and agent based model will be using logistic based regression approach where it will identify the correlation between each factor on LULC and classify the available area into low density, medium density, high density residential or commercial area. In the modeling phase, transition rule, neighborhood effect, cell change factors are used to improve the representation of built-up classes. Significant improvement is observed in the built-up classes from 84 % to 89 %. However after incorporating agent based model with cellular automata model the accuracy improved from 89 % to 94 % in 3 classes of urban i.e. low density, medium density and commercial classes
A coarse-grained model for the simulations of biomolecular interactions in cellular environments
Xie, Zhong-Ru; Chen, Jiawen; Wu, Yinghao
2014-01-01
The interactions of bio-molecules constitute the key steps of cellular functions. However, in vivo binding properties differ significantly from their in vitro measurements due to the heterogeneity of cellular environments. Here we introduce a coarse-grained model based on rigid-body representation to study how factors such as cellular crowding and membrane confinement affect molecular binding. The macroscopic parameters such as the equilibrium constant and the kinetic rate constant are calibrated by adjusting the microscopic coefficients used in the numerical simulations. By changing these model parameters that are experimentally approachable, we are able to study the kinetic and thermodynamic properties of molecular binding, as well as the effects caused by specific cellular environments. We investigate the volumetric effects of crowded intracellular space on bio-molecular diffusion and diffusion-limited reactions. Furthermore, the binding constants of membrane proteins are currently difficult to measure. We provide quantitative estimations about how the binding of membrane proteins deviates from soluble proteins under different degrees of membrane confinements. The simulation results provide biological insights to the functions of membrane receptors on cell surfaces. Overall, our studies establish a connection between the details of molecular interactions and the heterogeneity of cellular environments
Kadakia, Ekta; Shah, Lipa; Amiji, Mansoor M
2017-07-01
Nanoemulsions have shown potential in delivering drug across epithelial and endothelial cell barriers, which express efflux transporters. However, their transport mechanisms are not entirely understood. Our goal was to investigate the cellular permeability of nanoemulsion-encapsulated drugs and apply mathematical modeling to elucidate transport mechanisms and sensitive nanoemulsion attributes. Transport studies were performed in Caco-2 cells, using fish oil nanoemulsions and a model substrate, rhodamine-123. Permeability data was modeled using a semi-mechanistic approach, capturing the following cellular processes: endocytotic uptake of the nanoemulsion, release of rhodamine-123 from the nanoemulsion, efflux and passive permeability of rhodamine-123 in aqueous solution. Nanoemulsions not only improved the permeability of rhodamine-123, but were also less sensitive to efflux transporters. The model captured bidirectional permeability results and identified sensitive processes, such as the release of the nanoemulsion-encapsulated drug and cellular uptake of the nanoemulsion. Mathematical description of cellular processes, improved our understanding of transport mechanisms, such as nanoemulsions don't inhibit efflux to improve drug permeability. Instead, their endocytotic uptake, results in higher intracellular drug concentrations, thereby increasing the concentration gradient and transcellular permeability across biological barriers. Modeling results indicated optimizing nanoemulsion attributes like the droplet size and intracellular drug release rate, may further improve drug permeability.
A Cellular Automata-based Model for Simulating Restitution Property in a Single Heart Cell.
Sabzpoushan, Seyed Hojjat; Pourhasanzade, Fateme
2011-01-01
Ventricular fibrillation is the cause of the most sudden mortalities. Restitution is one of the specific properties of ventricular cell. The recent findings have clearly proved the correlation between the slope of restitution curve with ventricular fibrillation. This; therefore, mandates the modeling of cellular restitution to gain high importance. A cellular automaton is a powerful tool for simulating complex phenomena in a simple language. A cellular automaton is a lattice of cells where the behavior of each cell is determined by the behavior of its neighboring cells as well as the automata rule. In this paper, a simple model is depicted for the simulation of the property of restitution in a single cardiac cell using cellular automata. At first, two state variables; action potential and recovery are introduced in the automata model. In second, automata rule is determined and then recovery variable is defined in such a way so that the restitution is developed. In order to evaluate the proposed model, the generated restitution curve in our study is compared with the restitution curves from the experimental findings of valid sources. Our findings indicate that the presented model is not only capable of simulating restitution in cardiac cell, but also possesses the capability of regulating the restitution curve.
Cellular automata and integrodifferential equation models for cell renewal in mosaic tissues
Bloomfield, J. M.; Sherratt, J. A.; Painter, K. J.; Landini, G.
2010-01-01
Mosaic tissues are composed of two or more genetically distinct cell types. They occur naturally, and are also a useful experimental method for exploring tissue growth and maintenance. By marking the different cell types, one can study the patterns formed by proliferation, renewal and migration. Here, we present mathematical modelling suggesting that small changes in the type of interaction that cells have with their local cellular environment can lead to very different outcomes for the composition of mosaics. In cell renewal, proliferation of each cell type may depend linearly or nonlinearly on the local proportion of cells of that type, and these two possibilities produce very different patterns. We study two variations of a cellular automaton model based on simple rules for renewal. We then propose an integrodifferential equation model, and again consider two different forms of cellular interaction. The results of the continuous and cellular automata models are qualitatively the same, and we observe that changes in local environment interaction affect the dynamics for both. Furthermore, we demonstrate that the models reproduce some of the patterns seen in actual mosaic tissues. In particular, our results suggest that the differing patterns seen in organ parenchymas may be driven purely by the process of cell replacement under different interaction scenarios. PMID:20375040
A new stochastic cellular automaton model on traffic flow and its jamming phase transition
Sakai, Satoshi; Nishinari, Katsuhiro; Iida, Shinji
2006-01-01
A general stochastic traffic cellular automaton (CA) model, which includes the slow-to-start effect and driver's perspective, is proposed in this paper. It is shown that this model includes well-known traffic CA models such as the Nagel-Schreckenberg model, the quick-start model and the slow-to-start model as specific cases. Fundamental diagrams of this new model clearly show metastable states around the critical density even when the stochastic effect is present. We also obtain analytic expressions of the phase transition curve in phase diagrams by using approximate flow-density relations at boundaries. These phase transition curves are in excellent agreement with numerical results
a Predator-Prey Model Based on the Fully Parallel Cellular Automata
He, Mingfeng; Ruan, Hongbo; Yu, Changliang
We presented a predator-prey lattice model containing moveable wolves and sheep, which are characterized by Penna double bit strings. Sexual reproduction and child-care strategies are considered. To implement this model in an efficient way, we build a fully parallel Cellular Automata based on a new definition of the neighborhood. We show the roles played by the initial densities of the populations, the mutation rate and the linear size of the lattice in the evolution of this model.
Embryonic stem cells as an ectodermal cellular model of human p63-related dysplasia syndromes.
Rostagno, P.; Wolchinsky, Z.; Vigano, A.M.; Shivtiel, S.; Zhou, Huiqing; 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
An agent-based model of cellular dynamics and circadian variability in human endotoxemia.
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.
Boundary Induced Phase Transition in Cellular Automata Models of Pedestrian Flow
Bukáček, M.; Hrabák, Pavel
2016-01-01
Roč. 11, č. 4 (2016), s. 327-338 ISSN 1557-5969 R&D Projects: GA ČR GA13-13502S Institutional support: RVO:67985556 Keywords : Adaptive time-span * Cellular automata model * Floor-field * Pedestrian flow * Phase transition * Principle of bonds Subject RIV: BD - Theory of Information Impact factor: 0.696, year: 2016
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...
A cellular automata model of traffic flow with variable probability of randomization
Zheng Wei-Fan; Zhang Ji-Ye
2015-01-01
Research on the stochastic behavior of traffic flow is important to understand the intrinsic evolution rules of a traffic system. By introducing an interactional potential of vehicles into the randomization step, an improved cellular automata traffic flow model with variable probability of randomization is proposed in this paper. In the proposed model, the driver is affected by the interactional potential of vehicles before him, and his decision-making process is related to the interactional potential. Compared with the traditional cellular automata model, the modeling is more suitable for the driver’s random decision-making process based on the vehicle and traffic situations in front of him in actual traffic. From the improved model, the fundamental diagram (flow–density relationship) is obtained, and the detailed high-density traffic phenomenon is reproduced through numerical simulation. (paper)
Application of a novel cellular automaton porosity prediction model to aluminium castings
Atwood, R.C.; Chirazi, A.; Lee, P.D.
2002-01-01
A multiscale model was developed to predict the formation of porosity within a solidifying aluminium-silicon alloy. The diffusion of silicon and dissolved gas was simulated on a microscopic scale combined with cellular automaton models of gas porosity formation within the growing three-dimensional solidification microstructure. However, due to high computational cost, the modelled volume is limited to the millimetre range. This renders the application of direct modelling of complex shape castings unfeasible. Combining the microstructural modelling with a statistical response-surface prediction method allows application of the microstructural model results to industrial scale casts by incorporating them in commercial solidification software. (author)
On the derivation of approximations to cellular automata models and the assumption of independence.
Davies, K J; Green, J E F; Bean, N G; Binder, B J; Ross, J V
2014-07-01
Cellular automata are discrete agent-based models, generally used in cell-based applications. There is much interest in obtaining continuum models that describe the mean behaviour of the agents in these models. Previously, continuum models have been derived for agents undergoing motility and proliferation processes, however, these models only hold under restricted conditions. In order to narrow down the reason for these restrictions, we explore three possible sources of error in deriving the model. These sources are the choice of limiting arguments, the use of a discrete-time model as opposed to a continuous-time model and the assumption of independence between the state of sites. We present a rigorous analysis in order to gain a greater understanding of the significance of these three issues. By finding a limiting regime that accurately approximates the conservation equation for the cellular automata, we are able to conclude that the inaccuracy between our approximation and the cellular automata is completely based on the assumption of independence. Copyright © 2014 Elsevier Inc. All rights reserved.
Modeling and Analysis of Cellular Networks using Stochastic Geometry: A Tutorial
Elsawy, Hesham; Salem, Ahmed Sultan; Alouini, Mohamed-Slim; Win, Moe Z.
2016-01-01
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 baseline single-tier downlink cellular network with single antenna base stations and universal frequency reuse. Then, it characterizes signal-to-interference-plus-noise-ratio (SINR) and its related performance metrics. In particular, a unified approach to conduct error probability, outage probability, and transmission 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 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. To this end, the paper highlights the state-of-the- art research and points out future research directions.
Modeling and Analysis of Cellular Networks using Stochastic Geometry: A Tutorial
Elsawy, Hesham
2016-11-03
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 baseline single-tier downlink cellular network with single antenna base stations and universal frequency reuse. Then, it characterizes signal-to-interference-plus-noise-ratio (SINR) and its related performance metrics. In particular, a unified approach to conduct error probability, outage probability, and transmission 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 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. To this end, the paper highlights the state-of-the- art research and points out future research directions.
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
Modeling cell adhesion and proliferation: a cellular-automata based approach.
Vivas, J; Garzón-Alvarado, D; Cerrolaza, M
Cell adhesion is a process that involves the interaction between the cell membrane and another surface, either a cell or a substrate. Unlike experimental tests, computer models can simulate processes and study the result of experiments in a shorter time and lower costs. One of the tools used to simulate biological processes is the cellular automata, which is a dynamic system that is discrete both in space and time. This work describes a computer model based on cellular automata for the adhesion process and cell proliferation to predict the behavior of a cell population in suspension and adhered to a substrate. The values of the simulated system were obtained through experimental tests on fibroblast monolayer cultures. The results allow us to estimate the cells settling time in culture as well as the adhesion and proliferation time. The change in the cells morphology as the adhesion over the contact surface progress was also observed. The formation of the initial link between cell and the substrate of the adhesion was observed after 100 min where the cell on the substrate retains its spherical morphology during the simulation. The cellular automata model developed is, however, a simplified representation of the steps in the adhesion process and the subsequent proliferation. A combined framework of experimental and computational simulation based on cellular automata was proposed to represent the fibroblast adhesion on substrates and changes in a macro-scale observed in the cell during the adhesion process. The approach showed to be simple and efficient.
Optical scatter imaging of cellular and mitochondrial swelling in brain tissue models of stroke
Johnson, Lee James
2001-08-01
The severity of brain edema resulting from a stroke can determine a patient's survival and the extent of their recovery. Cellular swelling is the microscopic source of a significant part of brain edema. Mitochondrial swelling also appears to be a determining event in the death or survival of the cells that are injured during a stroke. Therapies for reducing brain edema are not effective in many cases and current treatments of stroke do not address mitochondrial swelling at all. This dissertation is motivated by the lack of a complete understanding of cellular swelling resulting from stroke and the lack of a good method to begin to study mitochondrial swelling resulting from stroke in living brain tissue. In this dissertation, a novel method of detecting mitochondrial and cellular swelling in living hippocampal slices is developed and validated. The system is used to obtain spatial and temporal information about cellular and mitochondrial swelling resulting from various models of stroke. The effect of changes in water content on light scatter and absorption are examined in two models of brain edema. The results of this study demonstrate that optical techniques can be used to detect changes in water content. Mie scatter theory, the theoretical basis of the dual- angle scatter ratio imaging system, is presented. Computer simulations based on Mie scatter theory are used to determine the optimal angles for imaging. A detailed account of the early systems is presented to explain the motivations for the system design, especially polarization, wavelength and light path. Mitochondrial sized latex particles are used to determine the system response to changes in scattering particle size and concentration. The dual-angle scatter ratio imaging system is used to distinguish between osmotic and excitotoxic models of stroke injury. Such distinction cannot be achieved using the current techniques to study cellular swelling in hippocampal slices. The change in the scatter ratio is
Uniform and localized corrosion modelling by means of probabilistic cellular automata
Perez-Brokate, Cristian
2016-01-01
Numerical modelling is complementary tool for corrosion prediction. The objective of this work is to develop a corrosion model by means of a probabilistic cellular automata approach at a mesoscopic scale. In this work, we study the morphological evolution and kinetics of corrosion. This model couples electrochemical oxidation and reduction reactions. Regarding kinetics, cellular automata models are able to describe current as a function of the applied potential for a redox reaction on an inert electrode. The inclusion of probabilities allows the description of the stochastic nature of anodic and cathodic reactions. Corrosion morphology has been studied in different context: generalised corrosion, pitting corrosion and corrosion in an occluded environment. a general tendency of two regimes is found. a first regime of uniform corrosion where the anodic and cathodic reactions occur homogeneously over the surface. a second regime of localized corrosion when there is a spatial separation of anodic and cathodic zones, with an increase of anodic reaction rate. (author) [fr
Three-dimensional cellular automata as a model of a seismic fault
Gálvez, G; Muñoz, A
2017-01-01
The Earth's crust is broken into a series of plates, whose borders are the seismic fault lines and it is where most of the earthquakes occur. This plating system can in principle be described by a set of nonlinear coupled equations describing the motion of the plates, its stresses, strains and other characteristics. Such a system of equations is very difficult to solve, and nonlinear parts leads to a chaotic behavior, which is not predictable. In 1989, Bak and Tang presented an earthquake model based on the sand pile cellular automata. The model though simple, provides similar results to those observed in actual earthquakes. In this work the cellular automata in three dimensions is proposed as a best model to approximate a seismic fault. It is noted that the three-dimensional model reproduces similar properties to those observed in real seismicity, especially, the Gutenberg-Richter law. (paper)
Parallel Genetic Algorithms for calibrating Cellular Automata models: Application to lava flows
D'Ambrosio, D.; Spataro, W.; Di Gregorio, S.; Calabria Univ., Cosenza; Crisci, G.M.; Rongo, R.; Calabria Univ., Cosenza
2005-01-01
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
Simulation of a plane wavefront propagating in cardiac tissue using a cellular automata model
Barbosa, Carlos R Hall
2003-01-01
We present a detailed description of a cellular automata model for the propagation of action potential in a planar cardiac tissue, which is very fast and easy to use. The model incorporates anisotropy in the electrical conductivity and a spatial variation of the refractory time. The transmembrane potential distribution is directly derived from the cell states, and the intracellular and extracellular potential distributions are calculated for the particular case of a plane wavefront. Once the potential distributions are known, the associated current densities are calculated by Ohm's law, and the magnetic field is determined at a plane parallel to the cardiac tissue by applying the law of Biot and Savart. The results obtained for propagation speed and for magnetic field amplitude with the cellular automata model are compared with values predicted by the bidomain formulation, for various angles between wavefront propagation and fibre direction, characterizing excellent agreement between the models
Stochastic processes, multiscale modeling, and numerical methods for computational cellular biology
2017-01-01
This book focuses on the modeling and mathematical analysis of stochastic dynamical systems along with their simulations. The collected chapters will review fundamental and current topics and approaches to dynamical systems in cellular biology. This text aims to develop improved mathematical and computational methods with which to study biological processes. At the scale of a single cell, stochasticity becomes important due to low copy numbers of biological molecules, such as mRNA and proteins that take part in biochemical reactions driving cellular processes. When trying to describe such biological processes, the traditional deterministic models are often inadequate, precisely because of these low copy numbers. This book presents stochastic models, which are necessary to account for small particle numbers and extrinsic noise sources. The complexity of these models depend upon whether the biochemical reactions are diffusion-limited or reaction-limited. In the former case, one needs to adopt the framework of s...
Cellular self-assembly and biomaterials-based organoid models of development and diseases.
Shah, Shivem B; Singh, Ankur
2017-04-15
Organogenesis and morphogenesis have informed our understanding of physiology, pathophysiology, and avenues to create new curative and regenerative therapies. Thus far, this understanding has been hindered by the lack of a physiologically relevant yet accessible model that affords biological control. Recently, three-dimensional ex vivo cellular cultures created through cellular self-assembly under natural extracellular matrix cues or through biomaterial-based directed assembly have been shown to physically resemble and recapture some functionality of target organs. These "organoids" have garnered momentum for their applications in modeling human development and disease, drug screening, and future therapy design or even organ replacement. This review first discusses the self-organizing organoids as materials with emergent properties and their advantages and limitations. We subsequently describe biomaterials-based strategies used to afford more control of the organoid's microenvironment and ensuing cellular composition and organization. In this review, we also offer our perspective on how multifunctional biomaterials with precise spatial and temporal control could ultimately bridge the gap between in vitro organoid platforms and their in vivo counterparts. Several notable reviews have highlighted PSC-derived organoids and 3D aggregates, including embryoid bodies, from a development and cellular assembly perspective. The focus of this review is to highlight the materials-based approaches that cells, including PSCs and others, adopt for self-assembly and the controlled development of complex tissues, such as that of the brain, gut, and immune system. Copyright © 2017 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.
Cellular automaton modelling of ductile iron microstructure in the thin wall casting
Burbelko, A A; Gurgul, D; Kapturkiewicz, W; Górny, M
2012-01-01
The mathematical model of the globular eutectic solidification in 2D was designed. Proposed model is based on the Cellular Automaton Finite Differences (CA-FD) calculation method. Model has been used for studies of the primary austenite and of globular eutectic grains growth during the ductile iron solidification in the thin wall casting. Model takes into account, among other things, non-uniform temperature distribution in the casting wall cross-section, kinetics of the austenite and graphite grains nucleation, and non-equilibrium nature of the interphase boundary migration.
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.
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.
Cantone, Martina; Santos, Guido; Wentker, Pia; Lai, Xin; Vera, Julio
2017-01-01
Even today two bacterial lung infections, namely pneumonia and tuberculosis, are among the 10 most frequent causes of death worldwide. These infections still lack effective treatments in many developing countries and in immunocompromised populations like infants, elderly people and transplanted patients. The interaction between bacteria and the host is a complex system of interlinked intercellular and the intracellular processes, enriched in regulatory structures like positive and negative feedback loops. Severe pathological condition can emerge when the immune system of the host fails to neutralize the infection. This failure can result in systemic spreading of pathogens or overwhelming immune response followed by a systemic inflammatory response. Mathematical modeling is a promising tool to dissect the complexity underlying pathogenesis of bacterial lung infection at the molecular, cellular and tissue levels, and also at the interfaces among levels. In this article, we introduce mathematical and computational modeling frameworks that can be used for investigating molecular and cellular mechanisms underlying bacterial lung infection. Then, we compile and discuss published results on the modeling of regulatory pathways and cell populations relevant for lung infection and inflammation. Finally, we discuss how to make use of this multiplicity of modeling approaches to open new avenues in the search of the molecular and cellular mechanisms underlying bacterial infection in the lung.
Vaca-González, J J; Gutiérrez, M L; Guevara, J M; Garzón-Alvarado, D A
2017-01-01
Articular cartilage is characterized by low cell density of only one cell type, chondrocytes, and has limited self-healing properties. When articular cartilage is affected by traumatic injuries, a therapeutic strategy such as autologous chondrocyte implantation is usually proposed for its treatment. This approach requires in vitro chondrocyte expansion to yield high cell number for cell transplantation. To improve the efficiency of this procedure, it is necessary to assess cell dynamics such as migration, proliferation and cell death during culture. Computational models such as cellular automata can be used to simulate cell dynamics in order to enhance the result of cell culture procedures. This methodology has been implemented for several cell types; however, an experimental validation is required for each one. For this reason, in this research a cellular automata model, based on random-walk theory, was devised in order to predict articular chondrocyte behavior in monolayer culture during cell expansion. Results demonstrated that the cellular automata model corresponded to cell dynamics and computed-accurate quantitative results. Moreover, it was possible to observe that cell dynamics depend on weighted probabilities derived from experimental data and cell behavior varies according to the cell culture period. Thus, depending on whether cells were just seeded or proliferated exponentially, culture time probabilities differed in percentages in the CA model. Furthermore, in the experimental assessment a decreased chondrocyte proliferation was observed along with increased passage number. This approach is expected to having other uses as in enhancing articular cartilage therapies based on tissue engineering and regenerative medicine.
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.
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......, hollow, lattice structure and rotated lattice structure. Compression test is applied to the specimens while they are deformed. The analytical approach includes finite element (FE), geometrical and mathematical models for prediction of collapse strength. The results from the the models are verified...
Modeling virtualized downlink cellular networks with ultra-dense small cells
Ibrahim, Hazem
2015-09-11
The unrelenting increase in the mobile users\\' populations and traffic demand drive cellular network operators to densify their infrastructure. Network densification increases the spatial frequency reuse efficiency while maintaining the signal-to-interference-plus-noise-ratio (SINR) performance, hence, increases the spatial spectral efficiency and improves the overall network performance. However, control signaling in such dense networks consumes considerable bandwidth and limits the densification gain. Radio access network (RAN) virtualization via control plane (C-plane) and user plane (U-plane) splitting has been recently proposed to lighten the control signaling burden and improve the network throughput. In this paper, we present a tractable analytical model for virtualized downlink cellular networks, using tools from stochastic geometry. We then apply the developed modeling framework to obtain design insights for virtualized RANs and quantify associated performance improvement. © 2015 IEEE.
Denker, Elsa; Jiang, Di
2012-05-01
Biological tubes are a prevalent structural design across living organisms. They provide essential functions during the development and adult life of an organism. Increasing progress has been made recently in delineating the cellular and molecular mechanisms underlying tubulogenesis. This review aims to introduce ascidian notochord morphogenesis as an interesting model system to study the cell biology of tube formation, to a wider cell and developmental biology community. We present fundamental morphological and cellular events involved in notochord morphogenesis, compare and contrast them with other more established tubulogenesis model systems, and point out some unique features, including bipolarity of the notochord cells, and using cell shape changes and cell rearrangement to connect lumens. We highlight some initial findings in the molecular mechanisms of notochord morphogenesis. Based on these findings, we present intriguing problems and put forth hypotheses that can be addressed in future studies. Copyright © 2012 Elsevier Ltd. All rights reserved.
Modeling and Experimental Study of Soft Error Propagation Based on Cellular Automaton
He, Wei; Wang, Yueke; Xing, Kefei; Yang, Jianwei
2016-01-01
Aiming to estimate SEE soft error performance of complex electronic systems, a soft error propagation model based on cellular automaton is proposed and an estimation methodology based on circuit partitioning and error propagation is presented. Simulations indicate that different fault grade jamming and different coupling factors between cells are the main parameters influencing the vulnerability of the system. Accelerated radiation experiments have been developed to determine the main paramet...
Long-range inverse two-spin correlations in one-dimensional Potts lattices
Tejero, C.F.; Cuesta, J.A.; Brito, R.
1989-01-01
The inverse two-spin correlation function of a one-dimensional three-state Potts lattice with constant nearest-neighbor interactions in a uniform external field is derived exactly. It is shown that the external field induces long-range correlations. The inverse two-spin correlation function decays in a monotonic exponential fashion for a ferromagnetic lattice, while it decays in an oscillatory exponential fashion for an antiferromagnetic lattice. With no external field the inverse two-spin correlation function has a finite range equal to that of the interactions
Bru, Antonio; Cardona, Pere-Joan
2010-01-01
Background Mycobacterium tuberculosis is a particularly aggressive microorganism and the host's defense is based on the induction of cellular immunity, in which the creation of a granulomatous structure has an important role. Methodology We present here a new 2D cellular automata model based on the concept of a multifunctional process that includes key factors such as the chemokine attraction of the cells; the role of innate immunity triggered by natural killers; the presence of neutrophils; apoptosis and necrosis of infected macrophages; the removal of dead cells by macrophages, which induces the production of foamy macrophages (FMs); the life cycle of the bacilli as a determinant for the evolution of infected macrophages; and the immune response. Results The results obtained after the inclusion of two degrees of tolerance to the inflammatory response triggered by the infection shows that the model can cover a wide spectrum, ranging from highly-tolerant (i.e. mice) to poorly-tolerant hosts (i.e. mini-pigs or humans). Conclusions This model suggest that stopping bacillary growth at the onset of the infection might be difficult and the important role played by FMs in bacillary drainage in poorly-tolerant hosts together with apoptosis and innate lymphocytes. It also shows the poor ability of the cellular immunity to control the infection, provides a clear protective character to the granuloma, due its ability to attract a sufficient number of cells, and explains why an already infected host can be constantly reinfected. PMID:20886087
Silver Nanoparticle-Mediated Cellular Responses in Various Cell Lines: An in Vitro Model
Xi-Feng Zhang
2016-09-01
Full Text Available Silver nanoparticles (AgNPs have attracted increased interest and are currently used in various industries including medicine, cosmetics, textiles, electronics, and pharmaceuticals, owing to their unique physical and chemical properties, particularly as antimicrobial and anticancer agents. Recently, several studies have reported both beneficial and toxic effects of AgNPs on various prokaryotic and eukaryotic systems. To develop nanoparticles for mediated therapy, several laboratories have used a variety of cell lines under in vitro conditions to evaluate the properties, mode of action, differential responses, and mechanisms of action of AgNPs. In vitro models are simple, cost-effective, rapid, and can be used to easily assess efficacy and performance. The cytotoxicity, genotoxicity, and biocompatibility of AgNPs depend on many factors such as size, shape, surface charge, surface coating, solubility, concentration, surface functionalization, distribution of particles, mode of entry, mode of action, growth media, exposure time, and cell type. Cellular responses to AgNPs are different in each cell type and depend on the physical and chemical nature of AgNPs. This review evaluates significant contributions to the literature on biological applications of AgNPs. It begins with an introduction to AgNPs, with particular attention to their overall impact on cellular effects. The main objective of this review is to elucidate the reasons for different cell types exhibiting differential responses to nanoparticles even when they possess similar size, shape, and other parameters. Firstly, we discuss the cellular effects of AgNPs on a variety of cell lines; Secondly, we discuss the mechanisms of action of AgNPs in various cellular systems, and try to elucidate how AgNPs interact with different mammalian cell lines and produce significant effects; Finally, we discuss the cellular activation of various signaling molecules in response to AgNPs, and conclude with
Krzysztof Małecki
2017-12-01
Full Text Available A complex system is a set of mutually interacting elements for which it is possible to construct a mathematical model. This article focuses on the cellular automata theory and the graph theory in order to compare various types of cellular automata and to analyse applications of graph structures together with cellular automata. It proposes a graph cellular automaton with a variable configuration of cells and relation-based neighbourhoods (r–GCA. The developed mechanism enables modelling of phenomena found in complex systems (e.g., transport networks, urban logistics, social networks taking into account the interaction between the existing objects. As an implementation example, modelling of moving vehicles has been made and r–GCA was compared to the other cellular automata models simulating the road traffic and used in the computer simulation process.
Referent 3D tumor model at cellular level in radionuclide therapy
Spaic, R.; Ilic, R.D.; Petrovic, B.J.
2002-01-01
Aim Conventional internal dosimetry has a lot of limitations because of tumor dose nonuniformity. The best approach for absorbed dose at cellular level for different tumors in radionuclide therapy calculation is Monte Carlo method. The purpose of this study is to introduce referent tumor 3D model at cellular level for Monte Carlo simulation study in radionuclide therapy. Material and Methods The moment when tumor is detectable and when same therapy can start is time period in which referent 3D tumor model at cellular level was defined. In accordance with tumor growth rate at that moment he was a sphere with same radius (10 000 μm). In that tumor there are cells or cluster of cells, which are randomly distributed spheres. Distribution of cells/cluster of cells can be calculated from histology data but it was assumed that this distribution is normal with the same mean value and standard deviation (100±50 mm). Second parameter, which was selected to define referent tumor, is volume density of cells (30%). In this referent tumor there are no necroses. Stroma is defined as space between spheres with same concentration of materials as in spheres. Results: Referent tumor defined on this way have about 2,2 10 5 cells or cluster of cells random distributed. Using this referent 3D tumor model and for same concentration of radionuclides (1:100) and energy of beta emitters (1000 keV) which are homogeneously distributed in labeled cells absorbed dose for all cells was calculated. Simulations are done using FOTELP Monte Carlo code, which is modified for this purposes. Results of absorbed dose in cells are given in numerical values (1D distribution) and as the images (2D or 3D distributions). Conclusion Geometrical module for Monte Carlo simulation study can be standardized by introducing referent 3D tumor model at cellular level. This referent 3D tumor model gives most realistic presentation of different tumors at the moment of their detectability. Referent 3D tumor model at
Caty, O.; Maire, E.; Youssef, S.; Bouchet, R.
2008-01-01
Closed-cell cellular materials exhibit several interesting properties. These properties are, however, very difficult to simulate and understand from the knowledge of the cellular microstructure. This problem is mostly due to the highly complex organization of the cells and to their very fine walls. X-ray tomography can produce three-dimensional (3-D) images of the structure, enabling one to visualize locally the damage of the cell walls that would result in the structure collapsing. These data could be used for meshing with continuum elements of the structure for finite element (FE) calculations. But when the density is very low, the walls are fine and the meshes based on continuum elements are not suitable to represent accurately the structure while preserving the representativeness of the model in terms of cell size. This paper presents a shell FE model obtained from tomographic 3-D images that allows bigger volumes of low-density closed-cell cellular materials to be calculated. The model is enriched by direct thickness measurement on the tomographic images. The values measured are ascribed to the shell elements. To validate and use the model, a structure composed of stainless steel hollow spheres is firstly compressed and scanned to observe local deformations. The tomographic data are also meshed with shells for a FE calculation. The convergence of the model is checked and its performance is compared with a continuum model. The global behavior is compared with the measures of the compression test. At the local scale, the model allows the local stress and strain field to be calculated. The calculated deformed shape is compared with the deformed tomographic images
A Model of How Different Biology Experts Explain Molecular and Cellular Mechanisms
Trujillo, Caleb M.; Anderson, Trevor R.; Pelaez, Nancy J.
2015-01-01
Constructing explanations is an essential skill for all science learners. The goal of this project was to model the key components of expert explanation of molecular and cellular mechanisms. As such, we asked: What is an appropriate model of the components of explanation used by biology experts to explain molecular and cellular mechanisms? Do explanations made by experts from different biology subdisciplines at a university support the validity of this model? Guided by the modeling framework of R. S. Justi and J. K. Gilbert, the validity of an initial model was tested by asking seven biologists to explain a molecular mechanism of their choice. Data were collected from interviews, artifacts, and drawings, and then subjected to thematic analysis. We found that biologists explained the specific activities and organization of entities of the mechanism. In addition, they contextualized explanations according to their biological and social significance; integrated explanations with methods, instruments, and measurements; and used analogies and narrated stories. The derived methods, analogies, context, and how themes informed the development of our final MACH model of mechanistic explanations. Future research will test the potential of the MACH model as a guiding framework for instruction to enhance the quality of student explanations. PMID:25999313
An improved multi-value cellular automata model for heterogeneous bicycle traffic flow
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.
An improved multi-value cellular automata model for heterogeneous bicycle traffic flow
Jin, Sheng; Qu, Xiaobo; Xu, Cheng; Ma, Dongfang; Wang, Dianhai
2015-01-01
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
Unified tractable model for downlink MIMO cellular networks using stochastic geometry
Afify, Laila H.
2016-07-26
Several research efforts are invested to develop stochastic geometry models for cellular networks with multiple antenna transmission and reception (MIMO). On one hand, there are models that target abstract outage probability and ergodic rate for simplicity. On the other hand, there are models that sacrifice simplicity to target more tangible performance metrics such as the error probability. Both types of models are completely disjoint in terms of the analytic steps to obtain the performance measures, which makes it challenging to conduct studies that account for different performance metrics. This paper unifies both techniques and proposes a unified stochastic-geometry based mathematical paradigm to account for error probability, outage probability, and ergodic rates in MIMO cellular networks. The proposed model is also unified in terms of the antenna configurations and leads to simpler error probability analysis compared to existing state-of-the-art models. The core part of the analysis is based on abstracting unnecessary information conveyed within the interfering signals by assuming Gaussian signaling. To this end, the accuracy of the proposed framework is verified against state-of-the-art models as well as system level simulations. We provide via this unified study insights on network design by reflecting system parameters effect on different performance metrics. © 2016 IEEE.
López, Leonardo; Burguerner, Germán; Giovanini, Leonardo
2014-04-12
The spread of an infectious disease is determined by biological and social factors. Models based on cellular automata are adequate to describe such natural systems consisting of a massive collection of simple interacting objects. They characterize the time evolution of the global system as the emergent behaviour resulting from the interaction of the objects, whose behaviour is defined through a set of simple rules that encode the individual behaviour and the transmission dynamic. An epidemic is characterized trough an individual-based-model built upon cellular automata. In the proposed model, each individual of the population is represented by a cell of the automata. This way of modeling an epidemic situation allows to individually define the characteristic of each individual, establish different scenarios and implement control strategies. A cellular automata model to study the time evolution of a heterogeneous populations through the various stages of disease was proposed, allowing the inclusion of individual heterogeneity, geographical characteristics and social factors that determine the dynamic of the desease. Different assumptions made to built the classical model were evaluated, leading to following results: i) for low contact rate (like in quarantine process or low density population areas) the number of infective individuals is lower than other areas where the contact rate is higher, and ii) for different initial spacial distributions of infected individuals different epidemic dynamics are obtained due to its influence on the transition rate and the reproductive ratio of disease. The contact rate and spatial distributions have a central role in the spread of a disease. For low density populations the spread is very low and the number of infected individuals is lower than in highly populated areas. The spacial distribution of the population and the disease focus as well as the geographical characteristic of the area play a central role in the dynamics of the
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.
Modelling land-use effects of future urbanization using cellular automata
Fuglsang, Morten; Münier, B.; Hansen, H.S.
2013-01-01
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......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...... 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...
Guided Inquiry and Consensus-Building Used to Construct Cellular Models
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.
Forest, Loïc; Demongeot, Jacques; Demongeota, Jacques
2006-05-01
The radial growth of conifer trees proceeds from the dynamics of a merismatic tissue called vascular cambium or cambium. Cambium is a thin layer of active proliferating cells. The purpose of this paper was to model the main characteristics of cambial activity and its consecutive radial growth. Cell growth is under the control of the auxin hormone indole-3-acetic. The model is composed of a discrete part, which accounts for cellular proliferation, and a continuous part involving the transport of auxin. Cambium is modeled in a two-dimensional cross-section by a cellular automaton that describes the set of all its constitutive cells. Proliferation is defined as growth and division of cambial cells under neighbouring constraints, which can eliminate some cells from the cambium. The cell-growth rate is determined from auxin concentration, calculated with the continuous model. We studied the integration of each elementary cambial cell activity into the global coherent movement of macroscopic morphogenesis. Cases of normal and abnormal growth of Pinus radiata (D. Don) are modelled. Abnormal growth includes deformed trees where gravity influences auxin transport, producing heterogeneous radial growth. Cross-sectional microscopic views are also provided to validate the model's hypothesis and results.
An improved cellular automata model for train operation simulation with dynamic acceleration
Li, Wen-Jun; Nie, Lei
2018-03-01
Urban rail transit plays an important role in the urban public traffic because of its advantages of fast speed, large transport capacity, high safety, reliability and low pollution. This study proposes an improved cellular automaton (CA) model by considering the dynamic characteristic of the train acceleration to analyze the energy consumption and train running time. Constructing an effective model for calculating energy consumption to aid train operation improvement is the basis for studying and analyzing energy-saving measures for urban rail transit system operation.
Stochastic modeling for dynamics of HIV-1 infection using cellular automata: A review.
Precharattana, Monamorn
2016-02-01
Recently, the description of immune response by discrete models has emerged to play an important role to study the problems in the area of human immunodeficiency virus type 1 (HIV-1) infection, leading to AIDS. As infection of target immune cells by HIV-1 mainly takes place in the lymphoid tissue, cellular automata (CA) models thus represent a significant step in understanding when the infected population is dispersed. Motivated by these, the studies of the dynamics of HIV-1 infection using CA in memory have been presented to recognize how CA have been developed for HIV-1 dynamics, which issues have been studied already and which issues still are objectives in future studies.
Modeling and Performance Analysis for Cell Access and Handoff Schemes in Two-Tier Cellular Networks
Kyungkoo Jun
2014-01-01
Full Text Available We investigate the effects of handoff on system performance in two-tier cellular networks. Two of the main performance metrics are new call blocking probability and handoff drop rate. We develop analytical models to evaluate the performance of two different handoff schemes. One scheme considers only femto-to-macrocell handoff while the other is bidirectional including macro-to-femtocell handoff. Our model is more elaborate than existing ones which have not considered the mobility of mobile stations. Numerical results show that the bidirectional scheme performs better than the femto-to-macrocell handoff as it achieves lower blocking probability and drop rate.
Modeling Mixed Bicycle Traffic Flow: A Comparative Study on the Cellular Automata Approach
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.
Esch, Jesse J; Shah, Pinak B; Cockrill, Barbara A; Farber, Harrison W; Landzberg, Michael J; Mehra, Mandeep R; Mullen, Mary P; Opotowsky, Alexander R; Waxman, Aaron B; Lock, James E; Marshall, Audrey C
2013-04-01
Patients with severe pulmonary arterial hypertension (PAH) face significant morbidity and death as a consequence of progressive right heart failure. Surgical shunt placement between the left PA and descending aorta (Potts shunt) appears promising for PAH palliation in children; however, surgical mortality is likely to be unacceptably high in adults with PAH. We describe a technique for transcatheter Potts shunt (TPS) creation by fluoroscopically guided retrograde needle perforation of the descending aorta at the site of apposition to the left PA to create a tract for deployment of a covered stent between these vessels. This covered stent-anchored by the vessel walls and surrounding tissue-serves as the shunt. TPS creation was considered in 7 patients and performed in 4. The procedure was technically successful in 3 patients; 1 patient died during the procedure as a result of uncontrolled hemothorax. One acute survivor, critically ill at the time of TPS creation, later died of comorbidities. The 2 mid-term survivors (follow-up of 10 and 4 months) are well at home, with symptomatic improvement and no late complications. The 3 candidate patients in whom the procedure was not performed died within 1 month of consideration, underscoring the tenuous nature of this population. TPS creation is feasible and may offer symptomatic relief to select patients with refractory PAH. Further study of this innovative approach is warranted. Copyright © 2013 International Society for Heart and Lung Transplantation. Published by Elsevier Inc. All rights reserved.
Smith, G.T.; Hubner, K.F.; Goodman, M.M.; Stubbs, J.B.
1992-01-01
Positron emission tomography (PET) has been used to measure tissue radiotracer concentration in vivo. Radiochemical distribution can be determined with compartmental model analysis. A two compartment model describes the kinetics of N-13 ammonia ( 13 NH 3 ) in the myocardium. The model consists of a vascular space, Q 1 and a space for 13 NH 3 bound within the tissue, Q 2 . Differential equations for the model can be written: X(t) = AX(t) + BU( t), Y(t)= CX(t)+ DU(t) (1) where X(t) is a column vector [Q 1 (t); Q 2 (t)], U(t) is the arterial input activity measured from the left ventricular blood pool, and Y(t) is the measured tissue activity using PET. Matrices A, B, C, and D are dependent on physiological parameters describing the kinetics of 13 NH 3 in the myocardium. Estimated parameter matrices in Equation 1 have been validated in dog experiments by measuring myocardial perfusion with dynamic PET scanning and intravenous injection of 13 NH 3 . Tracer concentrations for each compartment can be calculated by direct integration of Equation 1. If the cellular level distribution of each compartment is known, the concentration of tracer within the intracellular and extracellular space can be determined. Applications of this type of modeling include parameter estimation for measurement of physiological processes, organ level dosimetry, and determination of cellular radiotracer distribution
Züleyha, Artuç; Ziya, Merdan; Selçuk, Yeşiltaş; Kemal, Öztürk M.; Mesut, Tez
2017-11-01
Computational models for tumors have difficulties due to complexity of tumor nature and capacities of computational tools, however, these models provide visions to understand interactions between tumor and its micro environment. Moreover computational models have potential to develop strategies for individualized treatments for cancer. To observe a solid brain tumor, glioblastoma multiforme (GBM), we present a two dimensional Ising Model applied on Creutz cellular automaton (CCA). The aim of this study is to analyze avascular spherical solid tumor growth, considering transitions between non tumor cells and cancer cells are like phase transitions in physical system. Ising model on CCA algorithm provides a deterministic approach with discrete time steps and local interactions in position space to view tumor growth as a function of time. Our simulation results are given for fixed tumor radius and they are compatible with theoretical and clinic data.
Cellular Automata Modelling of Photo-Induced Oxidation Processes in Molecularly Doped Polymers
David M. Goldie
2016-11-01
Full Text Available The possibility of employing cellular automata (CA to model photo-induced oxidation processes in molecularly doped polymers is explored. It is demonstrated that the oxidation dynamics generated using CA models exhibit stretched-exponential behavior. This dynamical characteristic is in general agreement with an alternative analysis conducted using standard rate equations provided the molecular doping levels are sufficiently low to prohibit the presence of safe-sites which are impenetrable to dissolved oxygen. The CA models therefore offer the advantage of exploring the effect of dopant agglomeration which is difficult to assess from standard rate equation solutions. The influence of UV-induced bleaching or darkening upon the resulting oxidation dynamics may also be easily incorporated into the CA models and these optical effects are investigated for various photo-oxidation product scenarios. Output from the CA models is evaluated for experimental photo-oxidation data obtained from a series of hydrazone-doped polymers.
Cellular retention of radioactivity and increased radiation dose. Model experiments with EGF-dextran
Sundberg, Aasa Liljegren; Blomquist, Erik; Carlsson, Joergen; Steffen, Ann-Charlott; Gedda, Lars
2003-01-01
Targeting of tumor cells with radiolabeled biomolecules is a possible approach to inactivate disseminated tumor cells. However, rapid degradation of the biomolecules after cellular internalization and subsequent excretion of the radioactivity is a problem. We studied the possibility of using dextran as a carrier of radionuclides to improve the intracellular retention. An EGF-dextran conjugate, aimed for targeting of tumor cells overexpressing the EGF-receptor, was used as model. Retention tests were performed with 125 I on different parts: [ 125 I]-EGF-dextran-[ 125 I], [ 125 I]-EGF-dextran and EGF-dextran-[ 125 I]. Comparisons were made with [ 125 I]-EGF. The radiolabeled compounds were incubated with cultured glioma cells for different times. The cellular retention of radioactivity was then measured for up to 24 h. Expected radiation doses at the cellular level were calculated assuming that 131 I, instead of 125 I, was coupled to EGF and EGF-dextran. The results indicated that the EGF-part of the conjugate was degraded and the EGF-attached radioactivity was rapidly excreted, whereas radioactivity on dextran was retained intracellularly to a high degree, i.e. 70-80% of the radioactivity bound to dextran was still cell-associated after 24 h. The retention after 24 h was significantly higher (p < 0.001) when the radioactivity was on the dextran instead of the EGF-part. The radiolabeled EGF-dextran had a notably high specific radioactivity; up to 11 MBq/μg. There was potential for at least hundred times increased radiation dose per receptor interaction when the radioactivity was on the dextran part. The advantage with radioactivity on the dextran part was the high cellular retention and the high specific radioactivity (higher than previously reported for other residualizing labels) without severe loss of receptor specific binding. Thus, dextran seems suitable as a carrier of radionuclides aimed for therapy and gives potential for a highly increased radiation dose
A Local Land Use Competition Cellular Automata Model and Its Application
Jun Yang
2016-06-01
Full Text Available Cellular automaton (CA is an important method in land use and cover change studies, however, the majority of research focuses on the discovery of macroscopic factors affecting LUCC, which results in ignoring the local effects within the neighborhoods. This paper introduces a Local Land Use Competition Cellular Automata (LLUC-CA model, based on local land use competition, land suitability evaluation, demand analysis of the different land use types, and multi-target land use competition allocation algorithm to simulate land use change at a micro level. The model is applied to simulate land use changes at Jinshitan National Tourist Holiday Resort from 1988 to 2012. The results show that the simulation accuracies were 64.46%, 77.21%, 85.30% and 99.14% for the agricultural land, construction land, forestland and water, respectively. In addition, comparing the simulation results of the LLUC-CA and CA-Markov model with the real land use data, their overall spatial accuracies were found to be 88.74% and 86.82%, respectively. In conclusion, the results from this study indicated that the model was an acceptable method for the simulation of large-scale land use changes, and the approach used here is applicable to analyzing the land use change driven forces and assist in decision-making.
Ma, Xiao; Zheng, Wei-Fan; Jiang, Bao-Shan; Zhang, Ji-Ye
2016-10-01
With the development of traffic systems, some issues such as traffic jams become more and more serious. Efficient traffic flow theory is needed to guide the overall controlling, organizing and management of traffic systems. On the basis of the cellular automata model and the traffic flow model with look-ahead potential, a new cellular automata traffic flow model with negative exponential weighted look-ahead potential is presented in this paper. By introducing the negative exponential weighting coefficient into the look-ahead potential and endowing the potential of vehicles closer to the driver with a greater coefficient, the modeling process is more suitable for the driver’s random decision-making process which is based on the traffic environment that the driver is facing. The fundamental diagrams for different weighting parameters are obtained by using numerical simulations which show that the negative exponential weighting coefficient has an obvious effect on high density traffic flux. The complex high density non-linear traffic behavior is also reproduced by numerical simulations. Project supported by the National Natural Science Foundation of China (Grant Nos. 11572264, 11172247, 11402214, and 61373009).
Cellular automata model for traffic flow at intersections in internet of vehicles
Zhao, Han-Tao; Liu, Xin-Ru; Chen, Xiao-Xu; Lu, Jian-Cheng
2018-03-01
Considering the effect of the front vehicle's speed, the influence of the brake light and the conflict of the traffic flow, we established a cellular automata model called CE-NS for traffic flow at the intersection in the non-vehicle networking environment. According to the information interaction of Internet of Vehicles (IoV), introducing parameters describing the congestion and the accurate speed of the front vehicle into the CE-NS model, we improved the rules of acceleration, deceleration and conflict, and finally established a cellular automata model for traffic flow at intersections of IoV. The relationship between traffic parameters such as vehicle speed, flow and average travel time is obtained by numerical simulation of two models. Based on this, we compared the traffic situation of the non-vehicle networking environment with conditions of IoV environment, and analyzed the influence of the different degree of IoV on the traffic flow. The results show that the traffic speed is increased, the travel time is reduced, the flux of intersections is increased and the traffic flow is more smoothly under IoV environment. After the vehicle which achieves IoV reaches a certain proportion, the operation effect of the traffic flow begins to improve obviously.
Computational Modeling of Proteins based on Cellular Automata: A Method of HP Folding Approximation.
Madain, Alia; Abu Dalhoum, Abdel Latif; Sleit, Azzam
2018-06-01
The design of a protein folding approximation algorithm is not straightforward even when a simplified model is used. The folding problem is a combinatorial problem, where approximation and heuristic algorithms are usually used to find near optimal folds of proteins primary structures. Approximation algorithms provide guarantees on the distance to the optimal solution. The folding approximation approach proposed here depends on two-dimensional cellular automata to fold proteins presented in a well-studied simplified model called the hydrophobic-hydrophilic model. Cellular automata are discrete computational models that rely on local rules to produce some overall global behavior. One-third and one-fourth approximation algorithms choose a subset of the hydrophobic amino acids to form H-H contacts. Those algorithms start with finding a point to fold the protein sequence into two sides where one side ignores H's at even positions and the other side ignores H's at odd positions. In addition, blocks or groups of amino acids fold the same way according to a predefined normal form. We intend to improve approximation algorithms by considering all hydrophobic amino acids and folding based on the local neighborhood instead of using normal forms. The CA does not assume a fixed folding point. The proposed approach guarantees one half approximation minus the H-H endpoints. This lower bound guaranteed applies to short sequences only. This is proved as the core and the folds of the protein will have two identical sides for all short sequences.
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
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.
Cellular automaton modeling of ductile iron microstructure in the thin wall
A.A. Burbelko
2011-10-01
Full Text Available The mathematical model of the globular eutectic solidification in 2D was designed. Proposed model is based on the Cellular Automaton Finite Differences (CA-FD calculation method. Model has been used for studies of the primary austenite and of globular eutectic grains growth during the solidification of the ductile iron with different carbon equivalent in the thin wall casting. Model takes into account, among other things, non-uniform temperature distribution in the casting wall cross-section, kinetics of the austenite and graphite grains nucleation, and non-equilibrium nature of the interphase boundary migration. Solidification of the DI with different carbon equivalents was analyzed. Obtained results were compared with the solidification path calculated by CALPHAD method.
Burbelko A.A.
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 Automaton Finite Differences (CA-FD calculation method. Model has been used for studies of the primary austenite and of globular eutectic grains growth during the ductile iron solidification in the thin wall casting. Model takes into account, among other things, non-uniform temperature distribution in the casting wall cross-section, kinetics of the austenite and graphite grains nucleation, and non-equilibrium nature 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.
Continuum-level modelling of cellular adhesion and matrix production in aggregates.
Geris, Liesbet; Ashbourn, Joanna M A; Clarke, Tim
2011-05-01
Key regulators in tissue-engineering processes such as cell culture and cellular organisation are the cell-cell and cell-matrix interactions. As mathematical models are increasingly applied to investigate biological phenomena in the biomedical field, it is important, for some applications, that these models incorporate an adequate description of cell adhesion. This study describes the development of a continuum model that represents a cell-in-gel culture system used in bone-tissue engineering, namely that of a cell aggregate embedded in a hydrogel. Cell adhesion is modelled through the use of non-local (integral) terms in the partial differential equations. The simulation results demonstrate that the effects of cell-cell and cell-matrix adhesion are particularly important for the survival and growth of the cell population and the production of extracellular matrix by the cells, concurring with experimental observations in the literature.
Advanced spatial metrics analysis in cellular automata land use and cover change modeling
Zamyatin, Alexander; Cabral, Pedro
2011-01-01
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.
Idealized Mesoscale Model Simulations of Open Cellular Convection Over the Sea
Vincent, Claire Louise; Hahmann, Andrea N.; Kelly, Mark C.
2012-01-01
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...... case. By considering all sources of explicit diffusion in the model, the budgets were balanced. In comparison with previous work based on observational studies, the use of three-dimensional, gridded model data afforded the possibility of calculating all terms in the budgets, which showed...
Cellular-automata model of the dwarf shrubs populations and communities dynamics
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.
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.
Modeling and Experimental Study of Soft Error Propagation Based on Cellular Automaton
Wei He
2016-01-01
Full Text Available Aiming to estimate SEE soft error performance of complex electronic systems, a soft error propagation model based on cellular automaton is proposed and an estimation methodology based on circuit partitioning and error propagation is presented. Simulations indicate that different fault grade jamming and different coupling factors between cells are the main parameters influencing the vulnerability of the system. Accelerated radiation experiments have been developed to determine the main parameters for raw soft error vulnerability of the module and coupling factors. Results indicate that the proposed method is feasible.
Feng, Yongjiu; Tong, Xiaohua
2017-09-22
Defining transition rules is an important issue in cellular automaton (CA)-based land use modeling because these models incorporate highly correlated driving factors. Multicollinearity among correlated driving factors may produce negative effects that must be eliminated from the modeling. Using exploratory regression under pre-defined criteria, we identified all possible combinations of factors from the candidate factors affecting land use change. Three combinations that incorporate five driving factors meeting pre-defined criteria were assessed. With the selected combinations of factors, three logistic regression-based CA models were built to simulate dynamic land use change in Shanghai, China, from 2000 to 2015. For comparative purposes, a CA model with all candidate factors was also applied to simulate the land use change. Simulations using three CA models with multicollinearity eliminated performed better (with accuracy improvements about 3.6%) than the model incorporating all candidate factors. Our results showed that not all candidate factors are necessary for accurate CA modeling and the simulations were not sensitive to changes in statistically non-significant driving factors. We conclude that exploratory regression is an effective method to search for the optimal combinations of driving factors, leading to better land use change models that are devoid of multicollinearity. We suggest identification of dominant factors and elimination of multicollinearity before building land change models, making it possible to simulate more realistic outcomes.
An examination of adaptive cellular protective mechanisms using a multi-stage carcinogenesis model
Schollnberger, H.; Stewart, R. D.; Mitchel, R. E. J.; Hofmann, W.
2004-01-01
A multi-stage cancer model that describes the putative rate-limiting steps in carcinogenesis was developed and used to investigate the potential impact on lung cancer incidence of the hormesis mechanisms suggested by Feinendegen and Pollycove. In this deterministic cancer model, radiation and endogenous processes damage the DNA of target cells in the lung. Some fraction of the misrepaired our unrepaired DNA damage induces genomic instability and, ultimately, leads to the accumulation of malignant cells. The model accounts for cell birth and death processes. Ita also includes a rate of malignant transformation and a lag period for tumour formation. Cellular defence mechanisms are incorporated into the model by postulating dose and dose rate dependent radical scavenging. The accuracy of DNA damage repair also depends on dose and dose rate. Sensitivity studies were conducted to identify critical model inputs and to help define the shapes of the cumulative lung cancer incidence curves that may arise when dose and dose rate dependent cellular defence mechanisms are incorporated into a multi-stage cancer model. For lung cancer, both linear no-threshold (LNT) and non-LNT shaped responses can be obtained. The reported studied clearly show that it is critical to know whether or not and to what extent multiply damaged DNA sites are formed by endogenous processes. Model inputs that give rise to U-shaped responses are consistent with an effective cumulative lung cancer incidence threshold that may be as high as 300 mGy (4 mGy per year for 75 years). (Author) 11 refs
Oxidative Damage and Cellular Defense Mechanisms in Sea Urchin Models of Aging
Du, Colin; Anderson, Arielle; Lortie, Mae; Parsons, Rachel; Bodnar, Andrea
2013-01-01
The free radical or oxidative stress theory of aging proposes that the accumulation of oxidative cellular damage is a major contributor to the aging process and a key determinant of species longevity. This study investigates the oxidative stress theory in a novel model for aging research, the sea urchin. Sea urchins present a unique model for the study of aging due to the existence of species with tremendously different natural life spans including some species with extraordinary longevity and negligible senescence. Cellular oxidative damage, antioxidant capacity and proteasome enzyme activities were measured in the tissues of three sea urchin species: short-lived Lytechinus variegatus, long-lived Strongylocentrotus franciscanus and Strongylocentrotus purpuratus which has an intermediate lifespan. Levels of protein carbonyls and 4-hydroxynonenal (HNE) measured in tissues (muscle, nerve, esophagus, gonad, coelomocytes, ampullae) and 8-hydroxy-2’-deoxyguanosine (8-OHdG) measured in cell-free coelomic fluid showed no general increase with age. The fluorescent age-pigment lipofuscin measured in muscle, nerve and esophagus, increased with age however it appeared to be predominantly extracellular. Antioxidant mechanisms (total antioxidant capacity, superoxide dismutase) and proteasome enzyme activities were maintained with age. In some instances, levels of oxidative damage were lower and antioxidant activity higher in cells or tissues of the long-lived species compared to the short-lived species, however further studies are required to determine the relationship between oxidative damage and longevity in these animals. Consistent with the predictions of the oxidative stress theory of aging, the results suggest that negligible senescence is accompanied by a lack of accumulation of cellular oxidative damage with age and maintenance of antioxidant capacity and proteasome enzyme activities may be important mechanisms to mitigate damage. PMID:23707327
Lian, Yanping; Lin, Stephen; Yan, Wentao; Liu, Wing Kam; Wagner, Gregory J.
2018-01-01
In this paper, a parallelized 3D cellular automaton computational model is developed to predict grain morphology for solidification of metal during the additive manufacturing process. Solidification phenomena are characterized by highly localized events, such as the nucleation and growth of multiple grains. As a result, parallelization requires careful treatment of load balancing between processors as well as interprocess communication in order to maintain a high parallel efficiency. We give a detailed summary of the formulation of the model, as well as a description of the communication strategies implemented to ensure parallel efficiency. Scaling tests on a representative problem with about half a billion cells demonstrate parallel efficiency of more than 80% on 8 processors and around 50% on 64; loss of efficiency is attributable to load imbalance due to near-surface grain nucleation in this test problem. The model is further demonstrated through an additive manufacturing simulation with resulting grain structures showing reasonable agreement with those observed in experiments.
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.
Lian, Yanping; Lin, Stephen; Yan, Wentao; Liu, Wing Kam; Wagner, Gregory J.
2018-05-01
In this paper, a parallelized 3D cellular automaton computational model is developed to predict grain morphology for solidification of metal during the additive manufacturing process. Solidification phenomena are characterized by highly localized events, such as the nucleation and growth of multiple grains. As a result, parallelization requires careful treatment of load balancing between processors as well as interprocess communication in order to maintain a high parallel efficiency. We give a detailed summary of the formulation of the model, as well as a description of the communication strategies implemented to ensure parallel efficiency. Scaling tests on a representative problem with about half a billion cells demonstrate parallel efficiency of more than 80% on 8 processors and around 50% on 64; loss of efficiency is attributable to load imbalance due to near-surface grain nucleation in this test problem. The model is further demonstrated through an additive manufacturing simulation with resulting grain structures showing reasonable agreement with those observed in experiments.
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.
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.
STATISTIC MODEL OF DYNAMIC DELAY AND DROPOUT ON CELLULAR DATA NETWORKED CONTROL SYSTEM
MUHAMMAD A. MURTI
2017-07-01
Full Text Available Delay and dropout are important parameters influence overall control performance in Networked Control System (NCS. The goal of this research is to find a model of delay and dropout of data communication link in the NCS. Experiments have been done in this research to a water level control of boiler tank as part of the NCS based on internet communication network using High Speed Packet Access (HSPA cellular technology. By this experiments have been obtained closed-loop system response as well as data delay and dropout of data packets. This research contributes on modeling of the NCS which is combination of controlled plant and data communication link. Another contribution is statistical model of delay and dropout on the NCS.
Cellular automata models for diffusion of information and highway traffic flow
Fuks, Henryk
In the first part of this work we study a family of deterministic models for highway traffic flow which generalize cellular automaton rule 184. This family is parameterized by the speed limit m and another parameter k that represents degree of 'anticipatory driving'. We compare two driving strategies with identical maximum throughput: 'conservative' driving with high speed limit and 'anticipatory' driving with low speed limit. Those two strategies are evaluated in terms of accident probability. We also discuss fundamental diagrams of generalized traffic rules and examine limitations of maximum achievable throughput. Possible modifications of the model are considered. For rule 184, we present exact calculations of the order parameter in a transition from the moving phase to the jammed phase using the method of preimage counting, and use this result to construct a solution to the density classification problem. In the second part we propose a probabilistic cellular automaton model for the spread of innovations, rumors, news, etc., in a social system. We start from simple deterministic models, for which exact expressions for the density of adopters are derived. For a more realistic model, based on probabilistic cellular automata, we study the influence of a range of interaction R on the shape of the adoption curve. When the probability of adoption is proportional to the local density of adopters, and individuals can drop the innovation with some probability p, the system exhibits a second order phase transition. Critical line separating regions of parameter space in which asymptotic density of adopters is positive from the region where it is equal to zero converges toward the mean-field line when the range of the interaction increases. In a region between R=1 critical line and the mean-field line asymptotic density of adopters depends on R, becoming zero if R is too small (smaller than some critical value). This result demonstrates the importance of connectivity in
Tian, Jun-fang; Yuan, Zhen-zhou; Jia, Bin; Fan, Hong-qiang; Wang, Tao
2012-01-01
Velocity effect and critical velocity are incorporated into the average space gap cellular automaton model [J.F. Tian, et al., Phys. A 391 (2012) 3129], which was able to reproduce many spatiotemporal dynamics reported by the three-phase theory except the synchronized outflow of wide moving jams. The physics of traffic breakdown has been explained. Various congested patterns induced by the on-ramp are reproduced. It is shown that the occurrence of synchronized outflow, free outflow of wide moving jams is closely related with drivers time delay in acceleration at the downstream jam front and the critical velocity, respectively. -- Highlights: ► Velocity effect is added into average space gap cellular automaton model. ► The physics of traffic breakdown has been explained. ► The probabilistic nature of traffic breakdown is simulated. ► Various congested patterns induced by the on-ramp are reproduced. ► The occurrence of synchronized outflow of jams depends on drivers time delay.
Cigarette smoke-exposed saliva suppresses cellular and humoral immune responses in an animal model
Jafarzadeh, A.; Bakhshi, H.; Rezayati, M.T.; Nemati, M.
2009-01-01
To evaluate the effects of cigarette smoke (CS)-exposed saliva on cellular and antibody responses in an animal model. The stimulatory and non-stimulatory saliva samples were collected from 10 healthy subjects and were then exposed to CS for 20 or 80 minutes. The CS-exposed saliva samples were administrated intraperitoneally (i.p) to male Balb/c mice. Then the delayed type hypersensitivity (DTH) and antibody responses to sheep red blood cell (SRBC) was assessed. Moreover, the total white blood cells (WBC) counts and the blood lymphocytes counts were determined. The mean of DTH responses of animal groups received 20 minutes or 80 minutes CS-exposed saliva samples was significantly lower than that observed in control group. Moreover, The mean titer of anti-SRBC antibody was significantly lower in animal groups who received 80 minutes CS-exposed stimulatory or non-stimulatory saliva as compared to control group (P<0.04 and P<0.002, respectively). The mean counts of blood lymphocytes in 80 minutes CS exposed-stimulatory saliva group was also significantly lower as compared to control group (P<0.05). These results show that the CS-exposed saliva samples have profound suppressive effects on both cellular and humoral immune response in a mouse animal model (JPMA 59:760; 2009). (author)
Train flow chaos analysis based on an improved cellular automata model
Meng, Xuelei; Xiang, Wanli; Jia, Limin; Xu, Jie
2015-01-01
To control the chaos in the railway traffic flow and offer valuable information for the dispatchers of the railway system, an improved cellular model is presented to detect and analyze the chaos in the traffic flow. We first introduce the working mechanism of moving block system, analyzing the train flow movement characteristics. Then we improve the cellular model on the evolution rules to adjust the train flow movement. We give the train operation steps from three cases: the trains running on a railway section, a train will arrive in a station and a train will departure from a station. We simulate 4 trains to run on a high speed section fixed with moving block system and record the distances between the neighbor trains and draw the Poincare section to analyze the chaos in the train operation. It is concluded that there is not only chaos but order in the train operation system with moving blocking system and they can interconvert to each other. The findings have the potential value in train dispatching system construction and offer supporting information for the daily dispatching work.
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.
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.
Evaluation of the Cytotoxicity and Genotoxicity of Flavonolignans in Different Cellular Models
Michal Bijak
2017-12-01
Full Text Available Flavonolignans are the main components of silymarin, which represents 1.5–3% of the dry fruit weight of Milk thistle (Silybum marianum L. Gaernt.. In ancient Greece and Romania, physicians and herbalists used the Silybum marianum to treat a range of liver diseases. Besides their hepatoprotective action, silymarin flavonolignans have many other healthy properties, such as anti-platelet and anti-inflammatory actions. The aim of this study was to evaluate the toxic effect of flavonolignans on blood platelets, peripheral blood mononuclear cells (PBMCs and human lung cancer cell line—A549—using different molecular techniques. We established that three major flavonolignans: silybin, silychristin and silydianin, in concentrations of up to 100 µM, have neither a cytotoxic nor genotoxic effect on blood platelets, PMBCs and A549. We also saw that silybin and silychristin have a protective effect on cellular mitochondria, observed as a reduction of spontaneous mitochondrial DNA (mtDNA damage in A549, measured as mtDNA copies, and mtDNA lesions in ND1 and ND5 genes. Additionally, we observed that flavonolignans increase the blood platelets’ mitochondrial membrane potential and reduce the generation of reactive oxygen species in blood platelets. Our current findings show for the first time that the three major flavonolignans, silybin, silychristin and silydianin, do not have any cytotoxicity and genotoxicity in various cellular models, and that they actually protect cellular mitochondria. This proves that the antiplatelet and anti-inflammatory effect of these compounds is part of our molecular health mechanisms.
A Modified Cellular Automaton Approach for Mixed Bicycle Traffic Flow Modeling
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.
Cellular Automaton Modeling of Dendritic Growth Using a Multi-grid Method
Natsume, Y; Ohsasa, K
2015-01-01
A two-dimensional cellular automaton model with a multi-grid method was developed to simulate dendritic growth. In the present model, we used a triple-grid system for temperature, solute concentration and solid fraction fields as a new approach of the multi-grid method. In order to evaluate the validity of the present model, we carried out simulations of single dendritic growth, secondary dendrite arm growth, multi-columnar dendritic growth and multi-equiaxed dendritic growth. From the results of the grid dependency from the simulation of single dendritic growth, we confirmed that the larger grid can be used in the simulation and that the computational time can be reduced dramatically. In the simulation of secondary dendrite arm growth, the results from the present model were in good agreement with the experimental data and the simulated results from a phase-field model. Thus, the present model can quantitatively simulate dendritic growth. From the simulated results of multi-columnar and multi-equiaxed dendrites, we confirmed that the present model can perform simulations under practical solidification conditions. (paper)
Temperature Effects on Olive Fruit Fly Infestation in the FlySim Cellular Automata Model
Bruno, Vincenzo; Baldacchini, Valerio; di Gregorio, Salvatore
FlySim is a Cellular Automata model developed for simulating infestation of olive fruit flies (Bactrocera Oleae) on olive (Olea europaea) groves. The flies move into the groves looking for mature olives where eggs are spawn. This serious agricultural problem is mainly tackled by using chemical agents at the first signs of the infestation, but organic productions with no or few chemicals are strongly requested by the market. Oil made with infested olives is poor in quality, nor olives are suitable for selling in stores. The FlySim model simulates the diffusion of flies looking for mature olives and the growing of flies due to atmospheric conditions. Foreseeing an infestation is the best way to prevent it and to reduce the need of chemicals in agriculture. In this work we investigated the effects of temperature on olive fruit flies and resulting infestation during late spring and summer.
A cellular automation model for the change of public attitude regarding nuclear energy
Ohnishi, Teruaki
1991-01-01
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 cellular automation model for the change of public attitude regarding nuclear energy
Ohnishi, Teruaki (CRC Research Inst., Chiba (Japan))
1991-01-01
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).
Genome editing of human pluripotent stem cells to generate human cellular disease models
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.
Guzmán, H. A.; Lárraga, M. E.; Alvarez-Icaza, L.; Carvajal, J.
2018-02-01
In this paper, a reliable cellular automata model oriented to faithfully reproduce deceleration and acceleration according to realistic reactions of drivers, when vehicles with different deceleration capabilities are considered is presented. The model focuses on describing complex traffic phenomena by coding in its rules the basic mechanisms of drivers behavior, vehicles capabilities and kinetics, while preserving simplicity. In particular, vehiclés kinetics is based on uniform accelerated motion, rather than in impulsive accelerated motion as in most existing CA models. Thus, the proposed model calculates in an analytic way three safe preserving distances to determine the best action a follower vehicle can take under a worst case scenario. Besides, the prediction analysis guarantees that under the proper assumptions, collision between vehicles may not happen at any future time. Simulations results indicate that all interactions of heterogeneous vehicles (i.e., car-truck, truck-car, car-car and truck-truck) are properly reproduced by the model. In addition, the model overcomes one of the major limitations of CA models for traffic modeling: the inability to perform smooth approach to slower or stopped vehicles. Moreover, the model is also capable of reproducing most empirical findings including the backward speed of the downstream front of the traffic jam, and different congested traffic patterns induced by a system with open boundary conditions with an on-ramp. Like most CA models, integer values are used to make the model run faster, which makes the proposed model suitable for real time traffic simulation of large networks.
An Urban Cellular Automata Model for Simulating Dynamic States on a Local Scale
Jenni Partanen
2016-12-01
Full Text Available In complex systems, flexibility and adaptability to changes are crucial to the systems’ dynamic stability and evolution. Such resilience requires that the system is able to respond to disturbances by self-organizing, which implies a certain level of entropy within the system. Dynamic states (static, cyclical/periodic, complex, and chaotic reflect this generative capacity, and correlate with the level of entropy. For planning complex cities, we need to develop methods to guide such autonomous progress in an optimal manner. A classical apparatus, cellular automaton (CA, provides such a tool. Applications of CA help us to study temporal dynamics in self-organizing urban systems. By exploring the dynamic states of the model’s dynamics resulting from different border conditions it is possible to discover favorable set(s of rules conductive to the self-organizing dynamics and enable the system’s recovery at the time of crises. Level of entropy is a relevant measurement for evaluation of these dynamic states. The 2-D urban cellular automaton model studied here is based on the microeconomic principle that similar urban activities are attracted to each other, especially in certain self-organizing areas, and that the local dynamics of these enclaves affect the dynamics of the urban region by channeling flows of information, goods and people. The results of the modeling experiment indicate that the border conditions have a major impact on the model’s dynamics generating various dynamic states of the system. Most importantly, it seemed that the model could simulate a favorable, complex dynamic state with medium entropy level which may refer to the continuous self-organization of the system. The model provides a tool for exploring and understanding the effects of boundary conditions in the planning process as various scenarios are tested: resulting dynamics of the system can be explored with such “planning rules” prior to decisions, helping to
Iovine, G.; D'Ambrosio, D.
2003-04-01
Cellular Automata models do represent a valid method for the simulation of complex phenomena, when these latter can be described in "a-centric" terms - i.e. through local interactions within a discrete time-space. In particular, flow-type landslides (such as debris flows) can be viewed as a-centric dynamical system. SCIDDICA S4b, the last release of a family of two-dimensional hexagonal Cellular Automata models, has recently been developed for simulating debris flows characterised by strong inertial effects. It has been derived by progressively enriching an initial simplified CA model, originally derived for simulating very simple cases of slow-moving flow-type landslides. In S4b, by applying an empirical strategy, the inertial characters of the flowing mass have been translated into CA terms. In the transition function of the model, the distribution of landslide debris among the cells is computed by considering the momentum of the debris which move among the cells of the neighbourhood, and privileging the flow direction. By properly setting the value of one of the global parameters of the model (the "inertial factor"), the mechanism of distribution of the landslide debris among the cells can be influenced in order to emphasise the inertial effects, according to the energy of the flowing mass. Moreover, the high complexity of both the model and of the phenomena to be simulated (e.g. debris flows characterised by severe erosion along their path, and by strong inertial effects) suggested to employ an automated technique of evaluation, for the determination of the best set of global parameters. Accordingly, the calibration of the model has been performed through Genetic Algorithms, by considering several real cases of study: these latter have been selected among the population of landslides triggered in Campania (Southern Italy) in May 1998 and December 1999. Obtained results are satisfying: errors computed by comparing the simulations with the map of the real
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.
A Nanoflare-Based Cellular Automaton Model and the Observed Properties of the Coronal Plasma
Lopez-Fuentes, Marcelo; Klimchuk, James Andrew
2016-01-01
We use the cellular automaton model described in Lopez Fuentes and Klimchuk 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 SDOAIA instruments. The comparison is based on the statistical properties of synthetic and observed loop light curves. 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 amplitudes of 10 percent - 15 percent 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) between 2.7 and 4.3, in agreement with published observational values.
A NANOFLARE-BASED CELLULAR AUTOMATON MODEL AND THE OBSERVED PROPERTIES OF THE CORONAL PLASMA
Fuentes, Marcelo López [Instituto de Astronomía y Física del Espacio, CONICET-UBA, CC. 67, Suc. 28, 1428 Buenos Aires (Argentina); Klimchuk, James A., E-mail: lopezf@iafe.uba.ar [NASA Goddard Space Flight Center, Code 671, Greenbelt, MD 20771 (United States)
2016-09-10
We use the cellular automaton model described in López Fuentes and Klimchuk 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 light curves. 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 amplitudes of 10%–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) between 2.7 and 4.3, in agreement with published observational values.
Christensen, K.; Olami, Z.
1992-01-01
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
An empirical Bayesian approach for model-based inference of cellular signaling networks
Klinke David J
2009-11-01
Full Text Available Abstract Background A common challenge in systems biology is to infer mechanistic descriptions of biological process given limited observations of a biological system. Mathematical models are frequently used to represent a belief about the causal relationships among proteins within a signaling network. Bayesian methods provide an attractive framework for inferring the validity of those beliefs in the context of the available data. However, efficient sampling of high-dimensional parameter space and appropriate convergence criteria provide barriers for implementing an empirical Bayesian approach. The objective of this study was to apply an Adaptive Markov chain Monte Carlo technique to a typical study of cellular signaling pathways. Results As an illustrative example, a kinetic model for the early signaling events associated with the epidermal growth factor (EGF signaling network was calibrated against dynamic measurements observed in primary rat hepatocytes. A convergence criterion, based upon the Gelman-Rubin potential scale reduction factor, was applied to the model predictions. The posterior distributions of the parameters exhibited complicated structure, including significant covariance between specific parameters and a broad range of variance among the parameters. The model predictions, in contrast, were narrowly distributed and were used to identify areas of agreement among a collection of experimental studies. Conclusion In summary, an empirical Bayesian approach was developed for inferring the confidence that one can place in a particular model that describes signal transduction mechanisms and for inferring inconsistencies in experimental measurements.
TWO-DIMENSIONAL CELLULAR AUTOMATON MODEL FOR THE EVOLUTION OF ACTIVE REGION CORONAL PLASMAS
López Fuentes, Marcelo [Instituto de Astronomía y Física del Espacio, CONICET-UBA, CC. 67, Suc. 28, 1428 Buenos Aires (Argentina); Klimchuk, James A., E-mail: lopezf@iafe.uba.ar [NASA Goddard Space Flight Center, Code 671, Greenbelt, MD 20771 (United States)
2015-02-01
We study a two-dimensional 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 model to compute the response of the plasma to the heating events. Using the known response of the X-Ray 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 terms of the plasma cooling time, increases with strand length. We discuss the implications of our results for the problem of heating and evolution of active region coronal plasmas.
On the Geometric Modeling of the Uplink Channel in a Cellular System
K. B. Baltzis
2008-01-01
Full Text Available To meet the challenges of present and future wireless communications realistic propagation models that consider both spatial and temporal channel characteristics are used. However, the complexity of the complete characterization of the wireless medium has pointed out the importance of approximate but simple approaches. The geometrically based methods are typical examples of low–complexity but adequate solutions. Geometric modeling idealizes the aforementioned wireless propagation environment via a geometric abstraction of the spatial relationships among the transmitter, the receiver, and the scatterers. The paper tries to present an efficient way to simulate mobile channels using geometrical–based stochastic scattering models. In parallel with an overview of the most commonly used propagation models, the basic principles of the method as well the main assumptions made are presented. The study is focused on three well–known proposals used for the description of the Angle–of –Arrival and Time–of–Arrival statistics of the incoming multipaths in the uplink of a cellular communication system. In order to demonstrate the characteristics of these models illustrative examples are given. The physical mechanism and motivations behind them are also included providing us with a better understanding of the physical insight of the propagation medium.
Simple cellular automaton model for traffic breakdown, highway capacity, and synchronized flow
Kerner, Boris S.; Klenov, Sergey L.; Schreckenberg, Michael
2011-10-01
We present a simple cellular automaton (CA) model for two-lane roads explaining the physics of traffic breakdown, highway capacity, and synchronized flow. The model consists of the rules “acceleration,” “deceleration,” “randomization,” and “motion” of the Nagel-Schreckenberg CA model as well as “overacceleration through lane changing to the faster lane,” “comparison of vehicle gap with the synchronization gap,” and “speed adaptation within the synchronization gap” of Kerner's three-phase traffic theory. We show that these few rules of the CA model can appropriately simulate fundamental empirical features of traffic breakdown and highway capacity found in traffic data measured over years in different countries, like characteristics of synchronized flow, the existence of the spontaneous and induced breakdowns at the same bottleneck, and associated probabilistic features of traffic breakdown and highway capacity. Single-vehicle data derived in model simulations show that synchronized flow first occurs and then self-maintains due to a spatiotemporal competition between speed adaptation to a slower speed of the preceding vehicle and passing of this slower vehicle. We find that the application of simple dependences of randomization probability and synchronization gap on driving situation allows us to explain the physics of moving synchronized flow patterns and the pinch effect in synchronized flow as observed in real traffic data.
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.
Chavali, Arvind K; Gianchandani, Erwin P; Tung, Kenneth S; Lawrence, Michael B; Peirce, Shayn M; Papin, Jason A
2008-12-01
The immune system is comprised of numerous components that interact with one another to give rise to phenotypic behaviors that are sometimes unexpected. Agent-based modeling (ABM) and cellular automata (CA) belong to a class of discrete mathematical approaches in which autonomous entities detect local information and act over time according to logical rules. The power of this approach lies in the emergence of behavior that arises from interactions between agents, which would otherwise be impossible to know a priori. Recent work exploring the immune system with ABM and CA has revealed novel insights into immunological processes. Here, we summarize these applications to immunology and, particularly, how ABM can help formulate hypotheses that might drive further experimental investigations of disease mechanisms.
Cellular Automata Models of Traffic Behavior in Presence of Speed Breaking Structures
Ramachandran, Parthasarathy
2009-01-01
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)
Maytin, Edward; Anand, Sanjay; Sato, Nobuyuki; Mack, Judith; Ortel, Bernhard
2005-04-01
During ALA-based photodynamic therapy (PDT), a pro-drug (aminolevulinic acid; ALA) is taken up by tumor cells and metabolically converted to a photosensitizing intermediate (protoporphyrin IX; PpIX). ALA-based PDT, while an emerging treatment modality, remains suboptimal for most cancers (e.g. squamous cell carcinoma of the skin). Many treatment failures may be largely due to insufficient conversion of ALA to PpIX within cells. We discovered a novel way to increase the conversion of ALA to PpIX, by administering agents that can drive terminal differentiation (i.e., accelerate cellular maturation). Terminally-differentiated epithelial cells show higher levels of intracellular PpIX, apparently via increased levels of a rate-limiting enzyme, coproporphyrinogen oxidase (CPO). To study these mechanisms in a three-dimensional tissue, we developed an organotypic model that mimics true epidermal physiology in a majority of respects. A line of rat epidermal keratinocytes (REKs), when grown in raft cultures, displays all the features of a fully-differentiated epidermis. Addition of ALA to the culture medium results in ALA uptake and PpIX synthesis, with subsequent death of keratinocytes upon exposure to blue light. Using this model, we can manipulate cellular differentiation via three different approaches. (1) Vitamin D, a hormone that enhances keratinocyte differentiation; (2) Hoxb13, a nuclear transcription factor that affects the genetically-controlled differentiation program of stratifying cells (3) Hyaluronan, an abundant extracellular matrix molecule that regulates epidermal differentiation. Because the raft cultures contain only a single cell type (no blood, fibroblasts, etc.) the effects of terminal differentiation upon CPO, PpIX, and keratinocyte cell death can be specifically defined.
Guillemot, G.; Avettand-Fènoël, M.-N.; Iosta, A.; Foct, J.
2011-01-01
Hot-dipping galvanizing process is a widely used and efficient way to protect steel from corrosion. We propose to master the microstructure of zinc grains by investigating the relevant process parameters. In order to improve the texture of this coating, we model grain nucleation and growth processes and simulate the zinc solid phase development. A coupling scheme model has been applied with this aim. This model improves a previous two-dimensional model of the solidification process. It couples a cellular automaton (CA) approach and a finite element (FE) method. CA grid and FE mesh are superimposed on the same domain. The grain development is simulated at the micro-scale based on the CA grid. A nucleation law is defined using a Gaussian probability and a random set of nucleating cells. A crystallographic orientation is defined for each one with a choice of Euler's angle (Ψ,θ,φ). A small growing shape is then associated to each cell in the mushy domain and a dendrite tip kinetics is defined using the model of Kurz [2]. The six directions of basal plane and the two perpendicular directions develop in each mushy cell. During each time step, cell temperature and solid fraction are then determined at micro-scale using the enthalpy conservation relation and variations are reassigned at macro-scale. This coupling scheme model enables to simulate the three-dimensional growing kinetics of the zinc grain in a two-dimensional approach. Grain structure evolutions for various cooling times have been simulated. Final grain structure has been compared to EBSD measurements. We show that the preferentially growth of dendrite arms in the basal plane of zinc grains is correctly predicted. The described coupling scheme model could be applied for simulated other product or manufacturing processes. It constitutes an approach gathering both micro and macro scale models.
Orientation selection of equiaxed dendritic growth by three-dimensional cellular automaton model
Wei Lei [State Key Laboratory of Solidification Processing, Northwestern Polytechnical University, Xi' an 710072 (China); Lin Xin, E-mail: xlin@nwpu.edu.cn [State Key Laboratory of Solidification Processing, Northwestern Polytechnical University, Xi' an 710072 (China); Wang Meng; Huang Weidong [State Key Laboratory of Solidification Processing, Northwestern Polytechnical University, Xi' an 710072 (China)
2012-07-01
A three-dimensional (3-D) adaptive mesh refinement (AMR) cellular automata (CA) model is developed to simulate the equiaxed dendritic growth of pure substance. In order to reduce the mesh induced anisotropy by CA capture rules, a limited neighbor solid fraction (LNSF) method is presented. It is shown that the LNSF method reduced the mesh induced anisotropy based on the simulated morphologies for isotropic interface free energy. An expansion description using two interface free energy anisotropy parameters ({epsilon}{sub 1}, {epsilon}{sub 2}) is used in the present 3-D CA model. It is illustrated by present 3-D CA model that the positive {epsilon}{sub 1} favors the dendritic growth with the Left-Pointing-Angle-Bracket 100 Right-Pointing-Angle-Bracket preferred directions, and negative {epsilon}{sub 2} favors dendritic growth with the Left-Pointing-Angle-Bracket 110 Right-Pointing-Angle-Bracket preferred directions, which has a good agreement with the prediction of the spherical plot of the inverse of the interfacial stiffness. The dendritic growths with the orientation selection between Left-Pointing-Angle-Bracket 100 Right-Pointing-Angle-Bracket and Left-Pointing-Angle-Bracket 110 Right-Pointing-Angle-Bracket are also discussed using the different {epsilon}{sub 1} with {epsilon}{sub 2}=-0.02. It is found that the simulated morphologies by present CA model are as expected from the minimum stiffness criterion.
Development of in vitro models for cellular and molecular studies in toxicology and chemoprevention
Mace, K.; Offord, E.A.; Harris, C.C.; Pfeifer, A.M.A. [Nestle Research Center, Lausanne (Switzerland)
1998-12-31
Many natural dietary phytochemicals found compounds found in fruits, vegetables, spices and tea have been shown in recent years to be protective against cancer in various animal models. In the light of the potential impact of these compounds on human health it is important to elucidate the mechanisms involved. We therefore developed and characterized relevant in vitro models using immortalized human epithelial cell lines derived from target tissues in carcinogenesis, such as lung, liver and colon. Assays were established, allowing the evaluation of the cytotoxic and genotoxic effects of various procarcinogens, including nitrosamines, mycotoxins and heterocyclic amines on these metabolically-competent human epithelial cell lines. These cellular models appeared to be a useful tool to study the capacity of certain food components to block the initiation stage of carcinogenesis. The ability of carnosol and carnosic acid from rosemary as well as the synthetic dithiolethione, oltipraz, to block the formation of DNA adducts, and their effects on the expression of phase I and phase II enzymes was investigated. We have observed that both rosemary extracts and oltiprax inhibited benzo(a)pyrene- or aflatoxin B{sub 1}-induced DNA adduct formation by strongly inhibiting CYP{sub 450} activities and inducing the expression of glutathione S-transferase. These results in human cell models give some insight into the different mechanisms involved in the chemopreventive action of both natural and synthetic compounds in relation to phase I and phase II enzymes. (orig.)
Juckett, D A
1987-03-01
A model is presented which proposes a specific cause-and-effect relationship between a limited cell division potential and the maximum lifespan of humans and other mammals. It is based on the clonal succession hypothesis of Kay which states that continually replicating cell beds (e.g. bone marrow, intestinal crypts, epidermis) could be composed of cells with short, well-defined division potentials. In this model, the cells of these beds are proposed to exist in an ordered hierarchy which establishes a specific sequence for cell divisions throughout the organism's lifespan. The depletion of division potential at all hierarchical levels leads to a loss of bed function and sets an intrinsic limit to species longevity. A specific hierarchy for cell proliferation is defined which allows the calculation of time to bed depletion and, ultimately, to organism mortality. The model allows the existence of a small number (n) of critical cell beds within the organism and defines organism death as the inability of any one of these beds to produce cells. The model is consistent with all major observations related to cellular and organismic aging. In particular, it links the PDLs (population doubling limit) observed for various species to their mean lifespan; it explains the slow decline in PDL as a function of age of the donor; it establishes a thermodynamically stable maximum lifespan for a disease-free population; and it can explain why tissue transplants outlive donors or hosts.
Lira, Matthew
This dissertation explores the Knowledge in Pieces (KiP) theory to account for how students learn to coordinate knowledge of mathematical and physical models in biology education. The KiP approach characterizes student knowledge as a fragmented collection of knowledge elements as opposed to stable and theory-like knowledge. This dissertation sought to use this theoretical lens to account for how students understand and learn with mathematical models and representations, such as equations. Cellular physiology provides a quantified discipline that leverages concepts from mathematics, physics, and chemistry to understand cellular functioning. Therefore, this discipline provides an exemplary context for assessing how biology students think and learn with mathematical models. In particular, the resting membrane potential provides an exemplary concept well defined by models of dynamic equilibrium borrowed from physics and chemistry. In brief, membrane potentials, or voltages, "rest" when the electrical and chemical driving forces for permeable ionic species are equal in magnitude but opposite in direction. To assess students' understandings of this concept, this dissertation employed three studies: the first study employed the cognitive clinical interview to assess student thinking in the absence and presence of equations. The second study employed an intervention to assess student learning and the affordances of an innovative assessment. The third student employed a human-computer-interaction paradigm to assess how students learn with a novel multi-representational technology. Study 1 revealed that students saw only one influence--the chemical gradient--and that students coordinated knowledge of only this gradient with the related equations. Study 2 revealed that students benefited from learning with the multi-representational technology and that the assessment detected performance gains across both calculation and explanation tasks. Last, Study 3 revealed how students
Tsallis, C.; Santos, R.J.V. dos
1983-01-01
On conjectural grounds an equation that provides a very good approximation for the critical temperature of the fully-anisotropic homogeneous quenched bond-random q-state Potts ferromagnet in triangular and honeycomb lattices is presented. Almost all the exact particular results presently known for the square, triangular and honeycomb lattices are recovered; the numerical discrepancy is quite small for the few exceptions. Some predictions that we believe to be exact are made explicite as well. (Author) [pt
Garijo, N; Manzano, R; Osta, R; Perez, M A
2012-12-07
Cell migration and proliferation has been modelled in the literature as a process similar to diffusion. However, using diffusion models to simulate the proliferation and migration of cells tends to create a homogeneous distribution in the cell density that does not correlate to empirical observations. In fact, the mechanism of cell dispersal is not diffusion. Cells disperse by crawling or proliferation, or are transported in a moving ﬂuid. The use of cellular automata, particle models or cell-based models can overcome this limitation. This paper presents a stochastic cellular automata model to simulate the proliferation, migration and differentiation of cells. These processes are considered as completely stochastic as well as discrete. The model developed was applied to predict the behaviour of in vitro cell cultures performed with adult muscle satellite cells. Moreover, non homogeneous distribution of cells has been observed inside the culture well and, using the above mentioned stochastic cellular automata model, we have been able to predict this heterogeneous cell distribution and compute accurate quantitative results. Differentiation was also incorporated into the computational simulation. The results predicted the myotube formation that typically occurs with adult muscle satellite cells. In conclusion, we have shown how a stochastic cellular automata model can be implemented and is capable of reproducing the in vitro behaviour of adult muscle satellite cells. Copyright © 2012 Elsevier Ltd. All rights reserved.
Dynamic crushing of uniform and density graded cellular structures based on the circle arc model
Jianjun Zhang
Full Text Available AbstractA new circle-arc model was established to present the cellular structure. Dynamic response of models with density gradients under constant velocities is investigated by employing Ls-dyna 971. Compared with the uniform models, the quasi-static plateau stress of different layers seems a significant parameter correlated with the deformation mode except for inertia effect when the density gradient is introduced. The impact velocity becomes much more vital on the deformation of the unit cell than the density gradient. The stress at both the impact and stationary sides is investigated in details. Furthermore, the stress-strain curve is compared with the modified shock wave theory. The density gradient does have some remarkable influence on the energy absorption capability, and a certain density gradient is not always beneficial to the energy absorption. Irrespective of the impact velocity, there seems always a critical strain where the energy absorbed by all these specimens could approximate to nearly the same value. So the critical strain-velocity curve is plotted and gives the beneficial area for energy absorption pertinent to density gradients and impact velocity.
Chung, C A; Lin, Tze-Hung; Chen, Shih-Di; Huang, Hsing-I
2010-01-21
Mathematic models help interpret experimental results and accelerate tissue engineering developments. We develop in this paper a hybrid cellular automata model that combines the differential nutrient transport equation to investigate the nutrient limited cell construct development for cartilage tissue engineering. Individual cell behaviors of migration, contact inhibition and cell collision, coupled with the cell proliferation regulated by oxygen concentration were carefully studied. Simplified two-dimensional simulations were performed. Using this model, we investigated the influence of cell migration speed on the overall cell growth within in vitro cell scaffolds. It was found that intense cell motility can enhance initial cell growth rates. However, since cell growth is also significantly modulated by the nutrient contents, intense cell motility with conventional uniform cell seeding method may lead to declined cell growth in the final time because concentrated cell population has been growing around the scaffold periphery to block the nutrient transport from outside culture media. Therefore, homogeneous cell seeding may not be a good way of gaining large and uniform cell densities for the final results. We then compared cell growth in scaffolds with various seeding modes, and proposed a seeding mode with cells initially residing in the middle area of the scaffold that may efficiently reduce the nutrient blockage and result in a better cell amount and uniform cell distribution for tissue engineering construct developments.
Safety impacts of red light cameras at signalized intersections based on cellular automata models.
Chai, C; Wong, Y D; Lum, K M
2015-01-01
This study applies a simulation technique to evaluate the hypothesis that red light cameras (RLCs) exert important effects on accident risks. Conflict occurrences are generated by simulation and compared at intersections with and without RLCs to assess the impact of RLCs on several conflict types under various traffic conditions. Conflict occurrences are generated through simulating vehicular interactions based on an improved cellular automata (CA) model. The CA model is calibrated and validated against field observations at approaches with and without RLCs. Simulation experiments are conducted for RLC and non-RLC intersections with different geometric layouts and traffic demands to generate conflict occurrences that are analyzed to evaluate the hypothesis that RLCs exert important effects on road safety. The comparison of simulated conflict occurrences show favorable safety impacts of RLCs on crossing conflicts and unfavorable impacts for rear-end conflicts during red/amber phases. Corroborative results are found from broad analysis of accident occurrence. RLCs are found to have a mixed effect on accident risk at signalized intersections: crossing collisions are reduced, whereas rear-end collisions may increase. The specially developed CA model is found to be a feasible safety assessment tool.
A computational approach to modeling cellular-scale blood flow in complex geometry
Balogh, Peter; Bagchi, Prosenjit
2017-04-01
We present a computational methodology for modeling cellular-scale blood flow in arbitrary and highly complex geometry. Our approach is based on immersed-boundary methods, which allow modeling flows in arbitrary geometry while resolving the large deformation and dynamics of every blood cell with high fidelity. The present methodology seamlessly integrates different modeling components dealing with stationary rigid boundaries of complex shape, moving rigid bodies, and highly deformable interfaces governed by nonlinear elasticity. Thus it enables us to simulate 'whole' blood suspensions flowing through physiologically realistic microvascular networks that are characterized by multiple bifurcating and merging vessels, as well as geometrically complex lab-on-chip devices. The focus of the present work is on the development of a versatile numerical technique that is able to consider deformable cells and rigid bodies flowing in three-dimensional arbitrarily complex geometries over a diverse range of scenarios. After describing the methodology, a series of validation studies are presented against analytical theory, experimental data, and previous numerical results. Then, the capability of the methodology is demonstrated by simulating flows of deformable blood cells and heterogeneous cell suspensions in both physiologically realistic microvascular networks and geometrically intricate microfluidic devices. It is shown that the methodology can predict several complex microhemodynamic phenomena observed in vascular networks and microfluidic devices. The present methodology is robust and versatile, and has the potential to scale up to very large microvascular networks at organ levels.
Loewe Axel
2015-09-01
Full Text Available Vernakalant is a new antiarrhythmic agent for the treatment of atrial fibrillation. While it has proven to be effective in a large share of patients in clinical studies, its underlying mode of action is not fully understood. In this work, we aim to link experimental data from the subcellular, tissue, and system level using an in-silico approach. A Hill’s equation-based drug model was extended to cover the frequency dependence of sodium channel block. Two model variants were investigated: M1 based on subcellular data and M2 based on tissue level data. 6 action potential (AP markers were evaluated regarding their dose, frequency and substrate dependence. M1 comprising potassium, sodium, and calcium channel block reproduced the reported prolongation of the refractory period. M2 not including the effects on potassium channels reproduced reported AP morphology changes on the other hand. The experimentally observed increase of ERP accompanied by a shortening of APD90 was not reproduced. Thus, explanations for the drug-induced changes are provided while none of the models can explain the effects in their entirety. These results foster the understanding of vernakalant’s cellular mode of action and point out relevant gaps in our current knowledge to be addressed in future in-silico and experimental research on this aspiring antiarrhythmic agent.
Wilson Gómez Manrique
Full Text Available The present study aimed to describe and characterize the cellular components during the evolution of chronic granulomatous inflammation in the teleost fish pacus (P. mesopotamicus induced by Bacillus Calmette-Guerin (BCG, using S-100, iNOS and cytokeratin antibodies. 50 fish (120±5.0 g were anesthetized and 45 inoculated with 20 μL (40 mg/mL (2.0 x 10(6 CFU/mg and five inoculated with saline (0,65% into muscle tissue in the laterodorsal region. To evaluate the inflammatory process, nine fish inoculated with BCG and one control were sampled in five periods: 3rd, 7th, 14th, 21st and 33rd days post-inoculation (DPI. Immunohistochemical examination showed that the marking with anti-S-100 protein and anti-iNOS antibodies was weak, with a diffuse pattern, between the third and seventh DPI. From the 14th to the 33rd day, the marking became stronger and marked the cytoplasm of the macrophages. Positivity for cytokeratin was initially observed in the 14th DPI, and the stronger immunostaining in the 33rd day, period in which the epithelioid cells were more evident and the granuloma was fully formed. Also after the 14th day, a certain degree of cellular organization was observed, due to the arrangement of the macrophages around the inoculated material, with little evidence of edema. The arrangement of the macrophages around the inoculum, the fibroblasts, the lymphocytes and, in most cases, the presence of melanomacrophages formed the granuloma and kept the inoculum isolated in the 33rd DPI. The present study suggested that the granulomatous experimental model using teleost fish P. mesopotamicus presented a similar response to those observed in mammals, confirming its importance for studies of chronic inflammatory reaction.
Kihara, Takanori; Kashitani, Kosuke; Miyake, Jun
2017-07-14
Cell proliferation is a key characteristic of eukaryotic cells. During cell proliferation, cells interact with each other. In this study, we developed a cellular automata model to estimate cell-cell interactions using experimentally obtained images of cultured cells. We used four types of cells; HeLa cells, human osteosarcoma (HOS) cells, rat mesenchymal stem cells (MSCs), and rat smooth muscle A7r5 cells. These cells were cultured and stained daily. The obtained cell images were binarized and clipped into squares containing about 10 4 cells. These cells showed characteristic cell proliferation patterns. The growth curves of these cells were generated from the cell proliferation images and we determined the doubling time of these cells from the growth curves. We developed a simple cellular automata system with an easily accessible graphical user interface. This system has five variable parameters, namely, initial cell number, doubling time, motility, cell-cell adhesion, and cell-cell contact inhibition (of proliferation). Within these parameters, we obtained initial cell numbers and doubling times experimentally. We set the motility at a constant value because the effect of the parameter for our simulation was restricted. Therefore, we simulated cell proliferation behavior with cell-cell adhesion and cell-cell contact inhibition as variables. By comparing growth curves and proliferation cell images, we succeeded in determining the cell-cell interaction properties of each cell. Simulated HeLa and HOS cells exhibited low cell-cell adhesion and weak cell-cell contact inhibition. Simulated MSCs exhibited high cell-cell adhesion and positive cell-cell contact inhibition. Simulated A7r5 cells exhibited low cell-cell adhesion and strong cell-cell contact inhibition. These simulated results correlated with the experimental growth curves and proliferation images. Our simulation approach is an easy method for evaluating the cell-cell interaction properties of cells.
Hu, Wenhao; Zhang, Xuesong; Yu, Jiayi; Hu, Fanqi; Zhang, Hao; Wang, Yan
2018-01-15
In the late stage of Spinal tuberculosis, the bony destruction and vertebral collapse often leads to significant kyphosis, presenting clinically as a painful gibbus deformity, with increased instability, vertebral body translations and increased risk of neurologic involvement. Vertebral column decancellation is thought to be suitable for most patients with severe rigid kyphosis. Surgimap Spine, could offer a pragmatic graphical method for the surgical planning of osteotomies. The aim of this study was to evaluate the efficacy of Vertebral column decancellation planned preoperatively with the computer software-assistance in the patients with Pott's kyphosis. Between May 2012 and May 2015, 18 patients with Pott's kyphosis underwent the Vertebral column decancellation using Surgimap Spine for preoperative surgical planning. Preoperative and postoperative Konstam's angle, sagittal vertical angle, lumbar lordosis, thoracic kyphosis, pelvic tilt and pelvic incidence were measured. Visual analog scale and American Spinal Injury Association were documented. The Konstam's angles decreased from 88.1° (range, 70-105°) preoperatively to 18.5° (range, 7-31°) (P column decancellation is an effective treatment option for severe Pott's kyphosis. The surgical planning software Surgimap Spine can be a reliable and helpful tool that provides a simplified method to evaluate and analyze the spino-pelvic parameters and simulate the osteotomy procedure. According to individual character, the appropriate surgery strategy should be selected.
Monteagudo, Ángel; Santos, José
2015-01-01
Cancer can be viewed as an emergent behavior in terms of complex system theory and artificial life, Cellular Automata (CA) being the tool most used for studying and characterizing the emergent behavior. Different approaches with CA models were used to model cancer growth. The use of the abstract model of acquired cancer hallmarks permits the direct modeling at cellular level, where a cellular automaton defines the mitotic and apoptotic behavior of cells, and allows for an analysis of different dynamics of the cellular system depending on the presence of the different hallmarks. A CA model based on the presence of hallmarks in the cells, which includes a simulation of the behavior of Cancer Stem Cells (CSC) and their implications for the resultant growth behavior of the multicellular system, was employed. This modeling of cancer growth, in the avascular phase, was employed to analyze the effect of cancer treatments in a cancer stem cell context. The model clearly explains why, after treatment against non-stem cancer cells, the regrowth capability of CSCs generates a faster regrowth of tumor behavior, and also shows that a continuous low-intensity treatment does not favor CSC proliferation and differentiation, thereby allowing an unproblematic control of future tumor regrowth. The analysis performed indicates that, contrary to the current attempts at CSC control, trying to make CSC proliferation more difficult is an important point to consider, especially in the immediate period after a standard treatment for controlling non-stem cancer cell proliferation.
Ángel Monteagudo
Full Text Available Cancer can be viewed as an emergent behavior in terms of complex system theory and artificial life, Cellular Automata (CA being the tool most used for studying and characterizing the emergent behavior. Different approaches with CA models were used to model cancer growth. The use of the abstract model of acquired cancer hallmarks permits the direct modeling at cellular level, where a cellular automaton defines the mitotic and apoptotic behavior of cells, and allows for an analysis of different dynamics of the cellular system depending on the presence of the different hallmarks. A CA model based on the presence of hallmarks in the cells, which includes a simulation of the behavior of Cancer Stem Cells (CSC and their implications for the resultant growth behavior of the multicellular system, was employed. This modeling of cancer growth, in the avascular phase, was employed to analyze the effect of cancer treatments in a cancer stem cell context. The model clearly explains why, after treatment against non-stem cancer cells, the regrowth capability of CSCs generates a faster regrowth of tumor behavior, and also shows that a continuous low-intensity treatment does not favor CSC proliferation and differentiation, thereby allowing an unproblematic control of future tumor regrowth. The analysis performed indicates that, contrary to the current attempts at CSC control, trying to make CSC proliferation more difficult is an important point to consider, especially in the immediate period after a standard treatment for controlling non-stem cancer cell proliferation.
Searby, N. D.; Steele, C. R.; Globus, R. K.; Dalton, Bonnie P. (Technical Monitor)
2001-01-01
Bone forming cells, osteoblasts, respond to various mechanical forces, including mechanical strain and fluid-induced shear stress. This study examined whether osteoblasts detect changes in gravity as a mechanical force, as assessed by cellular morphology and dimensions of the cytoskeletal network. We used modeling to evaluate how gravity influences cell morphology given theoretical differences in densities between the surrounding medium, cytoplasm, and nucleus. A mechanical model was built based on analysis of axisymmetric shell structures (Fast4 software) to study the effects of 10 times gravity (10G) on cell height. The model indicated 0.02% decrease in overall cell height when the medium was 10% denser than the nucleus or cytoplasm, 5.9 x 10(exp-5)% decrease when the nucleus was 10% denser than the cytoplasm or medium, and 1.3 x 10(exp-5)% decrease when the cell cytoplasm was 10% denser than the nucleus or medium. To experimentally evaluate the influence of gravity, cultured primary fetal rat osteoblasts were grown to near confluence and centrifuged at 10G for 3 hours. Actin, microtubules, and nuclei were fluorescently labeled and analyzed by confocal microscopy to determine overall microtubule and actin network height. Centrifugation led to an apparent reduction in height of both the microtubule (-16%) and the actin (-20%) networks relative to stationary controls. Thus, both modeling and experiments indicate that hypergravity reduces the height of the osteoblast cell layer and their microtubule and actin networks. This combination of modeling and experimental analyses will help us to better understand the mechanical loading of osteoblasts.
Stochastic Geometric Coverage Analysis in mmWave Cellular Networks with a Realistic Channel Model
Rebato, Mattia; Park, Jihong; Popovski, Petar
2017-01-01
Millimeter-wave (mmWave) bands have been attracting growing attention as a possible candidate for next-generation cellular networks, since the available spectrum is orders of magnitude larger than in current cellular allocations. To precisely design mmWave systems, it is important to examine mmWa...
Cellular Automata Based Modeling for Evaluating Different Bus Stop Designs in China
Haoyang Ding
2015-01-01
Full Text Available A cellular automaton model is proposed to simulate mixed traffic flow composed of motor vehicles and bicycles near bus stops. Three typical types of bus stops which are common in China are considered in the model, including two types of curbside bus stops and one type of bus bay stops. Passenger transport capacity of three types of bus stops, which is applied to evaluate the bus stop design, is calculated based on the corresponding traffic flow rate. According to the simulation results, the flow rates of both motor vehicles and bicycles exhibit phase transition from free flow to the saturation one at the critical point. The results also show that the larger the interaction between motor vehicle and bicycle flow is near curbside bus stops, the more the value of saturated flows drops. Curbside bus stops are more suitable when the conflicts between two flows are small and the inflow rate of motor vehicles is low. On the contrary, bus bay stops should be applied due to their ability to reduce traffic conflicts. Findings of this study can provide useful suggestions on bus stop selection considering different inflow rate of motor vehicles and bicycles simultaneously.
Cellular automata model for urban road traffic flow considering pedestrian crossing street
Zhao, Han-Tao; Yang, Shuo; Chen, Xiao-Xu
2016-11-01
In order to analyze the effect of pedestrians' crossing street on vehicle flows, we investigated traffic characteristics of vehicles and pedestrians. Based on that, rules of lane changing, acceleration, deceleration, randomization and update are modified. Then we established two urban two-lane cellular automata models of traffic flow, one of which is about sections with non-signalized crosswalk and the other is on uncontrolled sections with pedestrians crossing street at random. MATLAB is used for numerical simulation of the different traffic conditions; meanwhile space-time diagram and relational graphs of traffic flow parameters are generated and then comparatively analyzed. Simulation results indicate that when vehicle density is lower than around 25 vehs/(km lane), pedestrians have modest impact on traffic flow, whereas when vehicle density is higher than about 60 vehs/(km lane), traffic speed and volume will decrease significantly especially on sections with non-signal-controlled crosswalk. The results illustrate that the proposed models reconstruct the traffic flow's characteristic with the situation where there are pedestrians crossing and can provide some practical reference for urban traffic management.
Emergent 1d Ising Behavior in AN Elementary Cellular Automaton Model
Kassebaum, Paul G.; Iannacchione, Germano S.
The fundamental nature of an evolving one-dimensional (1D) Ising model is investigated with an elementary cellular automaton (CA) simulation. The emergent CA simulation employs an ensemble of cells in one spatial dimension, each cell capable of two microstates interacting with simple nearest-neighbor rules and incorporating an external field. The behavior of the CA model provides insight into the dynamics of coupled two-state systems not expressible by exact analytical solutions. For instance, state progression graphs show the causal dynamics of a system through time in relation to the system's entropy. Unique graphical analysis techniques are introduced through difference patterns, diffusion patterns, and state progression graphs of the 1D ensemble visualizing the evolution. All analyses are consistent with the known behavior of the 1D Ising system. The CA simulation and new pattern recognition techniques are scalable (in both dimension, complexity, and size) and have many potential applications such as complex design of materials, control of agent systems, and evolutionary mechanism design.
Tectonic modeling of Konya-Beysehir Region (Turkey using cellular neural networks
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.
Load-aware modeling for uplink cellular networks in a multi-channel environment
AlAmmouri, Ahmad
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.
Phase transitions and hysteresis in a cellular automata-based model of opinion formation
Kacperski, K.; Holyst, J.A.
1996-01-01
A particular case of a cellular automata-based model of two-state opinion formation in social groups with a strong leader is studied. We consider a 2D Euclidian geometry of open-quotes social spaceclose quotes and mutual interactions ∝ 1/r n . The model shows an interesting dynamics which can be analytically calculated. There are two stable states of the system: a cluster around the leader and unification. Unstable clusters may also appear. A variation in parameters such as the leader's strength or the open-quotes social temperatureclose quotes can change the size of a cluster or, when they reach some critical values, make the system jump into another state. For a certain range of parameters the system exhibits bistability and hysteresis phenomena. We obtained explicit formulas for the cluster size, critical values, make the system jump into another state. For a certain range of parameters the system exhibits bistability and hysteresis phenomena. We obtained explicit formulas for the cluster size, critical leader's strength, and critical open-quotes social temperature.close quotes These analytical results are verified by computer simulations
Martelli, Alain; Napierala, Marek; Puccio, Hélène
2012-01-01
In 1996, a link was identified between Friedreich’s ataxia (FRDA), the most common inherited ataxia in men, and alterations in the gene encoding frataxin (FXN). Initial studies revealed that the disease is caused by a unique, most frequently biallelic, expansion of the GAA sequence in intron 1 of FXN. Since the identification of this link, there has been tremendous progress in understanding frataxin function and the mechanism of FRDA pathology, as well as in developing diagnostics and therapeutic approaches for the disease. These advances were the subject of the 4th International Friedreich’s Ataxia Conference held on 5th–7th May in the Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France. More than 200 scientists gathered from all over the world to present the results of research spanning all areas of investigation into FRDA (including clinical aspects, FRDA pathogenesis, genetics and epigenetics of the disease, development of new models of FRDA, and drug discovery). This review provides an update on the understanding of frataxin function, developments of animal and cellular models of the disease, and recent advances in trying to uncover potential molecules for therapy. PMID:22382366
[A Cellular Automata Model for a Community Comprising Two Plant Species of Different Growth Forms].
Frolov, P V; Zubkova, E V; Komarov, A S
2015-01-01
A cellular automata computer model for the interactions between two plant species of different growth forms--the lime hairgrass Deschampsia caespitosa (L.) P. Beauv., a sod cereal, and the moneywort Lysimachia nummularia L., a ground creeping perennial herb--is considered. Computer experiments on the self-maintenance of the populations of each species against the background of a gradual increase in the share of randomly eliminated individuals, coexistence of the populations of two species, and the effect of the phytogenous field have been conducted. As has been shown, all the studied factors determine the number of individuals and self-sustainability of the simulated populations by the degree of their impact. The limits of action have been determined for individual factors; within these limits, the specific features in plant reproduction and dispersal provide sustainable coexistence of the simulated populations. It has been demonstrated that the constructed model allows for studying the long-term developmental dynamics of the plants belonging to the selected growth forms.
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.
fA cellular automaton model of crystalline cellulose hydrolysis by cellulases
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
Magalhaes, A.C.N. de.
1982-01-01
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 (dt 0 /dp) sub(p = p sub(c)) (where t 0 identical to tanh J/K sub(B) T), and to a 0.15% (0.96%) error in (dt 0 /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) [pt
Hilburn, Monty D.
Successful lean manufacturing and cellular manufacturing execution relies upon a foundation of leadership commitment and strategic planning built upon solid data and robust analysis. The problem for this study was to create and employ a simple lean transformation planning model and review process that could be used to identify functional support staff resources required to plan and execute lean manufacturing cells within aerospace assembly and manufacturing sites. The lean planning model was developed using available literature for lean manufacturing kaizen best practices and validated through a Delphi panel of lean experts. The resulting model and a standardized review process were used to assess the state of lean transformation planning at five sites of an international aerospace manufacturing and assembly company. The results of the three day, on-site review were compared with baseline plans collected from each of the five sites to determine if there analyzed, with focus on three critical areas of lean planning: the number and type of manufacturing cells identified, the number, type, and duration of planned lean and continuous kaizen events, and the quantity and type of functional staffing resources planned to support the kaizen schedule. Summarized data of the baseline and on-site reviews was analyzed with descriptive statistics. ANOVAs and paired-t tests at 95% significance level were conducted on the means of data sets to determine if null hypotheses related to cell, kaizen event, and support resources could be rejected. The results of the research found significant differences between lean transformation plans developed by site leadership and plans developed utilizing the structured, on-site review process and lean transformation planning model. The null hypothesis that there was no difference between the means of pre-review and on-site cell counts was rejected, as was the null hypothesis that there was no significant difference in kaizen event plans. These
Sara Anjomani Virmouni
Full Text Available Friedreich ataxia (FRDA is an autosomal recessive neurodegenerative disorder, caused by a GAA repeat expansion mutation within intron 1 of the FXN gene. We have previously established and performed preliminary characterisation of several human FXN yeast artificial chromosome (YAC transgenic FRDA mouse models containing GAA repeat expansions, Y47R (9 GAA repeats, YG8R (90 and 190 GAA repeats and YG22R (190 GAA repeats.We now report extended cellular, molecular and functional characterisation of these FXN YAC transgenic mouse models. FXN transgene copy number analysis of the FRDA mice demonstrated that the YG22R and Y47R lines each have a single copy of the FXN transgene while the YG8R line has two copies. Single integration sites of all transgenes were confirmed by fluorescence in situ hybridisation (FISH analysis of metaphase and interphase chromosomes. We identified significant functional deficits, together with a degree of glucose intolerance and insulin hypersensitivity, in YG8R and YG22R FRDA mice compared to Y47R and wild-type control mice. We also confirmed increased somatic GAA repeat instability in the cerebellum and brain of YG22R and YG8R mice, together with significantly reduced levels of FXN mRNA and protein in the brain and liver of YG8R and YG22R compared to Y47R.Together these studies provide a detailed characterisation of our GAA repeat expansion-based YAC transgenic FRDA mouse models that will help investigations of FRDA disease mechanisms and therapy.
Screening Applications to Test Cellular Fitness in Transwell® Models After Nanoparticle Treatment.
Christ, Bastian; Fey, Christina; Cubukova, Alevtina; Walles, Heike; Dembski, Sofia; Metzger, Marco
2017-01-01
Nanoparticles (NPs) in biotechnology hold great promise for revolutionizing medical treatments and therapies. In order to bring NPs into clinical application there is a number of preclinical in vitro and in vivo tests, which have to be applied before. The initial in vitro evaluation includes a detailed physicochemical characterization as well as biocompatibility tests, among others. For determination of biocompatibility at the cellular level, the correct choice of the in vitro assay as well as NP pretreatment is absolutely essential. There are a variety of assay technologies available that use standard plate readers to measure metabolic markers to estimate the number of viable cells in culture. Each cell viability assay has its own set of advantages and disadvantages. Regardless of the assay method chosen, the major factors critical for reproducibility and success include: (1) choosing the right assay after comparing optical NP properties with the read-out method of the assay, (2) verifying colloidal stability of NPs in cell culture media, (3) preparing a sterile and stable NP dispersion in cell culture media used in the assay, (4) using a tightly controlled and consistent cell model allowing appropriate characterization of NPs. This chapter will briefly summarize these different critical points, which can occur during biocompatibility screening applications of NPs.
M.A. Al-Griw
2016-09-01
Full Text Available Exposures to a wide variety of environmental substances are negatively associated with many biological cell systems both in humans and rodents. Trichloroethane (TCE, a ubiquitous environmental toxicant, is used in large quantities as a dissolvent, metal degreaser, chemical intermediate, and component of consumer products. This increases the likelihood of human exposure to these compounds through dermal, inhalation and oral routes. The present in vivo study was aimed to investigate the possible cellular and molecular etiology of liver abnormality induced by early exposure to TCE using a murine model. The results showed a significant increase in liver weight. Histopathological examination revealed a TCE-induced hepatotoxicity which appeared as heavily congested central vein and blood sinusoids as well as leukocytic infiltration. Mitotic figures and apoptotic changes such as chromatin condensation and nuclear fragments were also identified. Cell death analysis demonstrates hepatocellular apoptosis was evident in the treated mice compared to control. TCE was also found to induce oxidative stress as indicated by an increase in the levels of lipid peroxidation, an oxidative stress marker. There was also a significant decrease in the DNA content of the hepatocytes of the treated groups compared to control. Agarose gel electrophoresis also provided further biochemical evidence of apoptosis by showing internucleosomal DNA fragmentation in the liver cells, indicating oxidative stress as the cause of DNA damage. These results suggest the need for a complete risk assessment of any new chemical prior to its arrival into the consumer market.
Tilda Barliya
2017-01-01
Full Text Available Purpose. To explore functional electroretinographic (ERG changes and associated cellular remodeling following experimental retinal detachment in a rabbit model. Methods. Retinal detachment was created in ten rabbits by injecting 0.1 ml balanced salt solution under the retina. Fundus imaging was performed 0, 3, 7, 14, and 21 days postoperatively. ERGs were recorded pre- and 7 and 21 days postoperatively. Eyes were harvested on day 21 and evaluated immunohistochemically (IHC for remodeling of second- and third-order neurons. Results. Retinal reattachment occurred within two weeks following surgery. No attenuation was observed in the photopic or scotopic a- and b-waves. A secondary wavefront on the descending slope of the scotopic b-wave was the only ERG result that was attenuated in detached retinas. IHC demonstrated anatomical changes in both ON and OFF bipolar cells. Bassoon staining was observed in the remodeled dendrites. Amacrine and horizontal cells did not alter, but Muller cells were clearly reactive with marked extension. Conclusion. Retinal detachment and reattachment were associated with functional and anatomical changes. Exploring the significance of the secondary scotopic wavefront and its association with the remodeling of 2nd- and 3rd-order neurons will shade more light on functional changes and recovery of the retina.
McCleery, W. Tyler; Mohd-Radzman, Nadiatul A.; Grieneisen, Veronica A.
Cells within tissues can be regarded as autonomous entities that respond to their local environment and signaling from neighbors. Cell coordination is particularly important in plants, where root architecture must strategically invest resources for growth to optimize nutrient acquisition. Thus, root cells are constantly adapting to environmental cues and neighbor communication in a non-linear manner. To explain such plasticity, we view the root as a swarm of coupled multi-cellular structures, ''metamers'', rather than as a continuum of identical cells. These metamers are individually programmed to achieve a local objective - developing a lateral root primordia, which aids in local foraging of nutrients. Collectively, such individual attempts may be halted, structuring root architecture as an emergent behavior. Each metamer's decision to branch is coordinated locally and globally through hormone signaling, including processes of controlled diffusion, active polar transport, and dynamic feedback. We present a physical model of the signaling mechanism that coordinates branching decisions in response to the environment. This work was funded by the European Commission 7th Framework Program, Project No. 601062, SWARM-ORGAN.
Modelling land use/cover changes with markov-cellular automata in Komering Watershed, South Sumatera
Kusratmoko, E.; Albertus, S. D. Y.; Supriatna
2017-01-01
This research has a purpose to study and develop a model that can representing and simulating spatial distribution pattern of land use change in Komering watershed. The Komering watershed is one of nine sub Musi river basin and is located in the southern part of Sumatra island that has an area of 8060,62 km2. Land use change simulations, achieved through Markov-cellular automata (CA) methodologies. Slope, elevation, distance from road, distance from river, distance from capital sub-district, distance from settlement area area were driving factors that used in this research. Land use prediction result in 2030 also shows decrease of forest acreage up to -3.37%, agricultural land decreased up to -2.13%, and open land decreased up to -0.13%. On the other hand settlement area increased up to 0.07%, and plantation land increased up to 5.56%. Based on the predictive result, land use unconformity percentage to RTRW in Komering watershed is 18.62 % and land use conformity is 58.27%. Based on the results of the scenario, where forest in protected areas and agriculture land are maintained, shows increase the land use conformity amounted to 60.41 % and reduce unconformity that occur in Komering watershed to 17.23 %.
Jahanishakib, Fatemeh; Mirkarimi, Seyed Hamed; Salmanmahiny, Abdolrassoul; Poodat, Fatemeh
2018-05-08
Efficient land use management requires awareness of past changes, present actions, and plans for future developments. Part of these requirements is achieved using scenarios that describe a future situation and the course of changes. This research aims to link scenario results with spatially explicit and quantitative forecasting of land use development. To develop land use scenarios, SMIC PROB-EXPERT and MORPHOL methods were used. It revealed eight scenarios as the most probable. To apply the scenarios, we considered population growth rate and used a cellular automata-Markov chain (CA-MC) model to implement the quantified changes described by each scenario. For each scenario, a set of landscape metrics was used to assess the ecological integrity of land use classes in terms of fragmentation and structural connectivity. The approach enabled us to develop spatial scenarios of land use change and detect their differences for choosing the most integrated landscape pattern in terms of landscape metrics. Finally, the comparison between paired forecasted scenarios based on landscape metrics indicates that scenarios 1-1, 2-2, 3-2, and 4-1 have a more suitable integrity. The proposed methodology for developing spatial scenarios helps executive managers to create scenarios with many repetitions and customize spatial patterns in real world applications and policies.
Modeling and Simulation of Polarization in Internet Group Opinions Based on Cellular Automata
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.
Nagatani, Takashi; Tainaka, Kei-ichi
2018-01-01
In most cases, physicists have studied the migration of biospecies by the use of random walk. In the present article, we apply cellular automaton of traffic model. For simplicity, we deal with an ecosystem contains a prey and predator, and use one-dimensional lattice with two layers. Preys stay on the first layer, but predators uni-directionally move on the second layer. The spatial and temporal evolution is numerically explored. It is shown that the migration has the important effect on populations of both prey and predator. Without migration, the phase transition between a prey-phase and coexisting-phase occurs. In contrast, the phase transition disappears by migration. This is because predator can survive due to migration. We find another phase transition for spatial distribution: in one phase, prey and predator form a stripe pattern of condensation and rarefaction, while in the other phase, they uniformly distribute. The self-organized stripe may be similar to the migration patterns in real ecosystems.
Assessment of freeway work zone safety with improved cellular automata model
Guohua Liang
2014-08-01
Full Text Available To accurately assess the safety of freeway work zones, this paper investigates the safety of vehicle lane change maneuvers with improved cellular automata model. Taking the traffic conflict and standard deviation of operating speed as the evaluation indexes, the study evaluates the freeway work zone safety. With improved deceleration probability in car-following raies and the addition of lanechanging rules under critical state, the lane-changing behavior under critical state is defined as a conflict count. Through 72 schemes of simulation runs, the possible states of the traffic flow are carefully studied. The results show that under the condition of constant saturation traffic conflict count and vehicle speed standard deviation reach their maximums when the mixed rate of heave vehicles is 40%. Meanwhile, in the case of constant heavy vehicles mix, traffic conflict count and vehicle speed standard deviation reach maximum values when saturation rate is 0. 75. Integrating ail simulation results, it is known the traffic safety in freeway work zones is classified into four levels : safe, relatively safe, relatively dangerous, and dangerous.
Broda, Ellen; Mickler, Frauke Martina; Lächelt, Ulrich; Morys, Stephan; Wagner, Ernst; Bräuchle, Christoph
2015-09-10
Sophisticated drug delivery systems are coated with targeting ligands to improve the specific adhesion to surface receptors on diseased cells. In our study, we developed a method with which we assessed the potential of peptide ligands to specifically bind to receptor overexpressing target cells. Therefore, a microfluidic setup was used where the cellular adhesion of nanoparticles with ligand and of control nanoparticles was observed in parallel under the same experimental conditions. The effect of the ligand on cellular binding was quantified by counting the number of adhered nanoparticles with ligand and differently labeled control nanoparticles on single cells after incubation under flow conditions. To provide easy-to-synthesize, stable and reproducible nanoparticles which mimic the surface characteristics of drug delivery systems and meet the requirements for quantitative analysis, latex beads based on amine-modified polystyrene were used as model nanoparticles. Two short peptides were tested to serve as targeting ligand on the beads by increasing the specific binding to HuH7 cells. The c-Met binding peptide cMBP2 was used for hepatocyte growth factor receptor (c-Met) targeting and the peptide B6 for transferrin receptor (TfR) targeting. The impact of the targeting peptide on binding was investigated by comparing the beads with ligand to different internal control beads: 1) without ligand and tailored surface charge (electrostatic control) and 2) with scrambled peptide and similar surface charge, but a different amino acid sequence (specificity control). Our results demonstrate that the method is very useful to select suitable targeting ligands for specific nanoparticle binding to receptor overexpressing tumor cells. We show that the cMBP2 ligand specifically enhances nanoparticle adhesion to target cells, whereas the B6 peptide mediates binding to tumor cells mainly by nonspecific interactions. All together, we suggest that cMBP2 is a suitable choice for
A new micromechanical approach of micropolar continuum modeling for 2-D periodic cellular material
Bin Niu; Jun Yan
2016-01-01
In this paper, we present a new united approach to formulate the equivalent micropolar constitutive relation of two-dimensional (2-D) periodic cellular material to capture its non-local properties and to explain the size effects in its structural analysis. The new united approach takes both the displacement compatibility and the equilibrium of forces and moments into consideration, where Taylor series expansion of the displacement and rotation fields and the extended aver-aging procedure with an explicit enforcement of equilibrium are adopted in the micromechanical analysis of a unit cell. In numerical examples, the effective micropolar constants obtained in this paper and others derived in the literature are used for the equivalent micropolar continuum simulation of cellular solids. The solutions from the equivalent analysis are compared with the discrete simulation solutions of the cellu-lar solids. It is found that the micropolar constants developed in this paper give satisfying results of equivalent analysis for the periodic cellular material.
D'Onofrio, Alberto
2009-01-01
In this paper we study and extend the mechanistic mean field theory of growth of cellular populations proposed by Mombach et al. [Mombach JCM, Lemke N, Bodmann BEJ, Idiart MAP. A mean-field theory of cellular growth. Europhys Lett 2002;59:923-928] (MLBI model), and we demonstrate that the original model and our generalizations lead to inferences of biological interest. In the first part of this paper, we show that the model in study is widely general since it admits, as particular cases, the main phenomenological models of cellular growth. In the second part of this work, we generalize the MLBI model to a wider family of models by allowing the cells to have a generic unspecified biologically plausible interaction. Then, we derive a relationship between this generic microscopic interaction function and the growth rate of the corresponding macroscopic model. Finally, we propose to use this relationship in order to help the investigation of the biological plausibility of phenomenological models of cancer growth.
Ground state entropy of the Potts antiferromagnet on triangular lattice strips
Chang Shuchiuan; Shrock, Robert
2001-01-01
We present exact calculations of the zero-temperature partition function (chromatic polynomial) P for the q-state Potts antiferromagnet on triangular lattice strips of arbitrarily great length L x vertices and of width L y vertices and, in the L x →∞ limit, the exponent of the ground state entropy, W=e S 0 /k B . The strips considered, with their boundary conditions (BC), are (a) (FBC y , PBC x ) = cyclic for L y =3, 4, (b) (FBC y , TPBC x ) = Moebius, L y =3, (c) (PBC y , PBC x ) = toroidal, L y =3, (d) (PBC y , TPBC x ) = Klein bottle, L y =3, (e) (PBC y , FBC x ) = cylindrical, L y =5, 6, and (f) (FBC y , FBC x ) = free, L y =5, where F, P, and TP denote free, periodic, and twisted periodic. Several interesting features are found, including the presence of terms in P proportional to cos(2πL x /3) for case (c). The continuous locus of points B where W is nonanalytic in the q plane is discussed for each case and a comparative discussion is given of the respective loci B for families with different boundary conditions. Numerical values of W are given for infinite-length strips of various widths and are shown to approach values for the 2D lattice rapidly. A remark is also made concerning a zero-free region for chromatic zeros. Some results are given for strips of other lattices
Duchna Hans-Werner
2009-11-01
Full Text Available Abstract Background Tuberculous spondylitis (Pott's disease is an ancient human disease. Because it is rare in high-income, tuberculosis (TB low incidence countries, misdiagnoses occur as sufficient clinical experience is lacking. Case presentation We describe a fatal case of a patient with spinal TB, who was mistakenly irradiated for suspected metastatic lung cancer of the spine in the presence of a solitary pulmonary nodule of the left upper lobe. Subsequently, the patient progressed to central nervous system TB, and finally, disseminated TB before the accurate diagnosis was established. Isolation and antimycobacterial chemotherapy were initiated after an in-hospital course of approximately three months including numerous health care related contacts and procedures. Conclusion The rapid diagnosis of spinal TB demands a high index of suspicion and expertise regarding the appropriate diagnostic procedures. Due to the devastating consequences of a missed diagnosis, Mycobacterium tuberculosis should be considered early in every case of spondylitis, intraspinal or paravertebral abscess. The presence of certain alarm signals like a prolonged history of progressive back pain, constitutional symptoms or pulmonary nodules on a chest radiograph, particularly in the upper lobes, may guide the clinical suspicion.
N-acetyl-L-cysteine prevents stress-induced desmin aggregation in cellular models of desminopathy.
Bertrand-David Segard
Full Text Available Mutations within the human desmin gene are responsible for a subcategory of myofibrillar myopathies called desminopathies. However, a single inherited mutation can produce different phenotypes within a family, suggesting that environmental factors influence disease states. Although several mouse models have been used to investigate organ-specific desminopathies, a more general mechanistic perspective is required to advance our knowledge toward patient treatment. To improve our understanding of disease pathology, we have developed cellular models to observe desmin behaviour in early stages of disease pathology, e.g., upon formation of cytoplasmic desmin aggregates, within an isogenic background. We cloned the wildtype and three mutant desmin cDNAs using a Tet-On Advanced® expression system in C2C12 cells. Mutations were selected based on positioning within desmin and capacity to form aggregates in transient experiments, as follows: DesS46Y (head domain; low aggregation, DesD399Y (central rod domain; high aggregation, and DesS460I (tail domain; moderate aggregation. Introduction of these proteins into a C2C12 background permitted us to compare between desmin variants as well as to determine the role of external stress on aggregation. Three different types of stress, likely encountered during muscle activity, were introduced to the cell models-thermal (heat shock, redox-associated (H2O2 and cadmium chloride, and mechanical (stretching stresses-after which aggregation was measured. Cells containing variant DesD399Y were more sensitive to stress, leading to marked cytoplasmic perinuclear aggregations. We then evaluated the capacity of biochemical compounds to prevent this aggregation, applying dexamethasone (an inducer of heat shock proteins, fisetin or N-acetyl-L-cysteine (antioxidants before stress induction. Interestingly, N-acetyl-L-cysteine pre-treatment prevented DesD399Y aggregation during most stress. N-acetyl-L-cysteine has recently been
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
2007-03-01
computer models of cell cycle regulation in a variety of organisms, including yeast cells, amphibian embryos, bacterial cells and human cells. These...and meiosis ), but they do not nullify the central role played by irreversible, alternating START and FINISH transitions in the cell cycle. 32...AFRL-IF-RS-TR-2007-69 Final Technical Report March 2007 EUKARYOTIC CELL CYCLE AS A TEST CASE FOR MODELING CELLULAR REGULATION IN A
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...... 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....
Probing cellular mechanoadaptation using cell-substrate de-adhesion dynamics: experiments and model.
S S, Soumya; Sthanam, Lakshmi Kavitha; Padinhateeri, Ranjith; Inamdar, Mandar M; Sen, Shamik
2014-01-01
Physical properties of the extracellular matrix (ECM) are known to regulate cellular processes ranging from spreading to differentiation, with alterations in cell phenotype closely associated with changes in physical properties of cells themselves. When plated on substrates of varying stiffness, fibroblasts have been shown to exhibit stiffness matching property, wherein cell cortical stiffness increases in proportion to substrate stiffness up to 5 kPa, and subsequently saturates. Similar mechanoadaptation responses have also been observed in other cell types. Trypsin de-adhesion represents a simple experimental framework for probing the contractile mechanics of adherent cells, with de-adhesion timescales shown to scale inversely with cortical stiffness values. In this study, we combine experiments and computation in deciphering the influence of substrate properties in regulating de-adhesion dynamics of adherent cells. We first show that NIH 3T3 fibroblasts cultured on collagen-coated polyacrylamide hydrogels de-adhere faster on stiffer substrates. Using a simple computational model, we qualitatively show how substrate stiffness and cell-substrate bond breakage rate collectively influence de-adhesion timescales, and also obtain analytical expressions of de-adhesion timescales in certain regimes of the parameter space. Finally, by comparing stiffness-dependent experimental and computational de-adhesion responses, we show that faster de-adhesion on stiffer substrates arises due to force-dependent breakage of cell-matrix adhesions. In addition to illustrating the utility of employing trypsin de-adhesion as a biophysical tool for probing mechanoadaptation, our computational results highlight the collective interplay of substrate properties and bond breakage rate in setting de-adhesion timescales.
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.
Jin Kyu Kim; Petin, V.G.; Mishra, K.P.
2007-01-01
Complete text of publication follows. Background: Organisms in their living environment are not exposed to merely a single stress agent. Several factors such as radiation and heat may simultaneously exert their stressful effect to the organisms. The combined exposure to two stressors can result in an enhanced effect that would be expected from the addition of the separate exposures to individual agents. Objective: This study has been undertaken to develop a theoretical model for assessment of combined effects of low dose radiation and mild heat for predictive cellular response assay. Rationale: Present study was motivated from the belief that synergism may occur in terms of lethal lesions arising from the interaction of non-lethal sub-lesions induced by individual agents. The sub-lesions induced by each agent may be negligible or undetectable. But, there exists a possibility of some cross talk between sublesions produced by radiation and heat. These processes may reflect the real mechanisms for inflicting the lethal damage by otherwise ignorable or undetectable insults to exposed organisms. Results: A theoretically developed mathematical model of the synergy was formulated which was tested for validation on the experimental data. The model predictions fairly closely corresponded with several experimental results. .The significance of synergistic effects for radiation biology has been demonstrated. A number of common peculiarities of synergistic interactions were found to play their roles. A unified biophysical concept for synergistic interaction has been suggested. Conclusions: For a constant dose rate, synergistic interaction between radiation and hyperthermia especially at low intensity is realized only within a certain range of temperature, independently of the target object analyzed. For temperatures below the range, the synergistic effect was not observed and cell killing was mainly determined by the damage induced by ionizing radiation. On the contrary, the
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...... cellular model. With the use of the developed hierarchical model, the influence of the microstructure, including microfibril angles (MFAs, which characterizes the orientation of the cellulose fibrils with respect to the cell axis), the thickness of the cell wall, the shape of the cell cross...... 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...
Mahshid, Rasoul; Hansen, Hans Nørgaard; Loft Højbjerre, Klaus
2016-01-01
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...... with experimental data and it is shown that they agree well. The results from this research show that using lattice structures significantly reduces the strength of material with respect to solid samples while indicating no serious increase of strength compared to hollow structures. In combination with an analysis...
Induced pluripotent stem cells as a cellular model for studying Down Syndrome
Brigida AL
2016-11-01
Full Text Available Down Syndrome (DS, or Trisomy 21 Syndrome, is one of the most common genetic diseases. It is a chromosomal abnormality caused by a duplication of chromosome 21. DS patients show the presence of a third copy (or a partial third copy of chromosome 21 (trisomy, as result of meiotic errors. These patients suffer of many health problems, such as intellectual disability, congenital heart disease, duodenal stenosis, Alzheimer's disease, leukemia, immune system deficiencies, muscle hypotonia and motor disorders. About one in 1000 babies born each year are affected by DS. Alterations in the dosage of genes located on chromosome 21 (also called HSA21 are responsible for the DS phenotype. However, the molecular pathogenic mechanisms of DS triggering are still not understood; newest evidences suggest the involvement of epigenetic mechanisms. For obvious ethical reasons, studies performed on DS patients, as well as on human trisomic tissues are limited. Some authors have proposed mouse models of this syndrome. However, not all the features of the syndrome are represented. Stem cells are considered the future of molecular and regenerative medicine. Several types of stem cells could provide a valid approach to offer a potential treatment for some untreatable human diseases. Stem cells also represent a valid system to develop new cell-based drugs and/or a model to study molecular disease pathways. Among stem cell types, patient-derived induced pluripotent stem (iPS cells offer some advantages for cell and tissue replacement, engineering and studying: self-renewal capacity, pluripotency and ease of accessibility to donor tissues. These cells can be reprogrammed into completely different cellular types. They are derived from adult somatic cells via reprogramming with ectopic expression of four transcription factors (Oct3/4, Sox2, c-Myc and Klf4; or, Oct3/4, Sox2, Nanog, and Lin28. By reprogramming cells from DS patients, it is possible to obtain new tissue with
Tadeo, Irene; Piqueras, Marta; Montaner, David; Villamón, Eva; Berbegall, Ana P; Cañete, Adela; Navarro, Samuel; Noguera, Rosa
2014-02-01
Risk classification and treatment stratification for cancer patients is restricted by our incomplete picture of the complex and unknown interactions between the patient's organism and tumor tissues (transformed cells supported by tumor stroma). Moreover, all clinical factors and laboratory studies used to indicate treatment effectiveness and outcomes are by their nature a simplification of the biological system of cancer, and cannot yet incorporate all possible prognostic indicators. A multiparametric analysis on 184 tumor cylinders was performed. To highlight the benefit of integrating digitized medical imaging into this field, we present the results of computational studies carried out on quantitative measurements, taken from stromal and cancer cells and various extracellular matrix fibers interpenetrated by glycosaminoglycans, and eight current approaches to risk stratification systems in patients with primary and nonprimary neuroblastoma. New tumor tissue indicators from both fields, the cellular and the extracellular elements, emerge as reliable prognostic markers for risk stratification and could be used as molecular targets of specific therapies. The key to dealing with personalized therapy lies in the mathematical modeling. The use of bioinformatics in patient-tumor-microenvironment data management allows a predictive model in neuroblastoma.
Tsallis, C.
1980-01-01
It is conjectured that a logarithmic provides a very accurate approximation of the yet unknown critical frontier of a fully anisotropic homogeneous quenched bond-mixed q-state Potts ferromagnet in square lattice, where the random coupling constant J is distributed according to the laws P(J) and P'(J) for 'horizontal' and 'vertical' bonds respectively. Such an equation contains as particular cases a great number of exact results as well as a few recent conjectures (which are definitively only approximate). (Author) [pt
Short-time dynamics of random-bond Potts ferromagnet with continuous self-dual quenched disorders
Pan, Z. Q.; Ying, H. P.; Gu, D. W.
2001-01-01
We present Monte Carlo simulation results of 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 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 $\\eta$, as well as the exponent $\\theta$. Our special attention is paid to the dynamic process for the $q...
Solar PV powered mobile cellular base station: Models and use cases in South Africa
Aderemi, BA
2017-09-01
Full Text Available The huge costs of operating a mobile cellular base station, and the negative impact of greenhouse gasses on the environment have made the solar PV renewable energy source a sought after. In addition to cost and environmental factor, abundant supply...
Zhang, Ziyu; Yuan, Lang; Lee, Peter D; Jones, Eric; Jones, Julian R
2014-11-01
Bone augmentation implants are porous to allow cellular growth, bone formation and fixation. However, the design of the pores is currently based on simple empirical rules, such as minimum pore and interconnects sizes. We present a three-dimensional (3D) transient model of cellular growth based on the Navier-Stokes equations that simulates the body fluid flow and stimulation of bone precursor cellular growth, attachment, and proliferation as a function of local flow shear stress. The model's effectiveness is demonstrated for two additive manufactured (AM) titanium scaffold architectures. The results demonstrate that there is a complex interaction of flow rate and strut architecture, resulting in partially randomized structures having a preferential impact on stimulating cell migration in 3D porous structures for higher flow rates. This novel result demonstrates the potential new insights that can be gained via the modeling tool developed, and how the model can be used to perform what-if simulations to design AM structures to specific functional requirements. © 2014 Wiley Periodicals, Inc.
H. Wang
2010-07-01
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 concentration (150 vs. 30 mg^{−1}. When embedding the perturbations in closed cells, local drizzle and pockets of open cell (POC formation respond faster to the aerosol reduction than to the moisture increase, but the latter generates stronger and more persistent drizzle. A 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
Jarlath E. Nally
2018-03-01
Full Text Available Pathogenic species of Leptospira cause leptospirosis, a bacterial zoonotic disease with a global distribution affecting over one million people annually. Rats are regarded as one of the most significant reservoir hosts of infection for human disease, and in the absence of clinical signs of infection, excrete large numbers of organisms in their urine. A unique biological equilibrium exists between pathogenic leptospires and reservoir hosts of infection, but surprisingly, little is known concerning the host's cellular immune response that facilitates persistent renal colonization. To address this deficiency, we established and applied an immunocompetent inbred rat model of persistent renal colonization; leptospires were detected in urine of experimentally infected rats by 3 weeks post-infection and remained positive until 8 weeks post-infection. However, there was little, if any, evidence of inflammation in colonized renal tubules. At 8 weeks post-infection, a robust antibody response was detected against lipopolysaccharide and protein outer membrane (OM components. Purified B and T cells derived from the spleen of infected and non-infected rats proliferated in response to stimulation with 0.5 μg of OM fractions of Leptospira, including CD4+ T cells, which comprised 40% of proliferating cells, compared to 25% in non-infected controls. However, analysis of gene expression did not determine which immunoregulatory pathways were activated. Lymphocytes purified from the lymph node draining the site of colonization, the renal lymph node, also showed an increase in percentage of proliferating B and T cells. However, in contrast to a phenotype of 40% CD4+ T cells in the spleen, the phenotype of proliferating T cells in the renal lymph node comprised 65% CD4+ T cells. These results confirm that the renal lymph node, the local lymphoid organ, is a dominant site containing Leptospira reactive CD4+ T cells and highlight the need to consider the local, vs
Shimura, K.; Terai, T.; Yamawaki, M.
2003-01-01
In this study, the kinetics of desorption of adsorbed hydrogen from an ideal metallic surface is modelled in Cellular Automaton (CA). The modelling is achieved by downgrading the surface to one dimension. The model consists of two parts that are surface migration and desorption. The former is attained by randomly sorting the particles at each time, the latter is realised by modelling the thermally-activated process. For the verification of this model, thermal desorption is simulated then the comparison with the chemical kinetics is carried out. Excellent agreement is observed from the result. The results show that this model is reasonable to express the recombinative desorption of two chemisorbed adatoms. Though, the application of this model is limited to the second-order reaction case. But it can be believed that the groundwork of modelling the transport dynamics of hydrogen through the surface under complex conditions is established
Gary Achtemeier
2012-01-01
A cellular automata fire model represents âelementsâ of fire by autonomous agents. A few simple algebraic expressions substituted for complex physical and meteorological processes and solved iteratively yield simulations for âsuper-diffusiveâ fire spread and coupled surface-layer (2-m) fireâatmosphere processes. Pressure anomalies, which are integrals of the thermal...
Path Loss, Shadow Fading, and Line-Of-Sight Probability Models for 5G Urban Macro-Cellular Scenarios
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...... measurements in Austin, US, and Aalborg, Denmark, at 2, 10, 18, and 38 GHz. A comparison of different LOS probability models is performed for the Aalborg environment. Both single-slope and dual-slope omnidirectional path loss models are investigated to analyze and contrast their root-mean-square (RMS) errors...
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.
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.
Ibrahim, Hazem
2016-09-19
The unrelenting increase in the population of mobile users and their traffic demands drive cellular network operators to densify their network infrastructure. Network densification shrinks the footprint of base stations (BSs) and reduces the number of users associated with each BS, leading to an improved spatial frequency reuse and spectral efficiency, and thus, higher network capacity. However, the densification gain comes at the expense of higher handover rates and network control overhead. Hence, user’s mobility can diminish or even nullifies the foreseen densification gain. In this context, splitting the control plane ( C -plane) and user plane ( U -plane) is proposed as a potential solution to harvest densification gain with reduced cost in terms of handover rate and network control overhead. In this paper, we use stochastic geometry to develop a tractable mobility-aware model for a two-tier downlink cellular network with ultra-dense small cells and C -plane/ U -plane split architecture. The developed model is then used to quantify the effect of mobility on the foreseen densification gain with and without C -plane/ U -plane split. To this end, we shed light on the handover problem in dense cellular environments, show scenarios where the network fails to support certain mobility profiles, and obtain network design insights.
Tosic, P.T.
2011-01-01
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)
Le mal de pott sous occipital révélé par un abcès rétro pharyngien a ...
Introduction : Pott's disease is the most frequent localisation of osteo-articular tuberculosis. The suboccipital localisation remains rare. Case report : A 12-years old boy, admitted for cervicalgy and dysphagia. His clinical exam revealed a swelling of posterior pharyngeal wall associated with a basicervical tumefaction ...
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.
Morales, Jorge; Alpaugh, Mary L
2009-01-01
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
F.C. Gruau; J.T. Tromp (John)
1999-01-01
textabstractWe consider the problem of establishing gravity in cellular automata. In particular, when cellular automata states can be partitioned into empty, particle, and wall types, with the latter enclosing rectangular areas, we desire rules that will make the particles fall down and pile up on
In silico modeling for tumor growth visualization.
Jeanquartier, Fleur; Jean-Quartier, Claire; Cemernek, David; Holzinger, Andreas
2016-08-08
Cancer is a complex disease. Fundamental cellular based studies as well as modeling provides insight into cancer biology and strategies to treatment of the disease. In silico models complement in vivo models. Research on tumor growth involves a plethora of models each emphasizing isolated aspects of benign and malignant neoplasms. Biologists and clinical scientists are often overwhelmed by the mathematical background knowledge necessary to grasp and to apply a model to their own research. We aim to provide a comprehensive and expandable simulation tool to visualizing tumor growth. This novel Web-based application offers the advantage of a user-friendly graphical interface with several manipulable input variables to correlate different aspects of tumor growth. By refining model parameters we highlight the significance of heterogeneous intercellular interactions on tumor progression. Within this paper we present the implementation of the Cellular Potts Model graphically presented through Cytoscape.js within a Web application. The tool is available under the MIT license at https://github.com/davcem/cpm-cytoscape and http://styx.cgv.tugraz.at:8080/cpm-cytoscape/ . In-silico methods overcome the lack of wet experimental possibilities and as dry method succeed in terms of reduction, refinement and replacement of animal experimentation, also known as the 3R principles. Our visualization approach to simulation allows for more flexible usage and easy extension to facilitate understanding and gain novel insight. We believe that biomedical research in general and research on tumor growth in particular will benefit from the systems biology perspective.
Azarbarmas, M.; Aghaie-Khafri, M.
2018-03-01
A comprehensive cellular automaton (CA) model should be coupled with a rate-dependent (RD) model for analyzing the RD deformation of alloys at high temperatures. In the present study, a new CA technique coupled with an RD model—namely, CARD—was developed. The proposed CARD model was used to simulate the dynamic recrystallization phenomenon during the hot deformation of the Inconel 718 superalloy. This model is capable of calculating the mean grain size and volume fraction of dynamic recrystallized grains, and estimating the phenomenological flow behavior of the material. In the presented model, an actual orientation definition comprising three Euler angles was used by implementing the electron backscatter diffraction data. For calculating the lattice rotation of grains, it was assumed that all slip systems of grains are active during the high-temperature deformation because of the intrinsic rate dependency of the procedure. Moreover, the morphological changes in grains were obtained using a topological module.
Schmidt, Carl R; Shires, Peter; Mootoo, Mary
2012-02-01
Irreversible electroporation (IRE) is a largely non-thermal method for the ablation of solid tumours. The ability of ultrasound (US) to measure the size of the IRE ablation zone was studied in a porcine liver model. Three normal pig livers were treated in vivo with a total of 22 ablations using IRE. Ultrasound was used within minutes after ablation and just prior to liver harvest at either 6 h or 24 h after the procedure. The area of cellular necrosis was measured after staining with nitroblue tetrazolium and the percentage of cell death determined by histomorphometry. Visible changes in the hepatic parenchyma were apparent by US after all 22 ablations using IRE. The mean maximum diameter of the ablation zone measured by US during the procedure was 20.1 ± 2.7 mm. This compared with a mean cellular necrosis zone maximum diameter of 20.3 ± 2.9 mm as measured histologically. The mean percentage of dead cells within the ablation zone was 77% at 6 h and 98% at 24 h after ablation. Ultrasound is a useful modality for measuring the ablation zone within minutes of applying IRE to normal liver tissue. The area of parenchymal change measured by US correlates with the area of cellular necrosis. © 2011 International Hepato-Pancreato-Biliary Association.
Limmer, Stefanie; Haller, Samantha; Drenkard, Eliana; Lee, Janice; Yu, Shen; Kocks, Christine; Ausubel, Frederick M.; Ferrandon, Dominique
2011-01-01
An in-depth mechanistic understanding of microbial infection necessitates a molecular dissection of host–pathogen relationships. Both Drosophila melanogaster and Pseudomonas aeruginosa have been intensively studied. Here, we analyze the infection of D. melanogaster by P. aeruginosa by using mutants in both host and pathogen. We show that orally ingested P. aeruginosa crosses the intestinal barrier and then proliferates in the hemolymph, thereby causing the infected flies to die of bacteremia. Host defenses against ingested P. aeruginosa included an immune deficiency (IMD) response in the intestinal epithelium, systemic Toll and IMD pathway responses, and a cellular immune response controlling bacteria in the hemocoel. Although the observed cellular and intestinal immune responses appeared to act throughout the course of the infection, there was a late onset of the systemic IMD and Toll responses. In this oral infection model, P. aeruginosa PA14 did not require its type III secretion system or other well-studied virulence factors such as the two-component response regulator GacA or the protease AprA for virulence. In contrast, the quorum-sensing transcription factor RhlR, but surprisingly not LasR, played a key role in counteracting the cellular immune response against PA14, possibly at an early stage when only a few bacteria are present in the hemocoel. These results illustrate the power of studying infection from the dual perspective of host and pathogen by revealing that RhlR plays a more complex role during pathogenesis than previously appreciated. PMID:21987808
Xia, Weiwei; Shen, Lianfeng
We propose two vertical handoff schemes for cellular network and wireless local area network (WLAN) integration: integrated service-based handoff (ISH) and integrated service-based handoff with queue capabilities (ISHQ). Compared with existing handoff schemes in integrated cellular/WLAN networks, the proposed schemes consider a more comprehensive set of system characteristics such as different features of voice and data services, dynamic information about the admitted calls, user mobility and vertical handoffs in two directions. The code division multiple access (CDMA) cellular network and IEEE 802.11e WLAN are taken into account in the proposed schemes. We model the integrated networks by using multi-dimensional Markov chains and the major performance measures are derived for voice and data services. The important system parameters such as thresholds to prioritize handoff voice calls and queue sizes are optimized. Numerical results demonstrate that the proposed ISHQ scheme can maximize the utilization of overall bandwidth resources with the best quality of service (QoS) provisioning for voice and data services.
Modeling Cellular Networks with Full Duplex D2D Communication: A Stochastic Geometry Approach
Ali, Konpal S.
2016-08-24
Full-duplex (FD) communication is optimistically promoted to double the spectral efficiency if sufficient self-interference cancellation (SIC) is achieved. However, this is not true when deploying FD-communication in a large-scale setup due to the induced mutual interference. Therefore, a large-scale study is necessary to draw legitimate conclusions about gains associated with FD-communication. This paper studies the FD operation for underlay device-to-device (D2D) communication sharing the uplink resources in cellular networks. We propose a disjoint fine-tuned selection criterion for the D2D and FD modes of operation. Then, we develop a tractable analytical paradigm, based on stochastic geometry, to calculate the outage probability and rate for cellular and D2D users. The results reveal that even in the case of perfect SIC, due to the increased interference injected to the network by FD-D2D communication, having all proximity UEs transmit in FD-D2D is not beneficial for the network. However, if the system parameters are carefully tuned, non-trivial network spectral-efficiency gains (64% shown) can be harvested. We also investigate the effects of imperfect SIC and D2D-link distance distribution on the harvested FD gains.
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)
S. Psakhie
2013-04-01
Full Text Available A general approach to realization of models of elasticity, plasticity and fracture of heterogeneous materials within the framework of particle-based numerical methods is proposed in the paper. It is based on building many-body forces of particle interaction, which provide response of particle ensemble correctly conforming to the response (including elastic-plastic behavior and fracture of simulated solids. Implementation of proposed approach within particle-based methods is demonstrated by the example of the movable cellular automaton (MCA method, which integrates the possibilities of particle-based discrete element method (DEM and cellular automaton methods. Emergent advantages of the developed approach to formulation of many-body interaction are discussed. Main of them are its applicability to various realizations of the concept of discrete elements and a possibility to realize various rheological models (including elastic-plastic or visco-elastic-plastic and models of fracture to study deformation and fracture of solid-phase materials and media. Capabilities of particle-based modeling of heterogeneous solids are demonstrated by the problem of simulation of deformation and fracture of particle-reinforced metal-ceramic composites.
Meireles, Sincler P. de; Santos, Adriano M.; Grynberg, Suely Epsztein; Nunes, Maria Eugenia S.
2011-01-01
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)
Majta, Janusz; Madej, Łukasz; Svyetlichnyy, Dmytro S.; Perzyński, Konrad; Kwiecień, Marcin, E-mail: mkwiecie@agh.edu.pl; Muszka, Krzysztof
2016-08-01
The potential of discrete cellular automata technique to predict the grain refinement in wires produced using combined metal forming process is presented and discussed within the paper. The developed combined metal forming process can be treated as one of the Severe Plastic Deformation (SPD) techniques that consists of three different modes of deformation: asymmetric drawing with bending, namely accumulated angular drawing (AAD), wire drawing (WD) and wire flattening (WF). To accurately replicate complex stress state both at macro and micro scales during subsequent deformations two stage modeling approach was used. First, the Finite Element Method (FEM), implemented in commercial ABAQUS software, was applied to simulate entire combined forming process at the macro scale level. Then, based on FEM results, the Cellular Automata (CA) method was applied for simulation of grain refinement at the microstructure level. Data transferred between FEM and CA methods included set of files with strain tensor components obtained from selected integration points in the macro scale model. As a result of CA simulation, detailed information on microstructure evolution during severe plastic deformation conditions was obtained, namely: changes of shape and sizes of modeled representative volume with imposed microstructure, changes of the number of grains, subgrains and dislocation cells, development of grain boundaries angle distribution as well as changes in the pole figures. To evaluate CA model predictive capabilities, results of computer simulation were compared with scanning electron microscopy and electron back scattered diffraction images (SEM/EBSD) studies of samples after AAD+WD+WF process.
Phase-Type Models of Channel-Holding Times in Cellular Communication Systems
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.......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...
Cutforth, Tyler; DeMille, Mellissa MC; Agalliu, Ilir; Agalliu, Dritan
2016-01-01
Streptococcus pyogenes infections have been associated with two autoimmune diseases of the CNS: Sydenham’s chorea (SC) and Pediatric Autoimmune Neuropsychiatric Disorders Associated with Streptococcus infections (PANDAS). Despite the high frequency of pharyngeal streptococcus infections among children, only a small fraction develops SC or PANDAS. This suggests that several factors in combination are necessary to trigger autoimmune complications: specific S. pyogenes strains that induce a strong immune response toward the host nervous system; genetic susceptibility that predispose children toward an autoimmune response involving movement or tic symptoms; and multiple infections of the throat or tonsils that lead to a robust Th17 cellular and humoral immune response when untreated. In this review, we summarize the evidence for each factor and propose that all must be met for the requisite neurovascular pathology and behavioral deficits found in SC/PANDAS. PMID:27110222
Investigation of cellular and molecular responses to pulsed focused ultrasound in a mouse model.
Scott R Burks
Full Text Available Continuous focused ultrasound (cFUS has been widely used for thermal ablation of tissues, relying on continuous exposures to generate temperatures necessary to induce coagulative necrosis. Pulsed FUS (pFUS employs non-continuous exposures that lower the rate of energy deposition and allow cooling to occur between pulses, thereby minimizing thermal effects and emphasizing effects created by non-thermal mechanisms of FUS (i.e., acoustic radiation forces and acoustic cavitation. pFUS has shown promise for a variety of applications including drug and nanoparticle delivery; however, little is understood about the effects these exposures have on tissue, especially with regard to cellular pro-homing factors (growth factors, cytokines, and cell adhesion molecules. We examined changes in murine hamstring muscle following pFUS or cFUS and demonstrate that pFUS, unlike cFUS, has little effect on the histological integrity of muscle and does not induce cell death. Infiltration of macrophages was observed 3 and 8 days following pFUS or cFUS exposures. pFUS increased expression of several cytokines (e.g., IL-1α, IL-1β, TNFα, INFγ, MIP-1α, MCP-1, and GMCSF creating a local cytokine gradient on days 0 and 1 post-pFUS that returns to baseline levels by day 3 post-pFUS. pFUS exposures induced upregulation of other signaling molecules (e.g., VEGF, FGF, PlGF, HGF, and SDF-1α and cell adhesion molecules (e.g., ICAM-1 and VCAM-1 on muscle vasculature. The observed molecular changes in muscle following pFUS may be utilized to target cellular therapies by increasing homing to areas of pathology.
Sina Haas
Full Text Available Proteomic analysis of myocardial tissue from patient population is suited to yield insights into cellular and molecular mechanisms taking place in cardiovascular diseases. However, it has been limited by small sized biopsies and complicated by high variances between patients. Therefore, there is a high demand for suitable model systems with the capability to simulate ischemic and cardiotoxic effects in vitro, under defined conditions. In this context, we established an in vitro ischemia/reperfusion cardiac disease model based on the contractile HL-1 cell line. To identify pathways involved in the cellular alterations induced by ischemia and thereby defining disease-specific biomarkers and potential target structures for new drug candidates we used fluorescence 2D-difference gel electrophoresis. By comparing spot density changes in ischemic and reperfusion samples we detected several protein spots that were differentially abundant. Using MALDI-TOF/TOF-MS and ESI-MS the proteins were identified and subsequently grouped by functionality. Most prominent were changes in apoptosis signalling, cell structure and energy-metabolism. Alterations were confirmed by analysis of human biopsies from patients with ischemic cardiomyopathy.With the establishment of our in vitro disease model for ischemia injury target identification via proteomic research becomes independent from rare human material and will create new possibilities in cardiac research.
Cao, Yuli; Risling, Mårten; Malm, Elisabeth; Sondén, Anders; Bolling, Magnus Frödin; Sköld, Mattias K
2016-01-01
The mechanisms involved in traumatic brain injury 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 model 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 h 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.
Study of cellular retention of HMPAO and ECD in a model simulating the blood-brain barrier
Ponce, C.; Pittet, N.; Slosman, D.O.
1997-01-01
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 14 C 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 14 C 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
Mark A. Wallet
2017-10-01
Full Text Available At least 57 independent loci within the human genome confer varying degrees of risk for the development of type 1 diabetes (T1D. The majority of these variants are thought to contribute to overall genetic risk by modulating host innate and adaptive immune responses, ultimately resulting in a loss of immunological tolerance to β cell antigens. Early efforts to link specific risk variants with functional alterations in host immune responses have employed animal models or genotype-selected individuals from clinical bioresource banks. While some notable genotype:phenotype associations have been described, there remains an urgent need to accelerate the discovery of causal variants and elucidate the molecular mechanisms by which susceptible alleles alter immune functions. One significant limitation has been the inability to study human T1D risk loci on an isogenic background. The advent of induced pluripotent stem cells (iPSCs and genome-editing technologies have made it possible to address a number of these outstanding questions. Specifically, the ability to drive multiple cell fates from iPSC under isogenic conditions now facilitates the analysis of causal variants in multiple cellular lineages. Bioinformatic analyses have revealed that T1D risk genes cluster within a limited number of immune signaling pathways, yet the relevant immune cell subsets and cellular activation states in which candidate risk genes impact cellular activities remain largely unknown. In this review, we summarize the functional impact of several candidate risk variants on host immunity in T1D and present an isogenic disease-in-a-dish model system for interrogating risk variants, with the goal of expediting precision therapeutics in T1D.
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.
Mendonça, J. R. G.
2018-04-01
We propose and investigate a one-parameter probabilistic mixture of one-dimensional elementary cellular automata under the guise of a model for the dynamics of a single-species unstructured population with nonoverlapping generations in which individuals have smaller probability of reproducing and surviving in a crowded neighbourhood but also suffer from isolation and dispersal. Remarkably, the first-order mean field approximation to the dynamics of the model yields a cubic map containing terms representing both logistic and weak Allee effects. The model has a single absorbing state devoid of individuals, but depending on the reproduction and survival probabilities can achieve a stable population. We determine the critical probability separating these two phases and find that the phase transition between them is in the directed percolation universality class of critical behaviour.
He Yizhu; Ding Hanlin; Liu Liufa; Shin, Keesam
2006-01-01
The morphology, topology and kinetics of normal grain growth in two-dimension were studied by computer simulation using a cellular automata (Canada) model based on the lowest energy principle. The thermodynamic energy that follows Maxwell-Boltzmann statistics has been introduced into this model for the calculation of energy change. The transition that can reduce the system energy to the lowest level is chosen to occur when there is more than one possible transition direction. The simulation results show that the kinetics of normal grain growth follows the Burke equation with the growth exponent m = 2. The analysis of topology further indicates that normal grain growth can be simulated fairly well by the present CA model. The vanishing of grains with different number of sides is discussed in the simulation
Shimura, K.; Terai, T.; Yamawaki, M.; Yamaguchi, K.
2003-01-01
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 Li 2 O surface and sweep-gas that is consisting of a noble gas, hydrogen gas and water vapour. (author)
Structural-mechanical model of wax crystal networks—a mesoscale cellular solid approach
Miyazaki, Yukihiro; Marangoni, Alejandro G
2014-01-01
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 × 10 9 Pa and E L (PW) = 1.64 × 10 9 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)
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.
Bamne, Mikhil N; Ponder, Christine A; Wood, Joel A; Mansour, Hader; Frank, Ellen; Kupfer, David J; Young, Michael W; Nimgaonkar, Vishwajit L
2013-09-01
Disruption of circadian function has been observed in several human disorders, including bipolar disorder (BD). Research into these disorders can be facilitated by human cellular models that evaluate external factors (zeitgebers) that impact circadian pacemaker activity. Incorporating a firefly luciferase reporter system into human fibroblasts provides a facile, bioluminescent readout that estimates circadian phase, while leaving the cells intact. We evaluated whether this system can be adapted to clinical BD research and whether it can incorporate zeitgeber challenge paradigms. Fibroblasts from patients with bipolar I disorder (BD-I) (n = 13) and controls (n = 12) were infected ex vivo with a lentiviral reporter incorporating the promoter sequences for Bmal1, a circadian gene to drive expression of the firefly luciferase gene. Following synchronization, the bioluminescence was used to estimate period length. Phase response curves (PRCs) were also generated following forskolin challenge and the phase response patterns were characterized. Period length and PRCs could be estimated reliably from the constructs. There were no significant case-control differences in period length, with a nonsignificant trend for differences in PRCs following the phase-setting experiments. An ex vivo cellular fibroblast-based model can be used to investigate circadian function in BD-I. It can be generated from specific individuals and this could usefully complement ongoing circadian clinical research. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.
Salvatori, Francesca; Pappadà, Mariangela; Breveglieri, Giulia; D'Aversa, Elisabetta; Finotti, Alessia; Lampronti, Ilaria; Gambari, Roberto; Borgatti, Monica
2018-05-15
Nonsense mutations promote premature translational termination, introducing stop codons within the coding region of mRNAs and causing inherited diseases, including thalassemia. For instance, in β 0 39 thalassemia the CAG (glutamine) codon is mutated to the UAG stop codon, leading to premature translation termination and to mRNA destabilization through the well described NMD (nonsense-mediated mRNA decay). In order to develop an approach facilitating translation and, therefore, protection from NMD, ribosomal read-through molecules, such as aminoglycoside antibiotics, have been tested on mRNAs carrying premature stop codons. These findings have introduced new hopes for the development of a pharmacological approach to the β 0 39 thalassemia therapy. While several strategies, designed to enhance translational read-through, have been reported to inhibit NMD efficiency concomitantly, experimental tools for systematic analysis of mammalian NMD inhibition by translational read-through are lacking. We developed a human cellular model of the β 0 39 thalassemia mutation with UPF-1 suppressed and showing a partial NMD suppression. This novel cellular model could be used for the screening of molecules exhibiting preferential read-through activity allowing a great rescue of the mutated transcripts.
Wu, Yanqing; Wang, Fang; Fu, Mao; Wang, Cheng; Quon, Michael J.
2015-01-01
Increasing prevalence of type 2 diabetes in women of childbearing age has led to a higher incidence of diabetes-associated birth defects. We established a model of type 2 diabetic embryopathy by feeding 4-week-old female mice a high-fat diet (HFD) (60% fat). After 15 weeks on HFD, the mice showed characteristics of type 2 diabetes mellitus (DM) and were mated with lean male mice. During pregnancy, control dams fed a normal diet (10% fat) were maintained on either normal diet or HFD, serving as a control group with elevated circulating free fatty acids. DM dams produced offspring at a rate of 11.3% for neural tube defect (NTD) formation, whereas no embryos in the control groups developed NTDs. Elevated markers of oxidative stress, endoplasmic reticulum stress, caspase activation, and neuroepithelial cell apoptosis (causal events in type 1 diabetic embryopathy) were observed in embryos of DM dams. DM dams treated with 200 mg/kg metformin in drinking water ameliorated fasting hyperglycemia, glucose intolerance, and insulin resistance with consequent reduction of cellular stress, apoptosis, and NTDs in their embryos. We conclude that cellular stress and apoptosis occur and that metformin effectively reduces type 2 diabetic embryopathy in a useful rodent model. PMID:25720389
A New Noncanonical Anionic Peptide That Translocates a Cellular Blood–Brain Barrier Model
Sara Neves-Coelho
2017-10-01
Full Text Available The capacity to transport therapeutic molecules across the blood–brain barrier (BBB represents a breakthrough in the development of tools for the treatment of many central nervous system (CNS-associated diseases. The BBB, while being protective against infectious agents, hinders the brain uptake of many drugs. Hence, finding safe shuttles able to overcome the BBB is of utmost importance. Herein, we identify a new BBB-translocating peptide with unique properties. For years it was thought that cationic sequences were mandatory for a cell-penetrating peptide (CPP to achieve cellular internalization. Despite being anionic at physiological pH, PepNeg (sequence (SGTQEEY is an efficient BBB translocator that is able to carry a large cargo (27 kDa, while maintaining BBB integrity. In addition, PepNeg is able to use two distinct methods of translocation, energy-dependent and -independent, suggesting that direct penetration might occur when low concentrations of peptide are presented to cells. The discovery of this new anionic trans-BBB peptide allows the development of new delivery systems to the CNS and contributes to the need to rethink the role of electrostatic attraction in BBB-translocation.
Hu, X.; Li, X.; Lu, L.
2017-12-01
Land use/cover change (LUCC) is an important subject in the research of global environmental change and sustainable development, while spatial simulation on land use/cover change is one of the key content of LUCC and is also difficult due to the complexity of the system. The cellular automata (CA) model had an irreplaceable role in simulating of land use/cover change process due to the powerful spatial computing power. However, the majority of current CA land use/cover models were binary-state model that could not provide more general information about the overall spatial pattern of land use/cover change. Here, a multi-state logistic-regression-based Markov cellular automata (MLRMCA) model and a multi-state artificial-neural-network-based Markov cellular automata (MANNMCA) model were developed and were used to simulate complex land use/cover evolutionary process in an arid region oasis city constrained by water resource and environmental policy change, the Zhangye city during the period of 1990-2010. The results indicated that the MANNMCA model was superior to MLRMCA model in simulated accuracy. These indicated that by combining the artificial neural network with CA could more effectively capture the complex relationships between the land use/cover change and a set of spatial variables. Although the MLRMCA model were also some advantages, the MANNMCA model was more appropriate for simulating complex land use/cover dynamics. The two proposed models were effective and reliable, and could reflect the spatial evolution of regional land use/cover changes. These have also potential implications for the impact assessment of water resources, ecological restoration, and the sustainable urban development in arid areas.
Mbbs, El Bashir Gusm Elbari Ahmed [Clinical Medicine, University of Khartoum, Khartoum (Sudan)
1997-04-01
Fifty patients admitted to Khartoum Teaching Hospital and Shaab Teaching Hospital in the period from October 1994- October 1996 and diagnosed as Pott's disease of spine were included in the study. Patients below the age of 15 years were excluded. Full history and physical examination were performed in each patients. Haemoglobin concentration, Packed cell volume . (PCV) Erythrocyte Sedimentation Rate (ESR), White Blood Cell Count total and differential were done for all patients together with chest X-Ray, spinal X-Ray A. P. and lateral views. Myelogram, CT Scan, Mantoux and CSF examinations were done when needed.The main age of the study group was 41.3{+-}17.6 years, with male to female ratio of 30-20 (3:2). Tuberculoses spondylitis affect the cervical spines in 2 cases (3.45%), the upper thoracic in 10 cases (17.24%), mid thoracic 20 times (34.48%), lower thoracic 20 cases (34>48%), lumber spines 6 cases (10.35%) and no lesion in the sacral spines. Pulmonary tuberculosis was found in 18 patients (36%) together with Pott's disease of the spine.All patients came with back pain, lower limbs weakness and the course of the disease was progressive, 35 patients (70%) were unable to walk, and the sphincters were affected in 37 patients (74%) of the cases.On medical treatment 37 patients (74%) showed progressive improvement, 5 patients (10%) remained static or deteriorated and 8 patients (16%) died. 2 of those who died had developed severe bed sores and anemia before death, 3 of them developed deep vein thrombosis (DVT) and died even though they started anticoagulant therapy, two patients developed drug induced hepatitis and died in spite of stopping the drugs, and one patient had got militry tuberculosis showed no adverse effect on outcome of treatment. Surgery done on two patients showed good outcome.(Author)
Mbbs, El Bashir Gusm Elbari Ahmed
1997-04-01
Fifty patients admitted to Khartoum Teaching Hospital and Shaab Teaching Hospital in the period from October 1994- October 1996 and diagnosed as Pott's disease of spine were included in the study. Patients below the age of 15 years were excluded. Full history and physical examination were performed in each patients. Haemoglobin concentration, Packed cell volume . (PCV) Erythrocyte Sedimentation Rate (ESR), White Blood Cell Count total and differential were done for all patients together with chest X-Ray, spinal X-Ray A. P. and lateral views. Myelogram, CT Scan, Mantoux and CSF examinations were done when needed.The main age of the study group was 41.3±17.6 years, with male to female ratio of 30-20 (3:2). Tuberculoses spondylitis affect the cervical spines in 2 cases (3.45%), the upper thoracic in 10 cases (17.24%), mid thoracic 20 times (34.48%), lower thoracic 20 cases (34>48%), lumber spines 6 cases (10.35%) and no lesion in the sacral spines. Pulmonary tuberculosis was found in 18 patients (36%) together with Pott's disease of the spine.All patients came with back pain, lower limbs weakness and the course of the disease was progressive, 35 patients (70%) were unable to walk, and the sphincters were affected in 37 patients (74%) of the cases.On medical treatment 37 patients (74%) showed progressive improvement, 5 patients (10%) remained static or deteriorated and 8 patients (16%) died. 2 of those who died had developed severe bed sores and anemia before death, 3 of them developed deep vein thrombosis (DVT) and died even though they started anticoagulant therapy, two patients developed drug induced hepatitis and died in spite of stopping the drugs, and one patient had got militry tuberculosis showed no adverse effect on outcome of treatment. Surgery done on two patients showed good outcome.(Author)
Wang, Feixiang; Jia, Yali; Liu, Jiajing; Zhai, Jinglei; Cao, Ning; Yue, Wen; He, Huixia; Pei, Xuetao
2017-06-01
Alzheimer's disease (AD) is an incurable neurodegenerative disease and many types of stem cells have been used in AD therapy with some favorable effects. In this study, we investigated the potential therapeutical effects of human dental pulp stem cells (hDPSCs) on AD cellular model which established by okadaic acid (OA)-induced damage to human neuroblastoma cell line, SH-SY5Y, in vitro for 24 h. After confirmed the AD cellular model, the cells were co-culture with hDPSCs by transwell co-culture system till 24 h for treatment. Then the cytomorphology of the hDPSCs-treated cells were found to restore gradually with re-elongation of retracted dendrites. Meanwhile, Cell Counting Kit-8 assay and Hoechst 33258 staining showed that hDPSCs caused significant increase in the viability and decrease in apoptosis of the model cells, respectively. Observation of DiI labeling also exhibited the prolongation dendrites in hDPSCs-treated cells which were obviously different from the retraction dendrites in AD model cells. Furthermore, specific staining of α-tubulin and F-actin demonstrated that the hDPSCs-treated cells had the morphology of restored neurons, with elongated dendrites, densely arranged microfilaments, and thickened microtubular fibrils. In addition, results from western blotting revealed that phosphorylation at Ser 396 of Tau protein was significantly suppressed by adding of hDPSCs. These results indicate that hDPSCs may promote regeneration of damaged neuron cells in vitro model of AD and may serve as a useful cell source for treatment of AD. © 2017 International Federation for Cell Biology.
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.
Jokar Arsanjani, Taghi; Javidan, Reza; Nazemosadat, Mohamad Jafar; Jokar Arsanjani, Jamal; Vaz, Eric
2015-05-01
Recent developments of geospatial technologies and models have provided environmentalists and naturalists with a wide variety of facilities and approaches for improved monitoring and management of environmental resources. Rich temporal remote sensing datasets, e.g., Landsat imagery as well as geospatial modeling techniques, facilitate the process of monitoring and modeling environmental phenomena. The main objective of this paper is to monitor the spatiotemporal patterns of fluctuations of a dynamic lake in the south of Iran - Bakhtegan Lake - which has been influenced by extreme climate change conditions. To do so, a temporal coverage of 12 Landsat images from 1973 to 2013, was used to delineate the boundaries of the lake over time and analyze the occurred changes. Next, a cellular automata (CA) approach was adopted for simulating two main processes: 'lake expansion' and 'lake shrinkage'. The CA model was then calibrated based on a statistical comparison of the simulated and actual images of one timestamp. Application of Kappa index analysis measures the performance of the model at a value of 83 percent. The calibrated CA model was then applied and the future status of the lake (by 2017) was modeled; this suggested a further 45 percent shrinkage in addition to its recent 42 percent shrinkage. In conclusion, the socio-ecological impacts and consequences of the lake's fluctuations are discussed in detail and some complementary recommendations are proposed.
Rohrbach, F; Vesztergombi, G
1997-01-01
In the near future, the computer performance will be completely determined by how long it takes to access memory. There are bottle-necks in memory latency and memory-to processor interface bandwidth. The IRAM initiative could be the answer by putting Processor-In-Memory (PIM). Starting from the massively parallel processing concept, one reached a similar conclusion. The MPPC (Massively Parallel Processing Collaboration) project and the 8K processor ASTRA machine (Associative String Test bench for Research \\& Applications) developed at CERN \\cite{kuala} can be regarded as a forerunner of the IRAM concept. The computing power of the ASTRA machine, regarded as an IRAM with 64 one-bit processors on a 64$\\times$64 bit-matrix memory chip machine, has been demonstrated by running statistical physics algorithms: one-dimensional stochastic cellular automata, as a simple model for dynamical phase transitions. As a relevant result for physics, the damage spreading of this model has been investigated.
Mitus, A. C.; Stopa, P.; Zaklukiewicz, W.; Pawlik, G.; Mysliwiec, J.; Kajzar, F.; Rau, I.
2015-08-01
One of many photonic applications of biopolymers as functional materials is random lasing resulting from an incorporation of highly luminescent dyes into biopolymeric matrix, which leads to a random but coherent light scattering in amplifying medium. In spite of numerous theoretical and experimental studies the origin of the coherence is still not clear and various scenarios are discussed. In particular, inhomogeneity of biopolymeric layers can hypothetically promote the feedback in the scattering of the emitted light resulting in coherent and incoherent random lasing. In this paper we analyze the light scattering in a model system of scattering centers of circular shapes and various dimensions using ray-tracing techniques. In the second part, which has mostly a tutorial character, we present the approach to the study of random lasing using a cellular automaton model of Wiersma et al.
Astrocytic gap junctional networks suppress cellular damage in an in vitro model of ischemia
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
Astrocytic gap junctional networks suppress cellular damage in an in vitro model of ischemia
Shinotsuka, Takanori; Yasui, Masato; Nuriya, Mutsuo
2014-01-01
Highlights: • Astrocytes exhibit characteristic changes in [Ca 2+ ] i under OGD. • Astrocytic [Ca 2+ ] 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 2+ ] i ) in astrocytes in mouse cortical slices under oxygen/glucose deprivation (OGD) condition using two-photon microscopy. Under OGD, astrocytes showed [Ca 2+ ] i oscillations followed by larger and sustained [Ca 2+ ] 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 2+ ] i increase after OGD exposure. Interestingly, the simultaneous recording of the neuronal membrane potential revealed that the onset of the sustained [Ca 2+ ] 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 2+ ] 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
Sipahi, Rifat; Zupanc, Günther K H
2018-05-14
Neural stem and progenitor cells isolated from the central nervous system form, under specific culture conditions, clonal cell clusters known as neurospheres. The neurosphere assay has proven to be a powerful in vitro system to study the behavior of such cells and the development of their progeny. However, the theory of neurosphere growth has remained poorly understood. To overcome this limitation, we have, in the present paper, developed a cellular automata model, with which we examined the effects of proliferative potential, contact inhibition, cell death, and clearance of dead cells on growth rate, final size, and composition of neurospheres. Simulations based on this model indicated that the proliferative potential of the founder cell and its progenitors has a major influence on neurosphere size. On the other hand, contact inhibition of proliferation limits the final size, and reduces the growth rate, of neurospheres. The effect of this inhibition is particularly dramatic when a stem cell becomes encapsulated by differentiated or other non-proliferating cells, thereby suppressing any further mitotic division - despite the existing proliferative potential of the stem cell. Conversely, clearance of dead cells through phagocytosis is predicted to accelerate growth by reducing contact inhibition. A surprising prediction derived from our model is that cell death, while resulting in a decrease in growth rate and final size of neurospheres, increases the degree of differentiation of neurosphere cells. It is likely that the cellular automata model developed as part of the present investigation is applicable to the study of tissue growth in a wide range of systems. Copyright © 2018 Elsevier Ltd. All rights reserved.
Unified tractable model for downlink MIMO cellular networks using stochastic geometry
Afify, Laila H.; Elsawy, Hesham; Al-Naffouri, Tareq Y.; Alouini, Mohamed-Slim
2016-01-01
for simplicity. On the other hand, there are models that sacrifice simplicity to target more tangible performance metrics such as the error probability. Both types of models are completely disjoint in terms of the analytic steps to obtain the performance measures
Using a cellular model to explore human-facilitated spread of risk of EAB in Minnesota
Anantha Prasad; Louis Iverson; Matthew Peters; Steve. Matthews
2011-01-01
The Emerald Ash Borer has made inroads to Minnesota in the past two years, killing ash trees. We use our spatially explicit cell based model called EAB-SHIFT to calculate the risk of infestation owing to flight characteristics and short distance movement of the insect (insect flight model, IFM), and the human facilitated agents like roads, campgrounds etc. (insect ride...
Stability of a general delayed virus dynamics model with humoral immunity and cellular infection
Elaiw, A. M.; Raezah, A. A.; Alofi, A. S.
2017-06-01
In this paper, we investigate the dynamical behavior of a general nonlinear model for virus dynamics with virus-target and infected-target incidences. The model incorporates humoral immune response and distributed time delays. The model is a four dimensional system of delay differential equations where the production and removal rates of the virus and cells are given by general nonlinear functions. We derive the basic reproduction parameter R˜0 G and the humoral immune response activation number R˜1 G and establish a set of conditions on the general functions which are sufficient to determine the global dynamics of the models. We use suitable Lyapunov functionals and apply LaSalle's invariance principle to prove the global asymptotic stability of the all equilibria of the model. We confirm the theoretical results by numerical simulations.
Fereydoun Naghibi
2016-12-01
Full Text Available This paper presents an advanced method in urban growth modeling to discover transition rules of cellular automata (CA using the artificial bee colony (ABC optimization algorithm. Also, comparisons between the simulation results of CA models optimized by the ABC algorithm and the particle swarm optimization algorithms (PSO as intelligent approaches were performed to evaluate the potential of the proposed methods. According to previous studies, swarm intelligence algorithms for solving optimization problems such as discovering transition rules of CA in land use change/urban growth modeling can produce reasonable results. Modeling of urban growth as a dynamic process is not straightforward because of the existence of nonlinearity and heterogeneity among effective involved variables which can cause a number of challenges for traditional CA. ABC algorithm, the new powerful swarm based optimization algorithms, can be used to capture optimized transition rules of CA. This paper has proposed a methodology based on remote sensing data for modeling urban growth with CA calibrated by the ABC algorithm. The performance of ABC-CA, PSO-CA, and CA-logistic models in land use change detection is tested for the city of Urmia, Iran, between 2004 and 2014. Validations of the models based on statistical measures such as overall accuracy, figure of merit, and total operating characteristic were made. We showed that the overall accuracy of the ABC-CA model was 89%, which was 1.5% and 6.2% higher than those of the PSO-CA and CA-logistic model, respectively. Moreover, the allocation disagreement (simulation error of the simulation results for the ABC-CA, PSO-CA, and CA-logistic models are 11%, 12.5%, and 17.2%, respectively. Finally, for all evaluation indices including running time, convergence capability, flexibility, statistical measurements, and the produced spatial patterns, the ABC-CA model performance showed relative improvement and therefore its superiority was
García-Gómez, Mónica L; Azpeitia, Eugenio; Álvarez-Buylla, Elena R
2017-04-01
The study of the concerted action of hormones and transcription factors is fundamental to understand cell differentiation and pattern formation during organ development. The root apical meristem of Arabidopsis thaliana is a useful model to address this. It has a stem cell niche near its tip conformed of a quiescent organizer and stem or initial cells around it, then a proliferation domain followed by a transition domain, where cells diminish division rate before transiting to the elongation zone; here, cells grow anisotropically prior to their final differentiation towards the plant base. A minimal model of the gene regulatory network that underlies cell-fate specification and patterning at the root stem cell niche was proposed before. In this study, we update and couple such network with both the auxin and cytokinin hormone signaling pathways to address how they collectively give rise to attractors that correspond to the genetic and hormonal activity profiles that are characteristic of different cell types along A. thaliana root apical meristem. We used a Boolean model of the genetic-hormonal regulatory network to integrate known and predicted regulatory interactions into alternative models. Our analyses show that, after adding some putative missing interactions, the model includes the necessary and sufficient components and regulatory interactions to recover attractors characteristic of the root cell types, including the auxin and cytokinin activity profiles that correlate with different cellular behaviors along the root apical meristem. Furthermore, the model predicts the existence of activity configurations that could correspond to the transition domain. The model also provides a possible explanation for apparently paradoxical cellular behaviors in the root meristem. For example, how auxin may induce and at the same time inhibit WOX5 expression. According to the model proposed here the hormonal regulation of WOX5 might depend on the cell type. Our results
Mónica L García-Gómez
2017-04-01
Full Text Available The study of the concerted action of hormones and transcription factors is fundamental to understand cell differentiation and pattern formation during organ development. The root apical meristem of Arabidopsis thaliana is a useful model to address this. It has a stem cell niche near its tip conformed of a quiescent organizer and stem or initial cells around it, then a proliferation domain followed by a transition domain, where cells diminish division rate before transiting to the elongation zone; here, cells grow anisotropically prior to their final differentiation towards the plant base. A minimal model of the gene regulatory network that underlies cell-fate specification and patterning at the root stem cell niche was proposed before. In this study, we update and couple such network with both the auxin and cytokinin hormone signaling pathways to address how they collectively give rise to attractors that correspond to the genetic and hormonal activity profiles that are characteristic of different cell types along A. thaliana root apical meristem. We used a Boolean model of the genetic-hormonal regulatory network to integrate known and predicted regulatory interactions into alternative models. Our analyses show that, after adding some putative missing interactions, the model includes the necessary and sufficient components and regulatory interactions to recover attractors characteristic of the root cell types, including the auxin and cytokinin activity profiles that correlate with different cellular behaviors along the root apical meristem. Furthermore, the model predicts the existence of activity configurations that could correspond to the transition domain. The model also provides a possible explanation for apparently paradoxical cellular behaviors in the root meristem. For example, how auxin may induce and at the same time inhibit WOX5 expression. According to the model proposed here the hormonal regulation of WOX5 might depend on the cell
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.
Magnetohydrodynamics cellular automata
Hatori, Tadatsugu.
1990-02-01
There has been a renewal of interest in cellular automata, partly because they give an architecture for a special purpose computer with parallel processing optimized to solve a particular problem. The lattice gas cellular automata are briefly surveyed, which are recently developed to solve partial differential equations such as hydrodynamics or magnetohydrodynamics. A new model is given in the present paper to implement the magnetic Lorentz force in a more deterministic and local procedure than the previous one. (author)
Magnetohydrodynamic cellular automata
Hatori, Tadatsugu [National Inst. for Fusion Science, Nagoya (Japan)
1990-03-01
There has been a renewal of interest in cellular automata, partly because they give an architecture for a special purpose computer with parallel processing optimized to solve a particular problem. The lattice gas cellular automata are briefly surveyed, which are recently developed to solve partial differential equations such as hydrodynamics or magnetohydrodynamics. A new model is given in the present paper to implement the magnetic Lorentz force in a more deterministic and local procedure than the previous one. (author).
Magnetohydrodynamic cellular automata
Hatori, Tadatsugu
1990-01-01
There has been a renewal of interest in cellular automata, partly because they give an architecture for a special purpose computer with parallel processing optimized to solve a particular problem. The lattice gas cellular automata are briefly surveyed, which are recently developed to solve partial differential equations such as hydrodynamics or magnetohydrodynamics. A new model is given in the present paper to implement the magnetic Lorentz force in a more deterministic and local procedure than the previous one. (author)
Features of microscopic pedestrian movement in a panic situation based on cellular automata model
Ibrahim, Najihah; Hassan, Fadratul Hafinaz
2017-10-01
Pedestrian movement is the one of the subset for the crowd management under simulation objective. During panic situation, pedestrian usually will create a microscopic movement that lead towards the self-organization. During self-organizing, the behavioral and physical factors had caused the mass effect on the pedestrian movement. The basic CA model will create a movement path for each pedestrian over a time step. However, due to the factors immerge, the CA model needs some enhancement that will establish a real simulation state. Hence, this concept paper will discuss on the enhanced features of CA model for microscopic pedestrian movement during panic situation for a better pedestrian simulation.
Preterm labor--modeling the uterine electrical activity from cellular level to surface recording.
Rihana, S; Marque, C
2008-01-01
Uterine electrical activity is correlated to the appearance of uterine contractions. forceful contractions appear at the end of term. Therefore, understanding the genesis and the propagation of uterine electrical activity may provide an efficient tool to diagnose preterm labor. Moreover, the control of uterine excitability seems to have important consequences in the control of preterm labor. Modeling the electrical activity in uterine tissue is thus an important step in understanding physiological uterine contractile mechanisms and to permit uterine EMG simulation. Our model presented in this paper, incorporates ion channel models at the cell level, the reaction diffusion equations at the tissue level and the spatiotemporal integration at the uterine EMG reconstructed level. This model validates some key physiological observation hypotheses concerning uterine excitability and propagation.
J. P. M. Whitty; J. Francis; J. Howe; B. Henderson
2014-01-01
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 t...
Daniel A Beard
2006-09-01
Full Text Available Observations on the relationship between cardiac work rate and the levels of energy metabolites adenosine triphosphate (ATP, adenosine diphosphate (ADP, and phosphocreatine (CrP have not been satisfactorily explained by theoretical models of cardiac energy metabolism. Specifically, the in vivo stability of ATP, ADP, and CrP levels in response to changes in work and respiratory rate has eluded explanation. Here a previously developed model of mitochondrial oxidative phosphorylation, which was developed based on data obtained from isolated cardiac mitochondria, is integrated with a spatially distributed model of oxygen transport in the myocardium to analyze data obtained from several laboratories over the past two decades. The model includes the components of the respiratory chain, the F0F1-ATPase, adenine nucleotide translocase, and the mitochondrial phosphate transporter at the mitochondrial level; adenylate kinase, creatine kinase, and ATP consumption in the cytoplasm; and oxygen transport between capillaries, interstitial fluid, and cardiomyocytes. The integrated model is able to reproduce experimental observations on ATP, ADP, CrP, and inorganic phosphate levels in canine hearts over a range of workload and during coronary hypoperfusion and predicts that cytoplasmic inorganic phosphate level is a key regulator of the rate of mitochondrial respiration at workloads for which the rate of cardiac oxygen consumption is less than or equal to approximately 12 mumol per minute per gram of tissue. At work rates corresponding to oxygen consumption higher than 12 mumol min(-1 g(-1, model predictions deviate from the experimental data, indicating that at high work rates, additional regulatory mechanisms that are not currently incorporated into the model may be important. Nevertheless, the integrated model explains metabolite levels observed at low to moderate workloads and the changes in metabolite levels and tissue oxygenation observed during graded
Jin, Cheng-Jie; Jiang, Rui; Yin, Jun-Lin; Dong, Li-Yun; Li, Dawei
2017-09-01
In the experiments of bi-directional pedestrian flow, it is often observed that pedestrians turn their bodies and change from walking straight to walking sideways, in order to mitigate or avoid the conflicts with opposite walking ones. When these conflicts disappear, pedestrians restore and walk straight again. In the turning states, the forward velocities of pedestrians are not affected. In order to simulate this body-turning behavior, we use a cellular automaton (CA) model named ITP model, which has been proposed before. But the occupied area of one pedestrian is set as 0.4 m∗0.2 m. After the introduction of new rules of turnings and restorations, the pedestrians become more intelligent and flexible during the lane formation process, and some improvements of the fundamental diagram of pedestrian flow can be found. The simulation results of two different scenarios under open boundary conditions are also presented, and compared with the experimental data. It is shown that the new model performs much better than the original model in various tests, which further confirms the validity of the new rules. We think this approach is one useful contribution to the pedestrian flow modeling.
PATHLOGIC-S: a scalable Boolean framework for modelling cellular signalling.
Liam G Fearnley
Full Text Available Curated databases of signal transduction have grown to describe several thousand reactions, and efficient use of these data requires the development of modelling tools to elucidate and explore system properties. We present PATHLOGIC-S, a Boolean specification for a signalling model, with its associated GPL-licensed implementation using integer programming techniques. The PATHLOGIC-S specification has been designed to function on current desktop workstations, and is capable of providing analyses on some of the largest currently available datasets through use of Boolean modelling techniques to generate predictions of stable and semi-stable network states from data in community file formats. PATHLOGIC-S also addresses major problems associated with the presence and modelling of inhibition in Boolean systems, and reduces logical incoherence due to common inhibitory mechanisms in signalling systems. We apply this approach to signal transduction networks including Reactome and two pathways from the Panther Pathways database, and present the results of computations on each along with a discussion of execution time. A software implementation of the framework and model is freely available under a GPL license.
Vanessa Almendro
2014-02-01
Full Text Available Cancer therapy exerts a strong selection pressure that shapes tumor evolution, yet our knowledge of how tumors change during treatment is limited. Here, we report the analysis of cellular heterogeneity for genetic and phenotypic features and their spatial distribution in breast tumors pre- and post-neoadjuvant chemotherapy. We found that intratumor genetic diversity was tumor-subtype specific, and it did not change during treatment in tumors with partial or no response. However, lower pretreatment genetic diversity was significantly associated with pathologic complete response. In contrast, phenotypic diversity was different between pre- and posttreatment samples. We also observed significant changes in the spatial distribution of cells with distinct genetic and phenotypic features. We used these experimental data to develop a stochastic computational model to infer tumor growth patterns and evolutionary dynamics. Our results highlight the importance of integrated analysis of genotypes and phenotypes of single cells in intact tissues to predict tumor evolution.
Almendro, Vanessa; Cheng, Yu-Kang; Randles, Amanda; Itzkovitz, Shalev; Marusyk, Andriy; Ametller, Elisabet; Gonzalez-Farre, Xavier; Muñoz, Montse; Russnes, Hege G.; Helland, Åslaug; Rye, Inga H.; Borresen-Dale, Anne-Lise; Maruyama, Reo; Van Oudenaarden, Alexander; Dowsett, Mitchell; Jones, Robin L.; Reis-Filho, Jorge; Gascon, Pere; Gönen, Mithat; Michor, Franziska; Polyak, Kornelia
2014-01-01
Cancer therapy exerts a strong selection pressure that shapes tumor evolution, yet our knowledge of how tumors change during treatment is limited. Here, we report the analysis of cellular heterogeneity for genetic and phenotypic features and their spatial distribution in breast tumors pre- and post-neoadjuvant chemotherapy. We found that intratumor genetic diversity was tumor-subtype specific, and it did not change during treatment in tumors with partial or no response. However, lower pretreatment genetic diversity was significantly associated with pathologic complete response. In contrast, phenotypic diversity was different between pre- and post-treatment samples. We also observed significant changes in the spatial distribution of cells with distinct genetic and phenotypic features. We used these experimental data to develop a stochastic computational model to infer tumor growth patterns and evolutionary dynamics. Our results highlight the importance of integrated analysis of genotypes and phenotypes of single cells in intact tissues to predict tumor evolution
Cloud computing models and their application in LTE based cellular systems
Staring, A.J.; Karagiannis, Georgios
2013-01-01
As cloud computing emerges as the next novel concept in computer science, it becomes clear that the model applied in large data storage systems used to resolve issues coming forth from an increasing demand, could also be used to resolve the very high bandwidth requirements on access network, core
"A Cellular Encounter": Constructing the Cell as a Whole System Using Illustrative Models
Cohen, Joel I.
2014-01-01
A standard part of biology curricula is a project-based assessment of cell structure and function. However, these are often individual assignments that promote little problem-solving or group learning and avoid the subject of organelle chemical interactions. I evaluate a model-based cell project designed to foster group and individual guided…
Baxter, Douglas A.; Byrne, John H.
2006-01-01
Feeding behavior of Aplysia provides an excellent model system for analyzing and comparing mechanisms underlying appetitive classical conditioning and reward operant conditioning. Behavioral protocols have been developed for both forms of associative learning, both of which increase the occurrence of biting following training. Because the neural…
Investigation of the Nonlinear Model of the Cellular Population System Development
M. S. Vinogradova
2014-01-01
Full Text Available An isolated population system is considered which consists of two types of human stem cells: normal cells and cells with chromosomal anomalies (abnormal. In the paper the nonlinear dynamic model which describes dynamics of cell populations developing in vitro is elaborated. The model allows to investigate the processes of the formation of the abnormal cells population from the abnormal cells population of normal cells as well as joint development of these populations. The model takes into account the limited resources.An important feature of the developed model is the use of biological characteristics of processes in the cell population system, such as the proportion of cells, divided over a specified time, the proportion of cells whish are not divided, and which are "lost" and which are passed in the population of abnormal cells from the normal population. This approach allows a more detailed analysis of the impact of various "primary" parameters on the evolution of the population system.Under cultivation of cell populations in vitro a struggle for resources primarily affects the processes of the cell reproduction. This is reflected in the existence of the dividing cells frequency dependence of the total population of normal and abnormal cells. For the account of such dependencies different non-linear functions are typically used. However, the use of such non-linear relationships leads to the difficulties in finding confidence intervals for the estimates of the model parameters at subsequent stages of research. At the same time, the problem of the system parameters estimating and finding of the corresponding confidence intervals for estimates can be solved easy in case when the nonlinear system is linear with respect to the unknown parameters. In the paper it is achieved due to the piecewise linear approximation of nonlinear dependencies.An important feature of the model is a different view of the right part of the differential equations system
Gkigkitzis, Ioannis
2013-01-01
The aim of this report is to provide a mathematical model of the mechanism for making binary fate decisions about cell death or survival, during and after Photodynamic Therapy (PDT) treatment, and to supply the logical design for this decision mechanism as an application of rate distortion theory to the biochemical processing of information by the physical system of a cell. Based on system biology models of the molecular interactions involved in the PDT processes previously established, and regarding a cellular decision-making system as a noisy communication channel, we use rate distortion theory to design a time dependent Blahut-Arimoto algorithm where the input is a stimulus vector composed of the time dependent concentrations of three PDT related cell death signaling molecules and the output is a cell fate decision. The molecular concentrations are determined by a group of rate equations. The basic steps are: initialize the probability of the cell fate decision, compute the conditional probability distribution that minimizes the mutual information between input and output, compute the cell probability of cell fate decision that minimizes the mutual information and repeat the last two steps until the probabilities converge. Advance to the next discrete time point and repeat the process. Based on the model from communication theory described in this work, and assuming that the activation of the death signal processing occurs when any of the molecular stimulants increases higher than a predefined threshold (50% of the maximum concentrations), for 1800s of treatment, the cell undergoes necrosis within the first 30 minutes with probability range 90.0%-99.99% and in the case of repair/survival, it goes through apoptosis within 3-4 hours with probability range 90.00%-99.00%. Although, there is no experimental validation of the model at this moment, it reproduces some patterns of survival ratios of predicted experimental data. Analytical modeling based on cell death
Hasegawa, Sumitaka; Maruyama, Kouichi; Takenaka, Hikaru; Furukawa, Takako; Saga, Tsuneo
2009-08-18
The recent success with small fish as an animal model of cancer with the aid of fluorescence technique has attracted cancer modelers' attention because it would be possible to directly visualize tumor cells in vivo in real time. Here, we report a medaka model capable of allowing the observation of various cell behaviors of transplanted tumor cells, such as cell proliferation and metastasis, which were visualized easily in vivo. We established medaka melanoma (MM) cells stably expressing GFP and transplanted them into nonirradiated and irradiated medaka. The tumor cells were grown at the injection sites in medaka, and the spatiotemporal changes were visualized under a fluorescence stereoscopic microscope at a cellular-level resolution, and even at a single-cell level. Tumor dormancy and metastasis were also observed. Interestingly, in irradiated medaka, accelerated tumor growth and metastasis of the transplanted tumor cells were directly visualized. Our medaka model provides an opportunity to visualize in vivo tumor cells "as seen in a culture dish" and would be useful for in vivo tumor cell biology.
Barik, Debashis; Ball, David A; Peccoud, Jean; Tyson, John J
2016-12-01
The cell division cycle of eukaryotes is governed by a complex network of cyclin-dependent protein kinases (CDKs) and auxiliary proteins that govern CDK activities. The control system must function reliably in the context of molecular noise that is inevitable in tiny yeast cells, because mistakes in sequencing cell cycle events are detrimental or fatal to the cell or its progeny. To assess the effects of noise on cell cycle progression requires not only extensive, quantitative, experimental measurements of cellular heterogeneity but also comprehensive, accurate, mathematical models of stochastic fluctuations in the CDK control system. In this paper we provide a stochastic model of the budding yeast cell cycle that accurately accounts for the variable phenotypes of wild-type cells and more than 20 mutant yeast strains simulated in different growth conditions. We specifically tested the role of feedback regulations mediated by G1- and SG2M-phase cyclins to minimize the noise in cell cycle progression. Details of the model are informed and tested by quantitative measurements (by fluorescence in situ hybridization) of the joint distributions of mRNA populations in yeast cells. We use the model to predict the phenotypes of ~30 mutant yeast strains that have not yet been characterized experimentally.
Debashis Barik
2016-12-01
Full Text Available The cell division cycle of eukaryotes is governed by a complex network of cyclin-dependent protein kinases (CDKs and auxiliary proteins that govern CDK activities. The control system must function reliably in the context of molecular noise that is inevitable in tiny yeast cells, because mistakes in sequencing cell cycle events are detrimental or fatal to the cell or its progeny. To assess the effects of noise on cell cycle progression requires not only extensive, quantitative, experimental measurements of cellular heterogeneity but also comprehensive, accurate, mathematical models of stochastic fluctuations in the CDK control system. In this paper we provide a stochastic model of the budding yeast cell cycle that accurately accounts for the variable phenotypes of wild-type cells and more than 20 mutant yeast strains simulated in different growth conditions. We specifically tested the role of feedback regulations mediated by G1- and SG2M-phase cyclins to minimize the noise in cell cycle progression. Details of the model are informed and tested by quantitative measurements (by fluorescence in situ hybridization of the joint distributions of mRNA populations in yeast cells. We use the model to predict the phenotypes of ~30 mutant yeast strains that have not yet been characterized experimentally.
Yuanyuan Yang
2015-05-01
Full Text Available Decadal to centennial land use and land cover change has been consistently singled out as a key element and an important driver of global environmental change, playing an essential role in balancing energy use. Understanding long-term human-environment interactions requires historical reconstruction of past land use and land cover changes. Most of the existing historical reconstructions have insufficient spatial and thematic detail and do not consider various land change types. In this context, this paper explored the possibility of using a cellular automata-Markov model in 90 m × 90 m spatial resolution to reconstruct historical land use in the 1930s in Zhenlai County, China. Then the three-map comparison methodology was employed to assess the predictive accuracy of the transition modeling. The model could produce backward projections by analyzing land use changes in recent decades, assuming that the present land use pattern is dynamically dependent on the historical one. The reconstruction results indicated that in the 1930s most of the study area was occupied by grasslands, followed by wetlands and arable land, while other land categories occupied relatively small areas. Analysis of the three-map comparison illustrated that the major differences among the three maps have less to do with the simulation model and more to do with the inconsistencies among the land categories during the study period. Different information provided by topographic maps and remote sensing images must be recognized.
Hildebrand, C.E.; Walters, R.A.
1977-01-01
Progress is reported on the following research projects: chromatin structure; the use of circular synthetic polydeoxynucleotides as substrates for the study of DNA repair enzymes; human cellular kinetic response following exposure to DNA-interactive compounds; histone phosphorylation and chromatin structure in cell proliferation; photoaddition products induced in chromatin by uv light; pollutants and genetic information transfer; altered RNA metabolism as a function of cadmium accumulation and intracellular distribution in cultured cells; and thymidylate chromophore destruction by water free radicals
Cellular track model of biological damage to mammalian cell cultures from galactic cosmic rays
Cucinotta, Francis A.; Katz, Robert; Wilson, John W.; Townsend, Lawrence W.; Nealy, John E.; Shinn, Judy L.
1991-01-01
The assessment of biological damage from the galactic cosmic rays (GCR) is a current interest for exploratory class space missions where the highly ionizing, high-energy, high-charge ions (HZE) particles are the major concern. The relative biological effectiveness (RBE) values determined by ground-based experiments with HZE particles are well described by a parametric track theory of cell inactivation. Using the track model and a deterministic GCR transport code, the biological damage to mammalian cell cultures is considered for 1 year in free space at solar minimum for typical spacecraft shielding. Included are the effects of projectile and target fragmentation. The RBE values for the GCR spectrum which are fluence-dependent in the track model are found to be more severe than the quality factors identified by the International Commission on Radiological Protection publication 26 and seem to obey a simple scaling law with the duration period in free space.
Cellular track model of biological damage to mammalian cell cultures from galactic cosmic rays
Cucinotta, F.A.; Katz, R.; Wilson, J.W.; Townsend, L.W.; Nealy, J.E.; Shinn, J.L.
1991-02-01
The assessment of biological damage from the galactic cosmic rays (GCR) is a current interest for exploratory class space missions where the highly ionizing, high-energy, high-charge ions (HZE) particles are the major concern. The relative biological effectiveness (RBE) values determined by ground-based experiments with HZE particles are well described by a parametric track theory of cell inactivation. Using the track model and a deterministic GCR transport code, the biological damage to mammalian cell cultures is considered for 1 year in free space at solar minimum for typical spacecraft shielding. Included are the effects of projectile and target fragmentation. The RBE values for the GCR spectrum which are fluence-dependent in the track model are found to be more severe than the quality factors identified by the International Commission on Radiological Protection publication 26 and seem to obey a simple scaling law with the duration period in free space
A cellular automata model for social-learning processes in a classroom context
Bordogna, C. M.; Albano, E. V.
2002-02-01
A model for teaching-learning processes that take place in the classroom is proposed and simulated numerically. Recent ideas taken from the fields of sociology, educational psychology, statistical physics and computational science are key ingredients of the model. Results of simulations are consistent with well-established empirical results obtained in classrooms by means of different evaluation tools. It is shown that students engaged in collaborative groupwork reach higher achievements than those attending traditional lectures only. However, in many cases, this difference is subtle and consequently very difficult to be detected using tests. The influence of the number of students forming the collaborative groups on the average knowledge achieved is also studied and discussed.
Efficient Uplink Modeling for Dynamic System-Level Simulations of Cellular and Mobile Networks
Lobinger Andreas
2010-01-01
Full Text Available A novel theoretical framework for uplink simulations is proposed. It allows investigations which have to cover a very long (real- time and which at the same time require a certain level of accuracy in terms of radio resource management, quality of service, and mobility. This is of particular importance for simulations of self-organizing networks. For this purpose, conventional system level simulators are not suitable due to slow simulation speeds far beyond real-time. Simpler, snapshot-based tools are lacking the aforementioned accuracy. The runtime improvements are achieved by deriving abstract theoretical models for the MAC layer behavior. The focus in this work is long term evolution, and the most important uplink effects such as fluctuating interference, power control, power limitation, adaptive transmission bandwidth, and control channel limitations are considered. Limitations of the abstract models will be discussed as well. Exemplary results are given at the end to demonstrate the capability of the derived framework.
Spitkovsky, D.M.; Talyzina, T.A.
1995-01-01
The model is based on the concept of programmed initiation of genetic damage in sub-populations of specific evolutionary reserve cells (ERC). The model quantitatively predicts a dose response of genetic lesions at low dose range and furnishes an explanation of the minimum observed in the dose-response curve at doses corresponding to one (on the average) event of energy deposition per ERC. The complex shape of the dose-response curve is demonstrated to result from superposition of processes in different sub-populations within the exposed cell population (at low doses mainly in ERC). Programmed initiation of genetic lesions in ERC requires two hits to cell membrane and probably, at the same time, to the cell nucleus. The equation for dicentric yield in human lymphocytes as a function of dose describes the experimental observations rather well. (Author)
Šilhár, Peter; Silvaggi, Nicholas R; Pellett, Sabine; Čapková, Kateřina; Johnson, Eric A; Allen, Karen N; Janda, Kim D
2013-03-01
Botulinum neurotoxins (BoNTs) are the most lethal biotoxins known to mankind and are responsible for the neuroparalytic disease botulism. Current treatments for botulinum poisoning are all protein based and thus have a limited window of treatment opportunity. Inhibition of the BoNT light chain protease (LC) has emerged as a therapeutic strategy for the treatment of botulism as it may provide an effective post exposure remedy. Using a combination of crystallographic and modeling studies a series of hydroxamates derived from 1-adamantylacetohydroxamic acid (3a) were prepared. From this group of compounds, an improved potency of about 17-fold was observed for two derivatives. Detailed mechanistic studies on these structures revealed a competitive inhibition model, with a K(i)=27 nM, which makes these compounds some of the most potent small molecule, non-peptidic BoNT/A LC inhibitors reported to date. Copyright © 2012 Elsevier Ltd. All rights reserved.
Wang, He Joe; Murray, Gary J; Jung, Mary Katherine
2015-01-01
Humans develop various clinical phenotypes of severe alcoholic liver disease, including alcoholic hepatitis and cirrhosis, generally after decades of heavy drinking. In such individuals, following each episode of drinking, their livers experience heightened intracellular and extracellular stresses that are closely associated with alcohol consumption and alcohol metabolism. This article focuses on the latest advances made in animal models on evolutionarily conserved homeostatic mechanisms for coping with and resolving these stress conditions. The mechanisms discussed include the stress-activated protein kinase JNK, energy regulator AMPK, autophagy and the inflammatory response. Over time, the host may respond variably to stress with protective mechanisms that are critical in determining an individual's vulnerability to developing severe alcoholic liver disease. A systematic review of these mechanisms and their temporal changes in animal models provides the basis for general conclusions, and raises questions for future studies. The relevance of these data to human conditions is also discussed.
Pönisch, Wolfram; Weber, Christoph A.; Juckeland, Guido; Biais, Nicolas; Zaburdaev, Vasily
2017-01-01
Neisseria gonorrhoeae is the causative agent of one of the most common sexually transmitted diseases, gonorrhea. Over the past two decades there has been an alarming increase of reported gonorrhea cases where the bacteria were resistant to the most commonly used antibiotics thus prompting for alternative antimicrobial treatment strategies. The crucial step in this and many other bacterial infections is the formation of microcolonies, agglomerates consisting of up to several thousands of cells. The attachment and motility of cells on solid substrates as well as the cell-cell interactions are primarily mediated by type IV pili, long polymeric filaments protruding from the surface of cells. While the crucial role of pili in the assembly of microcolonies has been well recognized, the exact mechanisms of how they govern the formation and dynamics of microcolonies are still poorly understood. Here, we present a computational model of individual cells with explicit pili dynamics, force generation and pili-pili interactions. We employ the model to study a wide range of biological processes, such as the motility of individual cells on a surface, the heterogeneous cell motility within the large cell aggregates, and the merging dynamics and the self-assembly of microcolonies. The results of numerical simulations highlight the central role of pili generated forces in the formation of bacterial colonies and are in agreement with the available experimental observations. The model can quantify the behavior of multicellular bacterial colonies on biologically relevant temporal and spatial scales and can be easily adjusted to include the geometry and pili characteristics of various bacterial species. Ultimately, the combination of the microbiological experimental approach with the in silico model of bacterial colonies might provide new qualitative and quantitative insights on the development of bacterial infections and thus pave the way to new antimicrobial treatments.
Gamze Varan
2018-01-01
Full Text Available Amphiphilic cyclodextrins are biocompatible oligosaccharides that can be used for drug delivery especially for the delivery of drugs with solubility problems thanks to their unique molecular structures. In this paper, Paclitaxel was used as a model anticancer drug to determine the inclusion complex properties of amphiphilic cyclodextrins with different surface charge. Paclitaxel-loaded cyclodextrin nanoparticles were characterized in terms of mean particle diameter, zeta potential, encapsulation efficacy, drug release profile and cell culture studies. It was determined that the nanoparticles prepared from the inclusion complex according to characterization studies have a longer release profile than the conventionally prepared nanoparticles. In order to mimic the tumor microenvironment, breast cancer cells and healthy fibroblast cells were used in 3-dimensional (3D cell culture studies. It was determined that the activities of nanoparticles prepared by conventional methods behave differently in 2-dimensional (2D and 3D cell cultures. In addition, it was observed that the nanoparticles prepared from the inclusion complex have a stronger anti-tumoral activity in the 3D multicellular tumor model than the drug solution. Furthermore, polycationic amphiphilic cyclodextrin nanoparticles can diffuse and penetrate through multilayer cells in a 3D tumor model, which is crucial for an eventual antitumor effect.
Frédéric Boudon
2015-01-01
Full Text Available The link between genetic regulation and the definition of form and size during morphogenesis remains largely an open question in both plant and animal biology. This is partially due to the complexity of the process, involving extensive molecular networks, multiple feedbacks between different scales of organization and physical forces operating at multiple levels. Here we present a conceptual and modeling framework aimed at generating an integrated understanding of morphogenesis in plants. This framework is based on the biophysical properties of plant cells, which are under high internal turgor pressure, and are prevented from bursting because of the presence of a rigid cell wall. To control cell growth, the underlying molecular networks must interfere locally with the elastic and/or plastic extensibility of this cell wall. We present a model in the form of a three dimensional (3D virtual tissue, where growth depends on the local modulation of wall mechanical properties and turgor pressure. The model shows how forces generated by turgor-pressure can act both cell autonomously and non-cell autonomously to drive growth in different directions. We use simulations to explore lateral organ formation at the shoot apical meristem. Although different scenarios lead to similar shape changes, they are not equivalent and lead to different, testable predictions regarding the mechanical and geometrical properties of the growing lateral organs. Using flower development as an example, we further show how a limited number of gene activities can explain the complex shape changes that accompany organ outgrowth.
Validity of the Cauchy-Born rule applied to discrete cellular-scale models of biological tissues
Davit, Y.
2013-04-30
The development of new models of biological tissues that consider cells in a discrete manner is becoming increasingly popular as an alternative to continuum methods based on partial differential equations, although formal relationships between the discrete and continuum frameworks remain to be established. For crystal mechanics, the discrete-to-continuum bridge is often made by assuming that local atom displacements can be mapped homogeneously from the mesoscale deformation gradient, an assumption known as the Cauchy-Born rule (CBR). Although the CBR does not hold exactly for noncrystalline materials, it may still be used as a first-order approximation for analytic calculations of effective stresses or strain energies. In this work, our goal is to investigate numerically the applicability of the CBR to two-dimensional cellular-scale models by assessing the mechanical behavior of model biological tissues, including crystalline (honeycomb) and noncrystalline reference states. The numerical procedure involves applying an affine deformation to the boundary cells and computing the quasistatic position of internal cells. The position of internal cells is then compared with the prediction of the CBR and an average deviation is calculated in the strain domain. For center-based cell models, we show that the CBR holds exactly when the deformation gradient is relatively small and the reference stress-free configuration is defined by a honeycomb lattice. We show further that the CBR may be used approximately when the reference state is perturbed from the honeycomb configuration. By contrast, for vertex-based cell models, a similar analysis reveals that the CBR does not provide a good representation of the tissue mechanics, even when the reference configuration is defined by a honeycomb lattice. The paper concludes with a discussion of the implications of these results for concurrent discrete and continuous modeling, adaptation of atom-to-continuum techniques to biological
Cellular mechanisms underlying the laxative effect of flavonol naringenin on rat constipation model.
Zi-Huan Yang
Full Text Available BACKGROUND & AIMS: Symptoms of constipation are extremely common, especially in the elderly. The present study aim to identify an efficacious treatment strategy for constipation by evaluating the secretion-promoting and laxative effect of a herbal compound, naringenin, on intestinal epithelial anion secretion and a rat constipation model, respectively. METHODS/PRINCIPAL FINDINGS: In isolated rat colonic crypts, mucosal addition of naringenin (100 microM elicited a concentration-dependent and sustained increase in the short-circuit current (I(SC, which could be inhibited in Cl- free solution or by bumetanide and DPC (diphenylamine-2-carboxylic acid, but not by DIDS (4, 4'- diisothiocyanatostilbene-2, 2'-disulfonic acid. Naringenin could increase intracellular cAMP content and PKA activity, consisted with that MDL-12330A (N-(Cis-2-phenyl-cyclopentyl azacyclotridecan-2-imine-hydrochloride pretreatment reduced the naringenin-induced I(SC. In addition, significant inhibition of the naringenin-induced I(SC by quinidine indicated that basolateral K+ channels were involved in maintaining this cAMP-dependent Cl- secretion. Naringenin-evoked whole cell current which exhibited a linear I-V relationship and time-and voltage- independent characteristics was inhibited by DPC, indicating that the cAMP activated Cl- conductance most likely CFTR (cystic fibrosis transmembrane conductance regulator was involved. In rat constipation model, administration of naringenin restored the level of fecal output, water content and mucus secretion compared to loperamide-administrated group. CONCLUSIONS: Taken together, our data suggest that naringenin could stimulate Cl- secretion in colonic epithelium via a signaling pathway involving cAMP and PKA, hence provide an osmotic force for subsequent colonic fluid secretion by which the laxative effect observed in the rat constipation model. Naringenin appears to be a novel alternative treatment strategy for constipation.
Final Report - Modeling the Physics of Damage Cluster Formation in a Cellular Environment
L.H. Toburen, Principal Investigator; J.L. Shinpaugh; M. Dingfelder; and G. Lapicki; Co-Investigators
2007-01-01
Modern tools of radiobiology are leading to many new discoveries regarding how cells and tissues respond to radiation exposure. We can now irradiate single cells and observe responses in adjacent cells. We can also measure clusters of radiation damage produced in DNA. Our primary objective has been to understand the underling physics associated with these new biological responses. The primary tools available to describe the initial spatial pattern of damage formed by the absorption of ionizing radiation are based on Monte Carlo simulation of the structure of charged particle tracks. Although many Monte Carlo codes exist and considerable progress is being made in the incorporation of detailed macromolecular target structures into these codes, much of the interaction physics is still based on gas phase measurements and/or untested theoretical calculations that focus on water as the transport medium. Our objectives were threefold, (1) to expand the applicability of Monte Carlo track structure simulation to tissue-like material beyond the current focus on water, (2) to incorporate the most recent experimental information on electron interactions in biologically relevant material, and (3) to compare recent measurements of electron emissions induced by charged particles in thin foils with Monte Carlo predictions. We addressed these research objectives in three ways. First we applied theoretical techniques, similar to those used to derive data for water, to obtain cross sections for other condensed phase materials. This served two purposes. One was to provide testability of the theoretical technique by comparison to existing experimental data for electron transport (similar data does not exist for water), and the other was to expand the target database for use in modeling tissue. Second, we carefully reviewed published data, and ongoing experiments, for electron interaction cross-sections in biologically relevant condensed phase material. Results for low-energy electron
Ying, Bo; Campbell, Robert B.
2014-01-01
Highlights: • siRNA-lipid nanoparticles are solid particles not lipid bilayers with aqueous core. • High, but not low, PEG content can prevent nanoparticle encapsulation of siRNA. • PEG reduces cellular toxicity of cationic nanoparticles in vitro. • PEG reduces zeta potential while improving gene silencing of siRNA nanoparticles. • Kinesin spindle protein can be an effective target for tumor vascular targeting. - Abstract: The ideal siRNA delivery system should selectively deliver the construct to the target cell, avoid enzymatic degradation, and evade uptake by phagocytes. In the present study, we evaluated the importance of polyethylene glycol (PEG) on lipid-based carrier systems for encapsulating, and delivering, siRNA to tumor vessels using cellular models. Lipid nanoparticles containing different percentage of PEG were evaluated based on their physical chemical properties, density compared to water, siRNA encapsulation, toxicity, targeting efficiency and gene silencing in vitro. siRNA can be efficiently loaded into lipid nanoparticles (LNPs) when DOTAP is included in the formulation mixture. However, the total amount encapsulated decreased with increase in PEG content. In the presence of siRNA, the final formulations contained a mixed population of particles based on density. The major population which contains the majority of siRNA exhibited a density of 4% glucose, and the minor fraction associated with a decreased amount of siRNA had a density less than PBS. The inclusion of 10 mol% PEG resulted in a greater amount of siRNA associated with the minor fraction. Finally, when kinesin spindle protein (KSP) siRNA was encapsulated in lipid nanoparticles containing a modest amount of PEG, the proliferation of endothelial cells was inhibited due to the efficient knock down of KSP mRNA. The presence of siRNA resulted in the formation of solid lipid nanoparticles when prepared using the thin film and hydration method. LNPs with a relatively modest amount of
New roles of glycosaminoglycans in α-synuclein aggregation in a cellular model of Parkinson disease.
Sonia Lehri-Boufala
Full Text Available The causes of Parkinson disease (PD remain mysterious, although some evidence supports mitochondrial dysfunctions and α-synuclein accumulation in Lewy bodies as major events. The abnormal accumulation of α-synuclein has been associated with a deficiency in the ubiquitin-proteasome system and the autophagy-lysosomal pathway. Cathepsin D (cathD, the major lysosomal protease responsible of α-synuclein degradation was described to be up-regulated in PD model. As glycosaminoglycans (GAGs regulate cathD activity, and have been recently suggested to participate in PD physiopathology, we investigated their role in α-synuclein accumulation by their intracellular regulation of cathD activity. In a classical neuroblastoma cell model of PD induced by MPP+, the genetic expression of GAGs-biosynthetic enzymes was modified, leading to an increase of GAGs amounts whereas intracellular level of α-synuclein increased. The absence of sulfated GAGs increased intracellular cathD activity and limited α-synuclein accumulation. GAGs effects on cathD further suggested that specific sequences or sulfation patterns could be responsible for this regulation. The present study identifies, for the first time, GAGs as new regulators of the lysosome degradation pathway, regulating cathD activity and affecting two main biological processes, α-synuclein aggregation and apoptosis. Finally, this opens new insights into intracellular GAGs functions and new fields of investigation for glycobiological approaches in PD and neurobiology.