Parallelizing the Cellular Potts Model on graphics processing units
Tapia, José Juan; D'Souza, Roshan M.
2011-04-01
The Cellular Potts Model (CPM) is a lattice based modeling technique used for simulating cellular structures in computational biology. The computational complexity of the model means that current serial implementations restrict the size of simulation to a level well below biological relevance. Parallelization on computing clusters enables scaling the size of the simulation but marginally addresses computational speed due to the limited memory bandwidth between nodes. In this paper we present new data-parallel algorithms and data structures for simulating the Cellular Potts Model on graphics processing units. Our implementations handle most terms in the Hamiltonian, including cell-cell adhesion constraint, cell volume constraint, cell surface area constraint, and cell haptotaxis. We use fine level checkerboards with lock mechanisms using atomic operations to enable consistent updates while maintaining a high level of parallelism. A new data-parallel memory allocation algorithm has been developed to handle cell division. Tests show that our implementation enables simulations of >10 cells with lattice sizes of up to 256 3 on a single graphics card. Benchmarks show that our implementation runs ˜80× faster than serial implementations, and ˜5× faster than previous parallel implementations on computing clusters consisting of 25 nodes. The wide availability and economy of graphics cards mean that our techniques will enable simulation of realistically sized models at a fraction of the time and cost of previous implementations and are expected to greatly broaden the scope of CPM applications.
Study of contact angle hysteresis using the Cellular Potts Model.
Mortazavi, Vahid; D'Souza, Roshan M; Nosonovsky, Michael
2013-02-28
We use the Cellular Potts Model (CPM) to study the contact angle (CA) hysteresis in multiphase (solid-liquid-vapour) systems. We simulate a droplet over the tilted patterned surface, and a bubble placed under the surface immersed in liquid. The difference between bubbles and droplets was discussed through their CA hysteresis. Dependency of CA hysteresis on the surface structure and other parameters was also investigated. This analysis allows decoupling of the 1D (pinning of the triple line) and 2D (adhesion hysteresis in the contact area) effects and provides new insight into the nature of CA hysteresis.
A hybrid parallel framework for the cellular Potts model simulations
Energy Technology Data Exchange (ETDEWEB)
Jiang, Yi [Los Alamos National Laboratory; He, Kejing [SOUTH CHINA UNIV; Dong, Shoubin [SOUTH CHINA UNIV
2009-01-01
The Cellular Potts Model (CPM) has been widely used for biological simulations. However, most current implementations are either sequential or approximated, which can't be used for large scale complex 3D simulation. In this paper we present a hybrid parallel framework for CPM simulations. The time-consuming POE solving, cell division, and cell reaction operation are distributed to clusters using the Message Passing Interface (MPI). The Monte Carlo lattice update is parallelized on shared-memory SMP system using OpenMP. Because the Monte Carlo lattice update is much faster than the POE solving and SMP systems are more and more common, this hybrid approach achieves good performance and high accuracy at the same time. Based on the parallel Cellular Potts Model, we studied the avascular tumor growth using a multiscale model. The application and performance analysis show that the hybrid parallel framework is quite efficient. The hybrid parallel CPM can be used for the large scale simulation ({approx}10{sup 8} sites) of complex collective behavior of numerous cells ({approx}10{sup 6}).
An efficient Cellular Potts Model algorithm that forbids cell fragmentation
Durand, Marc; Guesnet, Etienne
2016-11-01
The Cellular Potts Model (CPM) is a lattice based modeling technique which is widely used for simulating cellular patterns such as foams or biological tissues. Despite its realism and generality, the standard Monte Carlo algorithm used in the scientific literature to evolve this model preserves connectivity of cells on a limited range of simulation temperature only. We present a new algorithm in which cell fragmentation is forbidden for all simulation temperatures. This allows to significantly enhance realism of the simulated patterns. It also increases the computational efficiency compared with the standard CPM algorithm even at same simulation temperature, thanks to the time spared in not doing unrealistic moves. Moreover, our algorithm restores the detailed balance equation, ensuring that the long-term stage is independent of the chosen acceptance rate and chosen path in the temperature space.
Solving the Advection-Diffusion Equations in Biological Contexts using the Cellular Potts Model
Dan, D; Chen, K; Glazier, J A; Dan, Debasis; Mueller, Chris; Chen, Kun; Glazier, James A.
2005-01-01
The Cellular Potts Model (CPM) is a robust, cell-level methodology for simulation of biological tissues and morphogenesis. Both tissue physiology and morphogenesis depend on diffusion of chemical morphogens in the extra-cellular fluid or matrix (ECM). Standard diffusion solvers applied to the cellular potts model use finite difference methods on the underlying CPM lattice. However, these methods produce a diffusing field tied to the underlying lattice, which is inaccurate in many biological situations in which cell or ECM movement causes advection rapid compared to diffusion. Finite difference schemes suffer numerical instabilities solving the resulting advection-diffusion equations. To circumvent these problems we simulate advection-diffusion within the framework of the CPM using off-lattice finite-difference methods. We define a set of generalized fluid particles which detach advection and diffusion from the lattice. Diffusion occurs between neighboring fluid particles by local averaging rules which approxi...
Computational energetic model of morphogenesis based on multi-agent Cellular Potts Model.
Tripodi, Sébastien; Ballet, Pascal; Rodin, Vincent
2010-01-01
The Cellular Potts Model (CPM) is a cellular automaton (CA), developed by Glazier and Graner in 1992, to model the morphogenesis. In this model, the entities are the cells. It has already been improved in many ways; however, a key point in biological systems, not defined in CPM, is energetic exchange between entities. We integrate this energetic concept inside the CPM. We simulate a cell differentiation inside a growing cell tissue. The results are the emergence of dynamic patterns coming from the consumption and production of energy. A model described by CA is less scalable than one described by a multi-agent system (MAS). We have developed a MAS based on the CPM, where a cell agent is implemented from the cell of CPM together with several behaviours, in particular the consumption and production of energy from the consumption of molecules.
Dynamic exponents for potts model cluster algorithms
Coddington, Paul D.; Baillie, Clive F.
We have studied the Swendsen-Wang and Wolff cluster update algorithms for the Ising model in 2, 3 and 4 dimensions. The data indicate simple relations between the specific heat and the Wolff autocorrelations, and between the magnetization and the Swendsen-Wang autocorrelations. This implies that the dynamic critical exponents are related to the static exponents of the Ising model. We also investigate the possibility of similar relationships for the Q-state Potts model.
Partial order of frustrated Potts model
Energy Technology Data Exchange (ETDEWEB)
Igarashi, Ryo [CCSE, Japan Atomic Energy Agency, Higashi-Ueno, Taito, Tokyo 110-0015 (Japan); Ogata, Masao, E-mail: igarashi.ryo@jaea.go.j [Deaprtment of Physics, University of Tokyo, Hongo, Bunkyo, Tokyo 133-0033 (Japan)
2010-01-01
We investigate a 4-state ferromagnetic Potts model with a special type of geometrical frustration on a three dimensional diamond lattice. We find that the model undergoes unconventional phase transition; half of the spins in the system order in a two dimensional hexagonal-sheet-like structure while the remaining half of the spins stay disordered. The ordered sheets and the disordered sheets stack one after another. We obtain fairly large residual entropy using the Wang-Landau Monte Carlo simulation.
Phase transition and surface sublimation of a mobile Potts model.
Bailly-Reyre, A; Diep, H T; Kaufman, M
2015-10-01
We study in this paper the phase transition in a mobile Potts model by the use of Monte Carlo simulation. The mobile Potts model is related to a diluted Potts model, which is also studied here by a mean-field approximation. We consider a lattice where each site is either vacant or occupied by a q-state Potts spin. The Potts spin can move from one site to a nearby vacant site. In order to study the surface sublimation, we consider a system of Potts spins contained in a recipient with a concentration c defined as the ratio of the number of Potts spins N(s) to the total number of lattice sites N(L)=N(x)×N(y)×N(z). Taking into account the attractive interaction between the nearest-neighboring Potts spins, we study the phase transitions as functions of various physical parameters such as the temperature, the shape of the recipient, and the spin concentration. We show that as the temperature increases, surface spins are detached from the solid phase to form a gas in the empty space. Surface order parameters indicate different behaviors depending on the distance to the surface. At high temperatures, if the concentration is high enough, the interior spins undergo a first-order phase transition to an orientationally disordered phase. The mean-field results are shown as functions of temperature, pressure, and chemical potential, which confirm in particular the first-order character of the transition.
Antiferromagnetic Potts model on the Erdos-Renyi random graph
Contucci, Pierluig; Giardina', Cristian; Starr, Shannon
2011-01-01
We study the antiferromagnetic Potts model on the Erdos-Renyi random graph. By identifying a suitable interpolation structure and proving an extended variational principle we show that the replica symmetric solution is an upper bound for the limiting pressure which can be recovered in the framework of Derrida-Ruelle probability cascades. A comparison theorem with a mixed model made of a mean field Potts-antiferromagnet plus a Potts-Sherrington-Kirkpatrick model allows to show that the replica symmetric solution is exact at high temperatures.
Graphical representations of Ising and Potts models
Björnberg, Jakob E
2010-01-01
We study graphical representations for two related models. The first model is the transverse field quantum Ising model, an extension of the original Ising model which was introduced by Lieb, Schultz and Mattis in the 1960's. The second model is the space-time percolation process, which is closely related to the contact model for the spread of disease. We consider a `space-time' random-cluster model and explore a range of useful probabilistic techniques for studying it. The space-time Potts model emerges as a natural generalization of the quantum Ising model. The basic properties of the phase transitions in these models are treated, such as the fact that there is at most one unbounded FK-cluster, and the resulting lower bound on the critical value in $\\ZZ$. We also develop an alternative graphical representation of the quantum Ising model, called the random-parity representation. This representation is based on the random-current representation of the classical Ising model, and allows us to study in much great...
Dynamical behavior of the Niedermayer algorithm applied to Potts models
Girardi, D.; Penna, T. J. P.; Branco, N. S.
2012-01-01
In this work we make a numerical study of the dynamic universality class of the Niedermayer algorithm applied to the two-dimensional Potts model with 2, 3, and 4 states. This algorithm updates clusters of spins and has a free parameter, $E_0$, which controls the size of these clusters, such that $E_0=1$ is the Metropolis algorithm and $E_0=0$ regains the Wolff algorithm, for the Potts model. For $-1
Remarks on Khovanov Homology and the Potts Model
Kauffman, Louis H
2009-01-01
This paper is about Khovanov homology and its relationships with statistical mechanics models such as the Ising model and the Potts model. The paper gives a relatively self-contained introduction to Khovanov homology, and also to a reformulation of the Potts model in terms of a bracket state sum expansion on a knot diagram K(G) related to a planar graph G via the medial construction. We consider the original Khovanov homology and also the homology defined by Stosic via the dichromatic polynomial, and examine those values of the Potts model where the partition function can be expressed in terms of homological Euler characteristics. These points occur at imaginary temperature, and consequences of this phenomenon will be studied in subsequent work. This paper is dedicated to Oleg Viro on his 60-th birthday.
Spontaneous magnetization of the integrable chiral Potts model
Energy Technology Data Exchange (ETDEWEB)
Au-Yang, Helen; Perk, Jacques H H, E-mail: helenperk@yahoo.com, E-mail: perk@okstate.edu [Department of Physics, Oklahoma State University, 145 Physical Sciences, Stillwater, OK 74078-3072 (United States)
2011-11-04
We show how Z-invariance in the chiral Potts model provides a strategy to calculate the pair correlation in the general integrable chiral Potts model using only the superintegrable eigenvectors. When the distance between the two spins in the correlation function becomes infinite it becomes the square of the order parameter. In this way, we show that the spontaneous magnetization can be expressed in terms of the inner products of the eigenvectors of the N asymptotically degenerate maximum eigenvalues. Using our previous results on these eigenvectors, we are able to obtain the order parameter as a sum almost identical to the one given by Baxter. This gives the known spontaneous magnetization of the chiral Potts model by an entirely different approach. (paper)
Spontaneous Magnetization of the Integrable Chiral Potts Model
Au-Yang, Helen
2010-01-01
We show how $Z$-invariance in the chiral Potts model provides a strategy to calculate the pair correlation in the general integrable chiral Potts model using only the superintegrable eigenvectors. When the distance between the two spins in the correlation function becomes infinite it becomes the square of the order parameter. In this way, we show that the spontaneous magnetization can be expressed in terms of the inner products of the eigenvectors of the $N$ asymptotically degenerate maximum eigenvalues. Using our previous results on these eigenvectors, we are able to obtain the order parameter as a sum almost identical to the one given by Baxter. This gives the known spontaneous magnetization of the chiral Potts model by an entirely different approach.
Potts Flux Tube Model at Nonzero Chemical Potential
Condella, J; Condella, Jac; Tar, Carleton De
2000-01-01
We model the deconfinement phase transition in quantum chromodynamics at nonzero baryon number density and large quark mass by extending the flux tube model (three-state, three-dimensional Potts model) to nonzero chemical potential. In a direct numerical simulation we confirm mean-field-theory predictions that the deconfinement transition does not occur in a baryon-rich environment.
The three-state antiferromagnetic Potts model: scaling laws
Energy Technology Data Exchange (ETDEWEB)
Gottlob, A.P. [Kaiserslautern Univ. (Germany); Hasenbusch, M. [Cambridge Univ. (United Kingdom). Dept. of Applied Mathematics and Theoretical Physics (DAMTP)
1995-04-01
We present the results of a Monte Carlo study of the three-dimensional anti-ferromagnetic three-state Potts model. We computed the correlation length, the magnetic susceptibility and the specific heat for various coupling parameters in the high temperature phase of the model. From the scaling behaviour of these quantities we determine estimates for the critical temperature and critical exponents. ((orig.)).
F-Susy And The Three States Potts Model
Sedra, M B
2009-01-01
In view of its several involvements in various physical and mathematical contexts, 2D-fractional supersymmetry (F-susy) is once again considered in this work. We are, for instance, interested to study the three states Potts model $(k = 3)$ which represents with the tricritical Ising model $(k = 2)$ the two leading examples of more general spin $1/k$ fractional supersymmetric theories.
Saddle-point approach to the gauge Potts model
Energy Technology Data Exchange (ETDEWEB)
Camarata, C.; Epele, L.N.; Fanchiotti, H.; Garcia Canal, C.A.
1984-07-02
The q-state gauge Potts model in d dimensions is studied via saddle-point techniques. Corrections to the mean-field results, due to gaussian fluctuations, are computed. Results for the free energy, the critical coupling and the latent heat are presented. The limit q->infinite is discussed.
Potts models coupled to two-dimensional quantum gravity
Baillie, Clive F.
We perform Monte Carlo simulations using the Wolff cluster algorithm of the q=2 (Ising), 3 and 4 Potts models on dynamical phi-cubed graphs of spherical topology with up to 5000 nodes. We find that the measured critical exponents are in reasonable agreement with those from the exact solution of the Ising model and with those calculated from KPZ scaling for q=3,4 where no exact solution is available.
Application of nested sampling in statistical physics: the Potts model
Pfeifenberger, Manuel J
2016-01-01
We present a systematic benchmark study of the nested sampling algorithm on the basis of the Potts model. This model exhibits a first order phase transition for $q>4$ at the critical temperature. The numerical evaluation of the partition function and thermodynamic observables, which involves high dimensional sums of sharply structured multi-modal density functions, represents a major challenge to most standard numerical techniques, such as Markov Chain Monte Carlo. Nested sampling, on the other hand, is particularly suited for such problems. In this paper we will employ both, nested sampling and thermodynamic integration to evaluate the partition function of the Potts model. In both cases individual moves are based on Swendsen-Wang updates. A autocorrelation time analysis of both algorithms shows that the severe slowing down of thermodynamic integration around the critical temperature does not occur in nested sampling. In addition we show, how thermodynamic variables can be computed with high accuracy from th...
Multiple Potts Models Coupled to Two-Dimensional Quantum Gravity
Baillie, C F
1992-01-01
We perform Monte Carlo simulations using the Wolff cluster algorithm of {\\it multiple} $q=2,3,4$ state Potts models on dynamical phi-cubed graphs of spherical topology in order to investigate the $c>1$ region of two-dimensional quantum gravity. Contrary to naive expectation we find no obvious signs of pathological behaviour for $c>1$. We discuss the results in the light of suggestions that have been made for a modified DDK ansatz for $c>1$.
Multiple Potts models coupled to two-dimensional quantum gravity
Baillie, C. F.; Johnston, D. A.
1992-07-01
We perform Monte Carlo simulations using the Wolff cluster algorithm of multiple q=2, 3, 4 state Potts models on dynamical phi-cubed graphs of spherical topology in order to investigate the c>1 region of two-dimensional quantum gravity. Contrary to naive expectation we find no obvious signs of pathological behaviour for c>1. We discuss the results in the light of suggestions that have been made for a modified DDK ansatz for c>1.
Dynamical behavior of the Niedermayer algorithm applied to Potts models
Girardi, D.; Penna, T. J. P.; Branco, N. S.
2012-08-01
In this work, we make a numerical study of the dynamic universality class of the Niedermayer algorithm applied to the two-dimensional Potts model with 2, 3, and 4 states. This algorithm updates clusters of spins and has a free parameter, E0, which controls the size of these clusters, such that E0=1 is the Metropolis algorithm and E0=0 regains the Wolff algorithm, for the Potts model. For -1clusters of equal spins can be formed: we show that the mean size of the clusters of (possibly) turned spins initially grows with the linear size of the lattice, L, but eventually saturates at a given lattice size L˜, which depends on E0. For L≥L˜, the Niedermayer algorithm is in the same dynamic universality class of the Metropolis one, i.e, they have the same dynamic exponent. For E0>0, spins in different states may be added to the cluster but the dynamic behavior is less efficient than for the Wolff algorithm (E0=0). Therefore, our results show that the Wolff algorithm is the best choice for Potts models, when compared to the Niedermayer's generalization.
Boundary States of the Potts Model on Random Planar Maps
Atkin, Max; Wheater, John
2015-01-01
We revisit the 3-states Potts model on random planar triangulations as a Hermitian matrix model. As a novelty, we obtain an algebraic curve which encodes the partition function on the disc with both fixed and mixed spin boundary conditions. We investigate the critical behaviour of this model and find scaling exponents consistent with previous literature. We argue that the conformal field theory that describes the double scaling limit is Liouville quantum gravity coupled to the $(A_4,D_4)$ minimal model with extended $\\mathcal{W}_3$-symmetry.
Critical Interfaces in the Random-Bond Potts Model
Jacobsen, Jesper L.; Le Doussal, Pierre; Picco, Marco; Santachiara, Raoul; Wiese, Kay Jörg
2009-02-01
We study geometrical properties of interfaces in the random-temperature q-states Potts model as an example of a conformal field theory weakly perturbed by quenched disorder. Using conformal perturbation theory in q-2 we compute the fractal dimension of Fortuin-Kasteleyn (FK) domain walls. We also compute it numerically both via the Wolff cluster algorithm for q=3 and via transfer-matrix evaluations. We also obtain numerical results for the fractal dimension of spin clusters interfaces for q=3. These are found numerically consistent with the duality κspinκFK=16 as expressed in putative SLE parameters.
New Correlation Duality Relations for the Planar Potts Model
King, C.; Wu, F. Y.
2002-05-01
We introduce a new method to generate duality relations for correlation functions of the Potts model on a planar graph. The method extends previously known results, by allowing the consideration of the correlation function for arbitrarily placed vertices on the graph. We show that generally it is linear combinations of correlation functions, not the individual correlations, that are related by dualities. The method is illustrated in several non-trivial cases, and the relation to earlier results is explained. A graph-theoretical formulation of our results in terms of rooted dichromatic, or Tutte, polynomials is also given.
Gauge Potts model with generalized action: A Monte Carlo analysis
Energy Technology Data Exchange (ETDEWEB)
Fanchiotti, H.; Canal, C.A.G.; Sciutto, S.J.
1985-08-15
Results of a Monte Carlo calculation on the q-state gauge Potts model in d dimensions with a generalized action involving planar 1 x 1, plaquette, and 2 x 1, fenetre, loop interactions are reported. For d = 3 and q = 2, first- and second-order phase transitions are detected. The phase diagram for q = 3 presents only first-order phase transitions. For d = 2, a comparison with analytical results is made. Here also, the behavior of the numerical simulation in the vicinity of a second-order transition is analyzed.
Parallel family trees for transfer matrices in the Potts model
Navarro, Cristobal A; Kahler, Nancy Hitschfeld; Navarro, Gonzalo
2013-01-01
The computational cost of transfer matrix methods for the Potts model is directly related to the problem of \\textit{into how many ways can two adjacent blocks of a lattice be connected}. Answering this question leads to the generation of a combinatorial set of lattice configurations. This set defines the \\textit{configuration space} of the problem, and the smaller it is, the faster the transfer matrix method can be. The configuration space of generic transfer matrix methods for strip lattices in the Potts model is in the order of the Catalan numbers, leading to an asymptotic cost of $O(4^m)$ with $m$ being the width of the strip. Transfer matrix methods with a smaller configuration space indeed exist but they make assumptions on the temperature, number of spin states, or restrict the topology of the lattice in order to work. In this paper we propose a general and parallel transfer matrix method, based on family trees, that uses a sub-Catalan configuration space of size $O(3^m)$. The improvement is achieved by...
Anisotropic exchange-interaction model: From the Potts model to the exchange-interaction model
King, T. C.; Chen, H. H.
1995-04-01
A spin model called the anisotropic exchange-interaction model is proposed. The Potts model, the exchange-interaction model, and the spin-1/2 anisotropic Heisenberg model are special cases of the proposed model. Thermodynamic properties of the model on the bcc and the fcc lattices are determined by the constant-coupling approximation.
Generalized Potts-Models and their Relevance for Gauge Theories
Directory of Open Access Journals (Sweden)
Andreas Wipf
2007-01-01
Full Text Available We study the Polyakov loop dynamics originating from finite-temperature Yang-Mills theory. The effective actions contain center-symmetric terms involving powers of the Polyakov loop, each with its own coupling. For a subclass with two couplings we perform a detailed analysis of the statistical mechanics involved. To this end we employ a modified mean field approximation and Monte Carlo simulations based on a novel cluster algorithm. We find excellent agreement of both approaches. The phase diagram exhibits both first and second order transitions between symmetric, ferromagnetic and antiferromagnetic phases with phase boundaries merging at three tricritical points. The critical exponents ν and γ at the continuous transition between symmetric and antiferromagnetic phases are the same as for the 3-state spin Potts model.
Twelve-state Potts model in a magnetic field
Kassan-Ogly, F. A.; Filippov, B. N.; Proshkin, A. I.; Zarubin, A. V.
2015-02-01
In this work, we have obtained an exact solution to the one-dimensional modified 12-state Potts model using the Kramers-Wannier transfer matrix with allowance for the exchange interaction between nearest neighbors in an external magnetic field. Analytical expressions have been derived for the heat capacity, magnetization, magnetic susceptibility, magnetic entropy, and magnetocaloric effect as functions of temperature, magnitude and sign of exchange interaction, and the magnitude and direction of the magnetic field. The behavior of all of these parameters has been investigated in detail using numerical methods. The possibility of applying the results obtained to explain the observed magnetic properties of real cubic magnets with a NaCl structure and easy axes oriented along the [110] crystallographic directions has been discussed.
Monte Carlo Simulation of the Potts Model on a Dodecagonal Quasiperiodic Structure
Institute of Scientific and Technical Information of China (English)
WEN Zhang-Bin; HOU Zhi-Lin; FU Xiu-Jun
2011-01-01
By means of a Monte Carlo simulation, we study the three-state Potts model on a two-dimensional quasiperiodic structure based on a dodecagonal cluster covering pattern. The critical temperature and exponents are obtained from finite-size scaling analysis. It is shown that the Potts model on the quasiperiodic lattice belongs to the same universal class as those on periodic ones.%@@ By means of a Monte Carlo simulation, we study the three-state Potts model on a two-dimensional quasiperiodic structure based on a dodecagonal cluster covering pattern.The critical temperature and exponents are obtained from finite-size scaling analysis.It is shown that the Potts model on the quasiperiodic lattice belongs to the same universal class as those on periodic ones.
Lapinskas, Saulius; Rosengren, Anders
1994-06-01
Using the cluster-variation method we study the phase diagram of the Blume-Emergy-Griffiths (BEG) model on simple cubic and face-centered cubic lattices. For the simple cubic lattice the main attention is paid to reentrant phenomena and ferrimagnetic phases occurring in a certain range of coupling constants. The results are in close agreement with Monte-Carlo data, available for parts of the phase diagram. Several ferrimagnetic phases are obtained in the vicinity of the line in parameter space, at which the model reduces to the antiferromagnetic three-state Potts model. Our results imply the existence of three phase transitions in the antiferromagnetic Potts model on the simple-cubic lattice. The phase diagrams for the BEG model on the face-centered cubic lattice are obtained in the region of antiquadrupolar ordering. Also the several ordered phases of the antiferromagnetic Potts model on this lattice are discussed.
Scale-free random graphs and Potts model
Indian Academy of Sciences (India)
D-S Lee; K-I Goh; B Kahng; D Kim
2005-06-01
We introduce a simple algorithm that constructs scale-free random graphs efficiently: each vertex has a prescribed weight − (0 < < 1) and an edge can connect vertices and with rate . Corresponding equilibrium ensemble is identified and the problem is solved by the → 1 limit of the -state Potts model with inhomogeneous interactions for all pairs of spins. The number of loops as well as the giant cluster size and the mean cluster size are obtained in the thermodynamic limit as a function of the edge density. Various critical exponents associated with the percolation transition are also obtained together with finite-size scaling forms. The process of forming the giant cluster is qualitatively different between the cases of > 3 and 2 < < 3, where = 1 + -1 is the degree distribution exponent. While for the former, the giant cluster forms abruptly at the percolation transition, for the latter, however, the formation of the giant cluster is gradual and the mean cluster size for finite shows double peaks.
Energy Technology Data Exchange (ETDEWEB)
Jason D. Hales; Veena Tikare
2014-04-01
The Used Fuel Disposition (UFD) program has initiated a project to develop a hydride formation modeling tool using a hybrid Pottsphase field approach. The Potts model is incorporated in the SPPARKS code from Sandia National Laboratories. The phase field model is provided through MARMOT from Idaho National Laboratory.
a Numerical Test of Kpz Scaling:. Potts Models Coupled to Two-Dimensional Quantum Gravity
Baillie, C. F.; Johnston, D. A.
We perform Monte-Carlo simulations using the Wolff cluster algorithm of the q=2 (Ising), 3, 4 and q=10 Potts models on dynamical phi-cubed graphs of spherical topology with up to 5000 nodes. We find that the measured critical exponents are in reasonable agreement with those from the exact solution of the Ising model and with those calculated from KPZ scaling for q=3, 4 where no exact solution is available. Using Binder’s cumulant we find that the q=10 Potts model displays a first order phase transition on a dynamical graph, as it does on a fixed lattice. We also examine the internal geometry of the graphs generated in the simulation, finding a linear relationship between ring length probabilities and the central charge of the Potts model.
A Numerical Test of KPZ Scaling Potts Models Coupled to Two-Dimensional Quantum Gravity
Baillie, C F
1992-01-01
We perform Monte Carlo simulations using the Wolff cluster algorithm of the q=2 (Ising), 3, 4 and q=10 Potts models on dynamical phi-cubed graphs of spherical topology with up to 5000 nodes. We find that the measured critical exponents are in reasonable agreement with those from the exact solution of the Ising model and with those calculated from KPZ scaling for q=3,4 where no exact solution is available. Using Binder's cumulant we find that the q=10 Potts model displays a first order phase transition on a dynamical graph, as it does on a fixed lattice. We also examine the internal geometry of the graphs generated in the simulation, finding a linear relationship between ring length probabilities and the central charge of the Potts model
On phase transitions of the Potts model with three competing interactions on Cayley tree
Directory of Open Access Journals (Sweden)
S. Temir
2011-06-01
Full Text Available In the present paper we study a phase transition problem for the Potts model with three competing interactions, the nearest neighbors, the second neighbors and triples of neighbors and non-zero external field on Cayley tree of order two. We prove that for some parameter values of the model there is phase transition. We reduce the problem of describing by limiting Gibbs measures to the problem of solving a system of nonlinear functional equations. We extend the results obtained by Ganikhodjaev and Rozikov [Math. Phys. Anal. Geom., 2009, vol. 12, No. 2, 141-156] on phase transition for the Ising model to the Potts model setting.
Potts Model on Maple Leaf Lattice with Pure Three-Site Interaction
Institute of Scientific and Technical Information of China (English)
WANG Zhou-Fei; CHEN Li
2005-01-01
We use Monte Carlo method to study three-state Potts model on maple leaf lattice with pure three-site interaction. The critical behavior of both ferromagnetic and antiferromagnetic cases is studied. Our results confirm that the critical behavior of the ferromagnetic model is independent of the lattice details and lies in the universality class of the three-state ferromagnetic Potts model. For the antiferromagnetic case the transition is of the first order. We have calculated the energy jump and critical temperature in this area. We find there is a tricritical point separating the first order and second order phases for this system.
Super-Potts glass: A disordered model for glass-forming liquids
Angelini, Maria Chiara; Biroli, Giulio
2014-12-01
We introduce a disordered system, the super-Potts model, which is a more frustrated version of the Potts glass. Its elementary degrees of freedom are variables that can take M values and are coupled via pairwise interactions. Its exact solution on a completely connected lattice demonstrates that, for large enough M , it belongs to the class of mean-field systems solved by a one-step replica symmetry breaking ansatz. Numerical simulations by the parallel tempering technique show that in three dimensions it displays a phenomenological behavior similar to the one of glass-forming liquids. The super-Potts glass is therefore a disordered model allowing one to perform extensive and detailed studies of the random first-order transition in finite dimensions. We also discuss its behavior for small values of M , which is similar to the one of spin glasses in a field.
Translation-invariant and periodic Gibbs measures for the Potts model on a Cayley tree
Khakimov, R. M.; Khaydarov, F. Kh.
2016-11-01
We study translation-invariant Gibbs measures on a Cayley tree of order k = 3 for the ferromagnetic three-state Potts model. We obtain explicit formulas for translation-invariant Gibbs measures. We also consider periodic Gibbs measures on a Cayley tree of order k for the antiferromagnetic q-state Potts model. Moreover, we improve previously obtained results: we find the exact number of periodic Gibbs measures with the period two on a Cayley tree of order k ≥ 3 that are defined on some invariant sets.
Potts model on directed small-world Voronoi-Delaunay lattices
Marques, R. M.; Lima, F. W. S.; Costa Filho, Raimundo N.
2016-06-01
The critical properties of the Potts model with q = 3 and 4 states in two-dimensions on directed small-world Voronoi-Delaunay random lattices with quenched connectivity disorder are investigated. This disordered system is simulated by applying the Monte Carlo update heat bath algorithm. The Potts model on these directed small-world random lattices presents in fact a second-order phase transition with new critical exponents for q = 3 and value of the rewiring probability p = 0.01, but for q = 4 the system exhibits only a first-order phase transition independent of p (0 < p < 1).
Random matrix theory and higher genus integrability: the quantum chiral Potts model
Energy Technology Data Exchange (ETDEWEB)
Angles d' Auriac, J.Ch. [Centre de Recherches sur les Tres Basses Temperatures, BP 166, Grenoble (France)]. E-mail: dauriac@polycnrs-gre.fr; Maillard, J.M.; Viallet, C.M. [LPTHE, Tour 16, Paris (France)]. E-mails: maillard@lpthe.jussieu.fr; viallet@lpthe.jussieu.fr
2002-06-14
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)
Joint Image Reconstruction and Segmentation Using the Potts Model
Storath, Martin; Frikel, Jürgen; Unser, Michael
2014-01-01
We propose a new algorithmic approach to the non-smooth and non-convex Potts problem (also called piecewise-constant Mumford-Shah problem) for inverse imaging problems. We derive a suitable splitting into specific subproblems that can all be solved efficiently. Our method does not require a priori knowledge on the gray levels nor on the number of segments of the reconstruction. Further, it avoids anisotropic artifacts such as geometric staircasing. We demonstrate the suitability of our method for joint image reconstruction and segmentation from limited data in x-ray and photoacoustic tomography. For instance, our method is able to reconstruct the Shepp-Logan phantom from $7$ angular views only. We demonstrate the practical applicability in an experiment with real PET data.
Fluctuation complexity of agent-based financial time series model by stochastic Potts system
Hong, Weijia; Wang, Jun
2015-03-01
Financial market is a complex evolved dynamic system with high volatilities and noises, and the modeling and analyzing of financial time series are regarded as the rather challenging tasks in financial research. In this work, by applying the Potts dynamic system, a random agent-based financial time series model is developed in an attempt to uncover the empirical laws in finance, where the Potts model is introduced to imitate the trading interactions among the investing agents. Based on the computer simulation in conjunction with the statistical analysis and the nonlinear analysis, we present numerical research to investigate the fluctuation behaviors of the proposed time series model. Furthermore, in order to get a robust conclusion, we consider the daily returns of Shanghai Composite Index and Shenzhen Component Index, and the comparison analysis of return behaviors between the simulation data and the actual data is exhibited.
Energy Technology Data Exchange (ETDEWEB)
Battaile, C.C.; Buchheit, T.E.; Holm, E.A.; Neilsen, M.K.; Wellman, G.W.
1999-01-12
The microstructural evolution of heavily deformed polycrystalline Cu is simulated by coupling a constitutive model for polycrystal plasticity with the Monte Carlo Potts model for grain growth. The effects of deformation on boundary topology and grain growth kinetics are presented. Heavy deformation leads to dramatic strain-induced boundary migration and subsequent grain fragmentation. Grain growth is accelerated in heavily deformed microstructures. The implications of these results for the thermomechanical fatigue failure of eutectic solder joints are discussed.
Modulated Phase of a Potts Model with Competing Binary Interactions on a Cayley Tree
Ganikhodjaev, N.; Temir, S.; Akin, H.
2009-11-01
We study the phase diagram for Potts model on a Cayley tree with competing nearest-neighbor interactions J 1, prolonged next-nearest-neighbor interactions J p and one-level next-nearest-neighbor interactions J o . Vannimenus proved that the phase diagram of Ising model with J o =0 contains a modulated phase, as found for similar models on periodic lattices, but the multicritical Lifshitz point is at zero temperature. Later Mariz et al. generalized this result for Ising model with J o ≠0 and recently Ganikhodjaev et al. proved similar result for the three-state Potts model with J o =0. We consider Potts model with J o ≠0 and show that for some values of J o the multicritical Lifshitz point be at non-zero temperature. We also prove that as soon as the same-level interaction J o is nonzero, the paramagnetic phase found at high temperatures for J o =0 disappears, while Ising model does not obtain such property. To perform this study, an iterative scheme similar to that appearing in real space renormalization group frameworks is established; it recovers, as particular case, previous work by Ganikhodjaev et al. for J o =0. At vanishing temperature, the phase diagram is fully determined for all values and signs of J 1, J p and J o . At finite temperatures several interesting features are exhibited for typical values of J o / J 1.
Energy Technology Data Exchange (ETDEWEB)
Baxter, R J [Mathematical Sciences Institute, Australian National University, Canberra, ACT 0200 (Australia)
2010-04-09
For the Ising model, the calculation of the spontaneous magnetization leads to the problem of evaluating a determinant. Yang did this by calculating the eigenvalues in the large-lattice limit. Montroll, Potts and Ward expressed it as a Toeplitz determinant and used Szego's theorem: this is almost certainly the route originally travelled by Onsager. For the corresponding problem in the superintegrable chiral Potts model, neither approach appears to work: here we show that the determinant D{sub PQ} can be expressed as that of a product of two Cauchy-like matrices. One can then use the elementary exact formula for the Cauchy determinant. One of course regains the known result, originally conjectured in 1989.
First-order phase transition in $1d$ Potts model with long-range interactions
Uzelac, K.; Glumac, Z.
1998-01-01
The first-order phase transition in the one-dimensional $q$-state Potts model with long-range interactions decaying with distance as $1/r^{1+\\sigma}$ has been studied by Monte Carlo numerical simulations for $0 2$. On the basis of finite-size scaling analysis of interface free energy $\\Delta F_L$, specific heat and Binder's fourth order cumulant, we obtain the first-order transition which occurs for $\\sigma$ below a threshold value $\\sigma_c(q)$.
Julia sets and complex singularities in diamond-like hierarchical Potts models
Institute of Scientific and Technical Information of China (English)
QIAO; Jianyong
2005-01-01
We study the phase transition of the Potts model on diamond-like hierarchical lattices. It is shown that the set of the complex singularities is the Julia set of a rational mapping. An interesting problem is how are these singularities continued to the complex plane. In this paper, by the method of complex dynamics, we give a complete description about the connectivity of the set of the complex singularities.
Efficient Monte Carlo Methods for the Potts Model at Low Temperature
Molkaraie, Mehdi
2015-01-01
We consider the problem of estimating the partition function of the ferromagnetic $q$-state Potts model. We propose an importance sampling algorithm in the dual of the normal factor graph representing the model. The algorithm can efficiently compute an estimate of the partition function in a wide range of parameters; in particular, when the coupling parameters of the model are strong (corresponding to models at low temperature) or when the model contains a mixture of strong and weak couplings. We show that, in this setting, the proposed algorithm significantly outperforms the state of the art methods in the primal and in the dual domains.
Sums of Ramdom Matrices and the Potts Model on Random Planar Maps
Atkin, Max R; Wheater, John F
2015-01-01
We compute the partition function of the $q$-states Potts model on a random planar lattice with $p\\leq q$ allowed, equally weighted colours on a connected boundary. To this end, we employ its matrix model representation in the planar limit, generalising a result by Voiculescu for the addition of random matrices to a situation beyond free probability theory. We show that the partition functions with $p$ and $q-p$ colours on the boundary are related algebraically. Finally, we investigate the phase diagram of the model when $0\\leq q\\leq 4$ and comment on the conformal field theory description of the critical points.
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.
Interface tension of the 3d 4-state Potts model using the Wang-Landau algorithm
Hietanen, A
2011-01-01
We study the interface tension of the 4-state Potts model in three dimensions using the Wang- Landau algorithm. The interface tension is given by the ratio of the partition function with a twisted boundary condition in one direction and periodic boundary conditions in all other directions over the partition function with periodic boundary conditions in all directions. With the Wang-Landau algorithm we can explicitly calculate both partition functions and obtain the result for all temperatures. We find solid numerical evidence for perfect wetting. Our algorithm is tested by calculating thermodynamic quantities at the phase transition point.
Numerical study of Potts models with aperiodic modulations: influence on first-order transitions
Branco, Nilton; Girardi, Daniel
2012-02-01
We perform a numerical study of Potts models on a rectangular lattice with aperiodic interactions along one spatial direction. The number of states q is such that the transition is a first-order one for the uniform model. The Wolff algorithm is employed, for many lattice sizes, allowing for a finite-size scaling analyses to be carried out. Three different self-dual aperiodic sequences are employed, such that the exact critical temperature is known: this leads to precise results for the exponents. We analyze models with q=6 and 15 and show that the Harris-Luck criterion, originally introduced in the study of continuous transitions, is obeyed also for first-order ones. The new universality class that emerges for relevant aperiodic modulations depends on the number of states of the Potts model, as obtained elsewhere for random disorder, and on the aperiodic sequence. We determine the occurrence of log-periodic behavior, as expected for models with aperiodic modulated interactions.
Cumulants of the three-state Potts model and of nonequilibrium models with C{sub 3v} symmetry
Energy Technology Data Exchange (ETDEWEB)
Tome, Tania [Instituto de Fisica, Universidade de Sao Paulo, Sao Paulo, SP (Brazil); Petri, Alberto [Istituto di Acustica O M Corbino, Consiglio Nazionale delle Ricerche, Via del Fosso del Cavaliere, Rome (Italy)
2002-07-05
The critical behaviour of two-dimensional stochastic lattice gas models with C{sub 3v} symmetry is analysed. We study the cumulants of the order parameter for the three-state (equilibrium) Potts model and for two irreversible models whose dynamic rules are invariant under the symmetry operations of the point group C{sub 3v}. By means of extensive numerical analysis of the phase transition we show that irreversibility does not affect the critical behaviour of the systems. In particular, we find that the Binder reduced fourth-order cumulant takes a universal value U* which is the same for the three-state Potts model and for the irreversible models. The same universal behaviour is observed for the reduced third-order cumulant. (author)
Roan, Shi-shyr
2010-01-01
We study the eigenvector problem in homogeneous superintegrable chiral Potts model (CPM) by the symmetry principal. Using duality and degeneracy symmetries of $\\tau^{(2)}$-model, we construct the complete eigenvectors in superintegrable CPM for an arbitrary Onsager sector. By duality in CPM, the Bethe state and the Fabricius-McCoy current for a sector in $\\tau^{(2)}$-model are constructed by employing algebraic-Bethe-ansatz techniques on its equivalent XXZ chain. The algebra-generators for the $sl_2$-loop-algebra symmetry of a $\\tau^{(2)}$-sector are determined by the Fabricius-McCoy current. Together with the loop-algebra and Onsager-algebra symmetries, we obtain the local-vector representation of $\\tau^{(2)}$- and CPM-eigenvectors. In this paper we also present the complete and precise constraints of quantum numbers for $\\tau^{(2)}$-sectors. By examining the relationship between solutions of Bethe equations, a new reflective symmetry, besides the duality relation, is found in the superintegrable $\\tau^{(2)}...
Fermat Surface and Group Theory in Symmetry of Rapidity Family in Chiral Potts Model
Roan, Shi-shyr
2013-01-01
The present paper discusses various mathematical aspects about the rapidity symmetry in chiral Potts model (CPM) in the context of algebraic geometry and group theory . We re-analyze the symmetry group of a rapidity curve in $N$-state CPM, explore the universal group structure for all $N$, and further enlarge it to modular symmetries of the complete rapidity family in CPM. As will be shown in the article that all rapidity curves in $N$-state CPM constitute a Fermat hypersurface in $\\PZ^3$ of degree 2N as the natural generalization of the Fermat K3 elliptic surface $(N=2)$, we conduct a thorough algebraic geometry study about the rapidity fibration of Fermat surface and its reduced hyperelliptic fibration via techniques in algebraic surface theory. Symmetries of rapidity family in CPM and hyperelliptic family in $\\tau^{(2)}$-model are exhibited through the geometrical representation of the universal structural group in mathematics.
Reexamination of the long-range Potts model: a multicanonical approach.
Reynal, S; Diep, H T
2004-02-01
We investigate the critical behavior of the one-dimensional q-state Potts model with long-range (LR) interactions 1/r(d+sigma), using a multicanonical algorithm. The recursion scheme initially proposed by Berg is improved so as to make it suitable for a large class of LR models with unequally spaced energy levels. The choice of an efficient predictor and a reliable convergence criterion is discussed. We obtain transition temperatures in the first-order regime which are in far better agreement with mean-field predictions than in previous Monte Carlo studies. By relying on the location of spinodal points and resorting to scaling arguments, we determine the threshold value sigma(c)(q) separating the first- and second-order regimes to two-digit precision within the range 3sigma(c)(q)sigma<1.2, thus lending strong support to Sak's scenario.
High-precision percolation thresholds and Potts-model critical manifolds from graph polynomials
>Jesper Lykke Jacobsen,
2014-04-01
The critical curves of the q-state Potts model can be determined exactly for regular two-dimensional lattices G that are of the three-terminal type. This comprises the square, triangular, hexagonal and bow-tie lattices. Jacobsen and Scullard have defined a graph polynomial PB(q, v) that gives access to the critical manifold for general lattices. It depends on a finite repeating part of the lattice, called the basis B, and its real roots in the temperature variable v = eK - 1 provide increasingly accurate approximations to the critical manifolds upon increasing the size of B. Using transfer matrix techniques, these authors computed PB(q, v) for large bases (up to 243 edges), obtaining determinations of the ferromagnetic critical point vc > 0 for the (4, 82), kagome, and (3, 122) lattices to a precision (of the order 10-8) slightly superior to that of the best available Monte Carlo simulations. In this paper we describe a more efficient transfer matrix approach to the computation of PB(q, v) that relies on a formulation within the periodic Temperley-Lieb algebra. This makes possible computations for substantially larger bases (up to 882 edges), and the precision on vc is hence taken to the range 10-13. We further show that a large variety of regular lattices can be cast in a form suitable for this approach. This includes all Archimedean lattices, their duals and their medials. For all these lattices we tabulate high-precision estimates of the bond percolation thresholds pc and Potts critical points vc. We also trace and discuss the full Potts critical manifold in the (q, v) plane, paying special attention to the antiferromagnetic region v < 0. Finally, we adapt the technique to site percolation as well, and compute the polynomials PB(p) for certain Archimedean and dual lattices (those having only cubic and quartic vertices), using very large bases (up to 243 vertices). This produces the site percolation thresholds pc to a precision of the order of 10-9.
Phase diagram of a two-dimensional large- Q Potts model in an external field
Tsai, Shan-Ho; Landau, D. P.
2009-04-01
We use a two-dimensional Wang-Landau sampling algorithm to map out the phase diagram of a Q-state Potts model with Q⩽10 in an external field H that couples to one state. Finite-size scaling analyses show that for large Q the first-order phase transition point at H=0 is in fact a triple point at which three first-order phase transition lines meet. One such line is restricted to H=0; another line has H⩽0. The third line, which starts at the H=0 triple point, ends at a critical point (T,H) which needs to be located in a two-dimensional parameter space. The critical field H(Q) is positive and decreases with decreasing Q, which is in qualitative agreement with previous predictions.
Capillary wave approach to order-order fluid interfaces in the 3D three-state Potts model
Provero, P
1994-01-01
The physics of fluid interfaces between domains of different magnetization in the ordered phase of the 3D three-state Potts model is studied by means of a Monte Carlo simulation. It is shown that finite--size effects in the interface free energy are well described by the capillary wave model at two loop order, supporting the idea of the universality of this description of fluid interfaces in 3D statistical models.
Girardi, D.; Branco, N. S.
2011-06-01
We study the Potts model on a rectangular lattice with aperiodic modulations in its interactions along one direction. Numerical results are obtained using the Wolff algorithm and for many lattice sizes, allowing for a finite-size scaling analyses to be carried out. Three different self-dual aperiodic sequences are employed, which leads to more precise results, since the exact critical temperature is known. We analyze two models, with 6 and 15 number of states: both present first-order transitions on their uniform versions. We show that the Harris-Luck criterion, originally introduced in the study of continuous transitions, is obeyed also for first-order ones. Also, we show that the new universality class that emerges for relevant aperiodic modulations depends on the number of states of the Potts model, as obtained elsewhere for random disorder, and on the aperiodic sequence. We determine the occurrence of log-periodic behavior, as expected for models with aperiodic modulated interactions.
Random-field Potts model for the polar domains of lead magnesium niobate and lead scandium tantalate
Energy Technology Data Exchange (ETDEWEB)
Qian, H.; Bursill, L.A
1997-06-01
A random filed Potts model is used to establish the spatial relationship between the nanoscale distribution of charges chemical defects and nanoscale polar domains for the perovskite-based relaxor materials lead magnesium niobate (PMN) and lead scandium tantalate (PST). The random fields are not set stochastically but are determined initially by the distribution of B-site cations (Mg, Nb) or (Sc, Ta) generated by Monte Carlo NNNI-model simulations for the chemical defects. An appropriate random field Potts model is derived and algorithms developed for a 2D lattice. It is shown that the local fields are strongly correlated with the chemical domain walls and that polar domains as a function of decreasing temperature is simulated for the two cases of PMN and PST. The dynamics of the polar clusters is also discussed. 33 refs., 9 figs.
Yang-Lee zeros of the two- and three-state Potts model defined on phi3 Feynman diagrams.
de Albuquerque, Luiz C; Dalmazi, D
2003-06-01
We present both analytical and numerical results on the position of partition function zeros on the complex magnetic field plane of the q=2 state (Ising) and the q=3 state Potts model defined on phi(3) Feynman diagrams (thin random graphs). Our analytic results are based on the ideas of destructive interference of coexisting phases and low temperature expansions. For the case of the Ising model, an argument based on a symmetry of the saddle point equations leads us to a nonperturbative proof that the Yang-Lee zeros are located on the unit circle, although no circle theorem is known in this case of random graphs. For the q=3 state Potts model, our perturbative results indicate that the Yang-Lee zeros lie outside the unit circle. Both analytic results are confirmed by finite lattice numerical calculations.
Murtazaev, Akai K.; Babaev, Albert B.; Magomedov, Magomed A.; Kassan-Ogly, Felix A.; Proshkin, Alexey I.
2016-11-01
Using Monte Carlo simulations, we investigated phase transitions and frustrations in the three-state Potts model on a triangular lattice with allowance for antiferromagnetic exchange interactions between nearest-neighbors J1 and next-nearest-neighbors J2. The ratio of the next-nearest-neighbor and nearest-neighbor exchange constants r=J2/J1 is chosen within the range of 0≤r≤2. Based on the analysis of the entropy, specific heat, system state density function, and fourth order Binder cumulants, the phase transitions in the Potts model with interactions J1<0 and J2<0 are shown to be found in value ranges of 0≤r<0.2 and 1.25≤r≤2.0. In an intermediate range of 0.2≤r≤1.0 the phase transition fails and the frustrations are revealed.
Reconstruction of a real world social network using the Potts model and Loopy Belief Propagation
Directory of Open Access Journals (Sweden)
Cristian eBisconti
2015-11-01
Full Text Available The scope of this paper is to test the adoption of a statistical model derived from Condensed Matter Physics, aiming at the reconstruction of a networked structure from observations of the states of the nodes in the network.The inverse Potts model, normally applied to observations of quantum states, is here addressed to observations of the node states in a network and their (anticorrelations, thus inferring interactions as links connecting the nodes. Adopting the Bethe approximation, such an inverse problem is known to be tractable.Within this operational framework, we discuss and apply this network-reconstruction method to a small real-world social network, where it is easy to track statuses of its members: the Italian parliament, adopted as a case study. The dataset is made of (cosponsorships of law proposals by parliament members. In previous studies of similar activity-based networks, the graph structure was inferred directly from activity co-occurrences: here we compare our statistical reconstruction with standard methods, outlining discrepancies and advantages.
Phase diagram and two-particle structure of the $Z_3$-chiral Potts model
Von Gehlen, G
1992-01-01
We calculate the low-lying part of the spectrum of the $Z_3$-symmetrical chiral Potts quantum chain in its self-dual and integrable versions, using numerical diagonalisation of the hamiltonian for $N \\leq 12$ sites and extrapolation $N \\ra \\infty$. From the sequences of levels crossing we show that the massive phases have oscillatory correlation functions. We calculate the wave vector scaling exponent. In the high-temperature massive phase the pattern of the low-lying levels can be explained assuming the existence of two particles, with $Z_3$-charge $Q\\!=\\!1$ and $Q\\!=\\!2$, and their scattering states. In the superintegrable case the $Q\\!=\\!2$-particle has twice the mass of the $Q\\!=\\!1$-particle. Exponential convergence in $N$ is observed for the single particle gaps, while power convergence is seen for the scattering levels. In the high temperature limit of the self-dual model the parity violation in the particle dispersion relation is equivalent to the presence of a macroscopic momentum $P_m = \\pm \\vph/3$,...
Competitive heterogeneous nucleation onto a microscopic impurity in a Potts model
Asuquo, Cletus C.; McArthur, Danielle; Bowles, Richard K.
2016-08-01
Many metastable systems can nucleate to multiple competing stable or intermediate metastable states. In this work, a Potts model, subject to external fields, is used to study the competitive nucleation of two phases attempting to grow on a microscopic impurity. Monte Carlo simulations are used to calculate the free energy surfaces for the system under different conditions, where the relative stability of the phases is adjusted by changing the interaction parameters, and the nucleation rates obtained using multicomponent transition state theory (TST) are compared with the rates measured using the survival probability method. We find that the two methods predict similar nucleation rates when the free energy barrier used in the transition state theory is defined as the work required to form a critical embryo from the metastable phase. An analysis of the free energy surfaces also reveals that the competition between the nucleating phases leads to an effective drying of the impurity which slows down the nucleation rate compared to the single phase case.
Murase, Yohsuke; Ito, Nobuyasu
2008-01-01
Values of dynamic critical exponents are numerically estimated for various models with the nonequilibrium relaxation method to test the dynamic universality hypothesis. The dynamics used here are single-spin update with Metropolis-type transition probabities. The estimated values of nonequilibrium relaxation exponent of magnetization λm (=β/zν) of Ising models on bcc and fcc lattices are estimated to be 0.251(3) and 0.252(3), respectively, which are consistent with the value of the model on simple-cubic lattice, 0.250(2). The dynamic critical exponents of three-states Potts models on square, honeycomb and triangular lattices are also estimated to be 2.193(5), 2.198(4), and 2.199(3), respectively. They are consistent within the error bars. It is also confirmed that Ising models with regularly modulated coupling constants on square lattice have the same dynamic critical exponents with the uniformly ferromagnetic Ising model.
Komura, Yukihiro
2012-01-01
We present the multiple GPU computing with the common unified device architecture (CUDA) for the Swendsen-Wang multi-cluster algorithm of two-dimensional (2D) q-state Potts model. Extending our algorithm for single GPU computing [Comp. Phys. Comm. 183 (2012) 1155], we realize the GPU computation of the Swendsen-Wang multi-cluster algorithm for multiple GPUs. We implement our code on the large-scale open science supercomputer TSUBAME 2.0, and test the performance and the scalability of the simulation of the 2D Potts model. The performance on Tesla M2050 using 256 GPUs is obtained as 37.3 spin flips per a nano second for the q=2 Potts model (Ising model) at the critical temperature with the linear system size L=65536.
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.
Barton, J. P.; Cocco, S.; De Leonardis, E.; Monasson, R.
2014-07-01
The mean-field (MF) approximation offers a simple, fast way to infer direct interactions between elements in a network of correlated variables, a common, computationally challenging problem with practical applications in fields ranging from physics and biology to the social sciences. However, MF methods achieve their best performance with strong regularization, well beyond Bayesian expectations, an empirical fact that is poorly understood. In this work, we study the influence of pseudocount and L2-norm regularization schemes on the quality of inferred Ising or Potts interaction networks from correlation data within the MF approximation. We argue, based on the analysis of small systems, that the optimal value of the regularization strength remains finite even if the sampling noise tends to zero, in order to correct for systematic biases introduced by the MF approximation. Our claim is corroborated by extensive numerical studies of diverse model systems and by the analytical study of the m-component spin model for large but finite m. Additionally, we find that pseudocount regularization is robust against sampling noise and often outperforms L2-norm regularization, particularly when the underlying network of interactions is strongly heterogeneous. Much better performances are generally obtained for the Ising model than for the Potts model, for which only couplings incoming onto medium-frequency symbols are reliably inferred.
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).
Ding, Chengxiang; Fu, Zhe; Guo, Wenan; Wu, F Y
2010-06-01
In the preceding paper, one of us (F. Y. Wu) considered the Potts model and bond and site percolation on two general classes of two-dimensional lattices, the triangular-type and kagome-type lattices, and obtained closed-form expressions for the critical frontier with applications to various lattice models. For the triangular-type lattices Wu's result is exact, and for the kagome-type lattices Wu's expression is under a homogeneity assumption. The purpose of the present paper is twofold: First, an essential step in Wu's analysis is the derivation of lattice-dependent constants A,B,C for various lattice models, a process which can be tedious. We present here a derivation of these constants for subnet networks using a computer algorithm. Second, by means of a finite-size scaling analysis based on numerical transfer matrix calculations, we deduce critical properties and critical thresholds of various models and assess the accuracy of the homogeneity assumption. Specifically, we analyze the q -state Potts model and the bond percolation on the 3-12 and kagome-type subnet lattices (n×n):(n×n) , n≤4 , for which the exact solution is not known. Our numerical determination of critical properties such as conformal anomaly and magnetic correlation length verifies that the universality principle holds. To calibrate the accuracy of the finite-size procedure, we apply the same numerical analysis to models for which the exact critical frontiers are known. The comparison of numerical and exact results shows that our numerical values are correct within errors of our finite-size analysis, which correspond to 7 or 8 significant digits. This in turn infers that the homogeneity assumption determines critical frontiers with an accuracy of 5 decimal places or higher. Finally, we also obtained the exact percolation thresholds for site percolation on kagome-type subnet lattices (1×1):(n×n) for 1≤n≤6 .
Kauffman Knot Invariant from SO(N) or Sp(N) Chern-Simons theory and the Potts Model
Astorino, Marco
2010-01-01
The expectation value of Wilson loop operators in three-dimensional SO(N) Chern-Simons gauge theory gives a known knot invariant: the Kauffman polynomial. Here this result is derived, at the first order, via a simple variational method. With the same procedure the skein relation for Sp(N) are also obtained. Jones polynomial arises as special cases: Sp(2), SO(-2) and SL(2,R). These results are confirmed and extended up to the second order, by means of perturbation theory, which moreover let us establish a duality relation between SO(+/-N) and Sp(-/+N) invariants. A correspondence between the firsts orders in perturbation theory of SO(-2), Sp(2) or SU(2) Chern-Simons quantum holonomies and the partition function of the Q=4 Potts Model is built.
Multi-particle structure in the Z_n-chiral Potts models
Von Gehlen, G
1993-01-01
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 to infinity. 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 = Q m_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 ...
Nucleation in a Potts lattice gas model of crystallization from solution
Duff, Nathan; Peters, Baron
2009-11-01
Nucleation from solution is important in many pharmaceutical crystallization, biomineralization, material synthesis, and self-assembly processes. Simulation methodology has progressed rapidly for studies of nucleation in pure component and implicit solvent systems; however little progress has been made in the simulation of explicit solvent systems. The impasse stems from the inability of rare events simulation methodology to be combined with simulation techniques which maintain a constant chemical potential driving force (supersaturation) for nucleation. We present a Potts lattice gas (PLG) to aid in the development of new simulation strategies for nucleation from solution. The PLG captures common crystallization phase diagram features such as a eutectic point and solute/solvent melting points. Simulations of the PLG below the bulk solute melting temperature reveal a competition between amorphous and crystalline nuclei. As the temperature is increased toward the bulk melting temperature, the nucleation pathway changes from a one step crystalline nucleation pathway to a two step pathway, where an amorphous nucleus forms and then crystallizes. We explain these results in terms of classical nucleation theory with different size-dependant chemical potentials for the amorphous and crystalline nucleation pathways. The two step pathway may be particularly important when crystallization is favored only at postcritical sizes.
Monceau, Pascal
2006-09-01
The extension of the phase diagram of the q -state Potts model to noninteger dimension is investigated by means of Monte Carlo simulations on Sierpinski and Menger fractal structures. Both multicanonical and canonical simulations have been carried out with the help of the Wang-Landau and the Wolff cluster algorithms. Lower bounds are provided for the critical values qc of q where a first-order transition is expected in the cases of two structures whose fractal dimension is smaller than 2: The transitions associated with the seven-state and ten-state Potts models on Sierpinski carpets with fractal dimensions df≃1.8928 and df≃1.7925 , respectively, are shown to be second-order ones, the renormalization eigenvalue exponents yh are calculated, and bounds are provided for the renormalization eigenvalue exponents yt and the critical temperatures. Moreover, the results suggest that second-order transitions are expected to occur for very large values of q when the fractal dimension is lowered below 2—that is, in the case of hierarchically weakly connected systems with an infinite ramification order. At last, the transition associated with the four-state Potts model on a fractal structure with a dimension df≃2.631 is shown to be a weakly first-order one.
Murtazaev, A. K.; Babaev, A. B.; Aznaurova, G. Ya.
2008-04-01
The influence of quenched nonmagnetic impurities on phase transitions in the three-dimensional Potts model with the number of spin states q = 3 is investigated using the Wolff single-cluster algorithm of the Monte Carlo method. The systems with linear sizes L = 20-44 at the spin concentrations p = 1.0, 0.9, 0.8, and 0.7 are analyzed. It is demonstrated with the use of the method of fourth-order Binder cumulants that the second-order phase transition occurs in the model under consideration at the spin concentrations p = 0.9, 0.8, and 0.7 and that the first-order phase transition is observed in the pure model ( p = 1.0). The static critical exponents α (heat capacity), γ (susceptibility), β (magnetization), and ν (correlation length) are calculated in the framework of the finite-size scaling theory. The problem regarding the universality classes of the critical behavior of weakly diluted systems is discussed.
On Dynamical Systems and Phase Transitions for q + 1-state p-adic Potts Model on the Cayley Tree
Energy Technology Data Exchange (ETDEWEB)
Mukhamedov, Farrukh, E-mail: far75m@yandex.ru [International Islamic University Malaysia, Department of Computational and Theoretical Sciences, Faculty of Science (Malaysia)
2013-03-15
In the present paper, we study a new kind of p-adic measures for q + 1-state Potts model, called p-adic quasi Gibbs measure. For such a model, we derive a recursive relations with respect to boundary conditions. Note that we consider two mode of interactions: ferromagnetic and antiferromagnetic. In both cases, we investigate a phase transition phenomena from the associated dynamical system point of view. Namely, using the derived recursive relations we define a fractional p-adic dynamical system. In ferromagnetic case, we establish that if q is divisible by p, then such a dynamical system has two repelling and one attractive fixed points. We find basin of attraction of the fixed point. This allows us to describe all solutions of the nonlinear recursive equations. Moreover, in that case there exists the strong phase transition. If q is not divisible by p, then the fixed points are neutral, and this yields that the existence of the quasi phase transition. In antiferromagnetic case, there are two attractive fixed points, and we find basins of attraction of both fixed points, and describe solutions of the nonlinear recursive equation. In this case, we prove the existence of a quasi phase transition.
Energy Technology Data Exchange (ETDEWEB)
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.
Komura, Yukihiro
2014-01-01
We present sample CUDA programs for the GPU computing of the Swendsen-Wang multi-cluster spin flip algorithm. We deal with the classical spin models; the Ising model, the $q$-state Potts model, and the classical XY model. As for the lattice, both the 2D (square) lattice and the 3D (simple cubic) lattice are treated. We already reported the idea of the GPU implementation for 2D models [Comput. Phys. Commun. 183 (2012) 1155-1161]. We here explain the details of sample programs, and discuss the performance of the present GPU implementation for the 3D Ising and XY models. We also show the calculated results of the moment ratio for these models, and discuss phase transitions.
A Cellular Potts Model simulating cell migration on and in matrix environments
Scianna, M.; Preziosi, L.; Wolf, K.A.
2013-01-01
Cell migration on and through extracellular matrix is fundamental in a wide variety of physiological and pathological phenomena, and is exploited in scaffold-based tissue engineering. Migration is regulated by a number of extracellular matrix- or cell-derived biophysical parameters, such as matrix f
Quantitative characterization of morphological evolution in Q=2 Potts model aluminum thin films
Alsem, DH; Stach, EA; de Hosson, JTM; Aziz, MJ; Bartelt, NC; Berbezier,; Hannon, JB; Hearne, SJ
2003-01-01
In this research, we have focused on the morphological evolution of a model metal film / silicon substrate system. When aluminum (Al) is physical vapor deposited on (100) oriented single crystal silicon (Si) at 280degreesC it grows heteroepitaxially. Crystallographically, the resulting films are a P
Testing Conformal Theory:. 3-STATE Potts
Barkema, G. T.; McCabe, J.; Wydro, T.
2001-04-01
Conformal theory predictions and Monte Carlo measurements of structure constants in 3-state Potts model were reviewed. The results provide a direct confirmation of the quality of conformal theory predictions of universal 3-point amplitudes. The prediction of these type of universal amplitudes sparked much of the original interest in conformal models, but are almost untested outside of the Ising model. Structure constants, C123, are universal amplitudes that define 3-point correlations, i.e., = C123/ |X12|2(Δ1+Δ2-Δ3)·× cyclic perms. To predict the values of these universal numbers, one constructs a 4-point correlation as a sum of products of conformal blocks and then, determines coefficients that weight the sum by demanding that the 4-point correlation satisfy a bootstrap equation. The bootstrap equation imposes consistency of the 4-point correlation with operator product expansions in multiple channels. The 3-state Potts model was chosen, because this model is easy of simulate. But, this Potts model has an added complication, i.e., a discrete Z3 symmetry at criticality. The discrete symmetry had to be implemented to calculate structure constants. Conformal theory predicted that Cσσσ = 1.092 and Cɛσσ* = 0.546. Monte Carlo simulations were performed on 500 × 500 lattices on which sample configurations were generated by the cluster algorithm of Wolff. To obtain the structure constants both 2-point and 3-point correlations were measured. The 2-point correlations fixed non-universal normalizatons. The quality of the Monte-Carlo methods were tested by measuring structure constants of the Ising model-good agreement with known results was found. For 3-state Potts, the simulations found that Cσσσ = 1.116 ± 0.14 and Cɛσσ* = 0.61 ± 0.06. These results provide striking agreement with predictions and a confirmation of conformal field theory.
Energy Technology Data Exchange (ETDEWEB)
Andrade, Pedro H.A. de; Cabral, Manuela O.M., E-mail: andrade.pha@gmail.com [Universidade Federal de Pernambuco (DEN/UFPE), Recife, PE (Brazil). Departamento de Engenharia Nuclear; Vieira, Jose W.; Correia, Filipe L. de B., E-mail: jose.wilson59@uol.com.br [Instituto Federal de Educacao, Ciencia e Tecnologia de Pernambuco (IFPE), Recife, PE (Brazil); Lima, Fernando R. De A., E-mail: falima@cnen.gov.br [Centro Regional de Ciencias Nucleares do Nordeste (CRCN-NE/CNEN-PE), Recife, PE (brazil)
2015-07-01
Exposure Computational Models are composed basically of an anthropomorphic phantom, a Monte Carlo (MC) code, and an algorithm simulator of the radioactive source. Tomographic phantoms are developed from medical images and must be pre-processed and segmented before being coupled to a MC code (which simulates the interaction of radiation with matter). This work presents a methodology used for treatment of micro-CT images stack of a femur, obtained from a 30 year old female skeleton provided by the Imaging Laboratory for Anthropology of the University of Bristol, UK. These images contain resolution of 60 micrometers and from these a block containing only 160 x 60 x 160 pixels of trabecular tissues and bone marrow was cut and saved as ⁎.sgi file (header + ⁎.raw file). The Grupo de Dosimetria Numerica (Recife-PE, Brazil) developed a software named Digital Image Processing (DIP), in which a method for segmentation based on a physical model for particle interaction known as Potts Model (or q-Ising) was implemented. This model analyzes the statistical dependence between sites in a network. In Potts Model, when the values of spin variables at neighboring sites are identical, it is assigned an 'energy of interaction' between them. Otherwise, it is said that the sites do not interact. Making an analogy between network sites and the pixels of a digital image and, moreover, between the spins variables and the intensity of the gray scale, it was possible to apply this model to obtain texture descriptors and segment the image. (author)
Gautam, M P; Karki, P; Rijal, S; Singh, R
2005-01-01
Spinal tuberculosis is usually secondary to lung or abdominal involvement and may also be the first manifestation of tuberculosis. Spinal tuberculosis (often called Pott's disease) is by definition, an advanced disease, requiring meticulous assessment and aggressive systemic therapy. Physicians should keep the diagnosis in mind, especially in a patient from a group with a high rate of tuberculosis infection. This review aims on updating the knowledge on spinal tuberculosis and its management. Skeletal involvement has been reported to occur in approximately 10% of all patents with extrapulmonary tuberculosis, and half of these patients develop infection within the spinal column. Symptoms of spinal tuberculosis are back pain, weakness, weight loss, fever, fatigue, and malaise. It is much more prone to develop neurological manifestation, paraplegia of varying degree. The palpation of spinous process in routine clinical examination is the most rewarding clinical method and is an invaluable measure for early recognition. Diagnosis of spinal tuberculosis is made on the basis of typical clinical presentation along with systemic constitutional manifestation and the evidence of past exposure to tuberculosis or concomitant visceral tuberculosis. Magnetic resonance imaging can define the extent of abscess formation and spinal cord compression. The diagnosis is confirmed through percutaneous or open biopsy of the spinal lesion. Surgery is necessary as an adjunct to antibiotic therapy if the vertebral infection produces an abscess, vertebral collapse, or neurologic compression. Some patents need aggressive supportive care owing to tuberculous meningitis or encephalopathy. Moreover, the importance of immediate commencement of appropriate treatment and its continuation for adequate duration along with the proper counseling of the patient and family members should not be underestimated for successful and desired outcome.
Cellular models for Parkinson's disease.
Falkenburger, Björn H; Saridaki, Theodora; Dinter, Elisabeth
2016-10-01
Developing new therapeutic strategies for Parkinson's disease requires cellular models. Current models reproduce the two most salient changes found in the brains of patients with Parkinson's disease: The degeneration of dopaminergic neurons and the existence of protein aggregates consisting mainly of α-synuclein. Cultured cells offer many advantages over studying Parkinson's disease directly in patients or in animal models. At the same time, the choice of a specific cellular model entails the requirement to focus on one aspect of the disease while ignoring others. This article is intended for researchers planning to use cellular models for their studies. It describes for commonly used cell types the aspects of Parkinson's disease they model along with technical advantages and disadvantages. It might also be helpful for researchers from other fields consulting literature on cellular models of Parkinson's disease. Important models for the study of dopaminergic neuron degeneration include Lund human mesencephalic cells and primary neurons, and a case is made for the use of non-dopaminergic cells to model pathogenesis of non-motor symptoms of Parkinson's disease. With regard to α-synuclein aggregates, this article describes strategies to induce and measure aggregates with a focus on fluorescent techniques. Cellular models reproduce the two most salient changes of Parkinson's disease, the degeneration of dopaminergic neurons and the existence of α-synuclein aggregates. This article is intended for researchers planning to use cellular models for their studies. It describes for commonly used cell types and treatments the aspects of Parkinson's disease they model along with technical advantages and disadvantages. Furthermore, this article describes strategies to induce and measure aggregates with a focus on fluorescent techniques. This article is part of a special issue on Parkinson disease.
Vernier, Eric
2011-01-01
We obtain long series expansions for the bulk, surface and corner free energies for several two-dimensional statistical models, by combining Enting's finite lattice method (FLM) with exact transfer matrix enumerations. The models encompass all integrable curves of the Q-state Potts model on the square and triangular lattices, including the antiferromagnetic transition curves and the Ising model (Q=2) at temperature T, as well as a fully-packed O(n) type loop model on the square lattice. The expansions are around the trivial fixed points at infinite Q, n or 1/T. By using a carefully chosen expansion parameter, q << 1, all expansions turn out to be of the form \\prod_{k=1}^\\infty (1-q^k)^{\\alpha_k + k \\beta_k}, where the coefficients \\alpha_k and \\beta_k are periodic functions of k. Thanks to this periodicity property we can conjecture the form of the expansions to all orders (except in a few cases where the periodicity is too large). These expressions are then valid for all 0 <= q < 1. We analyse in...
Mathematical Modeling of Cellular Metabolism.
Berndt, Nikolaus; Holzhütter, Hermann-Georg
2016-01-01
Cellular metabolism basically consists of the conversion of chemical compounds taken up from the extracellular environment into energy (conserved in energy-rich bonds of organic phosphates) and a wide array of organic molecules serving as catalysts (enzymes), information carriers (nucleic acids), and building blocks for cellular structures such as membranes or ribosomes. Metabolic modeling aims at the construction of mathematical representations of the cellular metabolism that can be used to calculate the concentration of cellular molecules and the rates of their mutual chemical interconversion in response to varying external conditions as, for example, hormonal stimuli or supply of essential nutrients. Based on such calculations, it is possible to quantify complex cellular functions as cellular growth, detoxification of drugs and xenobiotic compounds or synthesis of exported molecules. Depending on the specific questions to metabolism addressed, the methodological expertise of the researcher, and available experimental information, different conceptual frameworks have been established, allowing the usage of computational methods to condense experimental information from various layers of organization into (self-) consistent models. Here, we briefly outline the main conceptual frameworks that are currently exploited in metabolism research.
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.
Cellular automata modelling of SEIRS
Institute of Scientific and Technical Information of China (English)
Liu Quan-Xing; Jin Zhen
2005-01-01
In this paper the SEIRS epidemic spread is analysed, and a two-dimensional probability cellular automata model for SEIRS is presented. Each cellular automation cell represents a part of the population that may be found in one of five states of individuals: susceptible, exposed (or latency), infected, immunized (or recovered) and death. Here studied are the effects of two cases on the epidemic spread. i.e. the effects of non-segregation and segregation on the latency and the infected of population. The conclusion is reached that the epidemic will persist in the case of non-segregation but it will decrease in the case of segregation. The proposed model can serve as a basis for the development of algorithms to simulate real epidemics based on real data. Last we find the density series of the exposed and the infected will fluctuate near a positive equilibrium point, when the constant for the immunized is less than its corresponding constant τ0. Our theoretical results are verified by numerical simulations.
Cellular systems biology profiling applied to cellular models of disease.
Giuliano, Kenneth A; Premkumar, Daniel R; Strock, Christopher J; Johnston, Patricia; Taylor, Lansing
2009-11-01
Building cellular models of disease based on the approach of Cellular Systems Biology (CSB) has the potential to improve the process of creating drugs as part of the continuum from early drug discovery through drug development and clinical trials and diagnostics. This paper focuses on the application of CSB to early drug discovery. We discuss the integration of protein-protein interaction biosensors with other multiplexed, functional biomarkers as an example in using CSB to optimize the identification of quality lead series compounds.
Cellular Automaton Modeling of Pattern Formation
Boerlijst, M.C.
2006-01-01
Book review Andreas Deutsch and Sabine Dormann, Cellular Automaton Modeling of Biological Pattern Formation, Characterization, Applications, and Analysis, Birkhäuser (2005) ISBN 0-8176-4281-1 331pp..
Potts disease: Diagnosis with magnetic resonance imaging
Energy Technology Data Exchange (ETDEWEB)
Pursey, Jacqueline [MRI Department, Gartnavel General Hospitial, 1053 Great Western road, Glasgow G12 0YN (United Kingdom)], E-mail: Jacqueline.pursey@ggc.scot.nhs.uk; Stewart, Sharon [School of Health and Social Care, Caledonian University, Glasgow (United Kingdom)
2010-02-15
The eponymously named Potts disease is a relatively rare form of Tuberculosis (TB) which affects the spine. TB of the spine is one of the earliest diseases known to man and in the 20th century was thought to be a disease which had been defeated by the advent of antitubercular drugs. Over the last two decades there have been several reports which indicate a revival of TB in both the developing and developed world. Factors which may be contributing to this are the spread of the HIV virus, increased immigration and the emergence of drug resistant strains of the TB bacteria. Potts disease has an insidious onset and often the radiographic findings are far advanced when a diagnosis is finally reached. MRI is able to detect changes to the vertebrae in Potts disease earlier than radiographs. This case report outlines the clinical presentation of a young male with Potts disease who was HIV negative, and the important role that MRI plays in diagnosis and therefore in appropriate and timely intervention. The typical magnetic resonance (MR) imaging features and the radiographic hallmarks of the disease will also be discussed.
A Modified Sensitive Driving Cellular Automaton Model
Institute of Scientific and Technical Information of China (English)
GE Hong-Xia; DAI Shi-Qiang; DONG Li-Yun; LEI Li
2005-01-01
A modified cellular automaton model for traffic flow on highway is proposed with a novel concept about the variable security gap. The concept is first introduced into the original Nagel-Schreckenberg model, which is called the non-sensitive driving cellular automaton model. And then it is incorporated with a sensitive driving NaSch model,in which the randomization brake is arranged before the deterministic deceleration. A parameter related to the variable security gap is determined through simulation. Comparison of the simulation results indicates that the variable security gap has different influence on the two models. The fundamental diagram obtained by simulation with the modified sensitive driving NaSch model shows that the maximumflow are in good agreement with the observed data, indicating that the presented model is more reasonable and realistic.
Cellular automata modeling of pedestrian's crossing dynamics
Institute of Scientific and Technical Information of China (English)
张晋; 王慧; 李平
2004-01-01
Cellular automata modeling techniques and the characteristics of mixed traffic flow were used to derive the 2-dimensional model presented here for simulation of pedestrian's crossing dynamics.A conception of "stop point" is introduced to deal with traffic obstacles and resolve conflicts among pedestrians or between pedestrians and the other vehicles on the crosswalk.The model can be easily extended,is very efficient for simulation of pedestrian's crossing dynamics,can be integrated into traffic simulation software,and has been proved feasible by simulation experiments.
Cellular automata models for synchronized traffic flow
Jiang Rui
2003-01-01
This paper presents a new cellular automata model for describing synchronized traffic flow. The fundamental diagrams, the spacetime plots and the 1 min average data have been analysed in detail. It is shown that the model can describe the outflow from the jams, the light synchronized flow as well as heavy synchronized flow with average speed greater than approximately 24 km h sup - sup 1. As for the synchronized flow with speed lower than 24 km h sup - sup 1 , it is unstable and will evolve into the coexistence of jams, free flow and light synchronized flow. This is consistent with the empirical findings (Kerner B S 1998 Phys. Rev. Lett. 81 3797).
Cellular automata modelling of hantarvirus infection
Energy Technology Data Exchange (ETDEWEB)
Abdul Karim, Mohamad Faisal [School of Distance Education, Universiti Sains Malaysia, Minden 11800, Penang (Malaysia)], E-mail: faisal@usm.my; Md Ismail, Ahmad Izani [School of Mathematical Sciences, Universiti Sains Malaysia, Minden 11800, Penang (Malaysia)], E-mail: izani@cs.usm.my; Ching, Hoe Bee [School of Mathematical Sciences, Universiti Sains Malaysia, Minden 11800, Penang (Malaysia)], E-mail: Bee_Ching_Janice_Hoe@dell.com
2009-09-15
Hantaviruses are a group of viruses which have been identified as being responsible for the outbreak of diseases such as the hantavirus pulmonary syndrome. In an effort to understand the characteristics and dynamics of hantavirus infection, mathematical models based on differential equations have been developed and widely studied. However, such models neglect the local characteristics of the spreading process and do not include variable susceptibility of individuals. In this paper, we develop an alternative approach based on cellular automata to analyze and study the spatiotemporal patterns of hantavirus infection.
Cellular Automata Model for Elastic Solid Material
Institute of Scientific and Technical Information of China (English)
DONG Yin-Feng; ZHANG Guang-Cai; XU Ai-Guo; GAN Yan-Biao
2013-01-01
The Cellular Automaton (CA) modeling and simulation of solid dynamics is a long-standing difficult problem.In this paper we present a new two-dimensional CA model for solid dynamics.In this model the solid body is represented by a set of white and black particles alternatively positioned in the x-and y-directions.The force acting on each particle is represented by the linear summation of relative displacements of the nearest-neighboring particles.The key technique in this new model is the construction of eight coefficient matrices.Theoretical and numerical analyses show that the present model can be mathematically described by a conservative system.So,it works for elastic material.In the continuum limit the CA model recovers the well-known Navier equation.The coefficient matrices are related to the shear module and Poisson ratio of the material body.Compared with previous CA model for solid body,this model realizes the natural coupling of deformations in the x-and y-directions.Consequently,the wave phenomena related to the Poisson ratio effects are successfully recovered.This work advances significantly the CA modeling and simulation in the field of computational solid dynamics.
Unusual Cause of Seizure: Pott Puffy Tumor.
Sade, Recep; Polat, Gokhan; Kantarci, Mecit
2016-09-01
Seizures is a comparatively common neurologic unwellness in children that has significant implications for development, parents, and society. The etiologic categories of seizures involve idiopathic, symptomatic, and cryptogenic. Pott puff tumor is a rare cause of seizures. The authors present a rare cause of the seizures.A 12-year-old boy presented with seizures. On physical examination there was swelling on his glabella. Laboratory testing indicated leukocytosis and increased C-reactive protein, and microbiological testing showed the presence of pathogenic streptococcus sp. Brain magnetic resonance imaging was performed. T1-weighted image with gadolinium enhancement revealed frontal bone defects and subcutaneous abscess and left frontal swelling. On the diffusion-weighted imaging, the abscess has relatively homogeneous increased signal intensity b1000. The apparent diffusion coefficient map reveals low intensity. Intracranial spread also showed contrast-enhanced image (). Magnetic resonance imaging typically reveals an intracranial abscess.Pott puffy tumor is an unusual clinical existence characterized by osteomyelitis of the frontal bone. The very common symptoms are headache, swelling fever, and nasal discharge. Frontal sinus infection may induce osteomyelitis, subperiosteal, and epidural abscess.
Statistical physical models of cellular motility
Banigan, Edward J.
Cellular motility is required for a wide range of biological behaviors and functions, and the topic poses a number of interesting physical questions. In this work, we construct and analyze models of various aspects of cellular motility using tools and ideas from statistical physics. We begin with a Brownian dynamics model for actin-polymerization-driven motility, which is responsible for cell crawling and "rocketing" motility of pathogens. Within this model, we explore the robustness of self-diffusiophoresis, which is a general mechanism of motility. Using this mechanism, an object such as a cell catalyzes a reaction that generates a steady-state concentration gradient that propels the object in a particular direction. We then apply these ideas to a model for depolymerization-driven motility during bacterial chromosome segregation. We find that depolymerization and protein-protein binding interactions alone are sufficient to robustly pull a chromosome, even against large loads. Next, we investigate how forces and kinetics interact during eukaryotic mitosis with a many-microtubule model. Microtubules exert forces on chromosomes, but since individual microtubules grow and shrink in a force-dependent way, these forces lead to bistable collective microtubule dynamics, which provides a mechanism for chromosome oscillations and microtubule-based tension sensing. Finally, we explore kinematic aspects of cell motility in the context of the immune system. We develop quantitative methods for analyzing cell migration statistics collected during imaging experiments. We find that during chronic infection in the brain, T cells run and pause stochastically, following the statistics of a generalized Levy walk. These statistics may contribute to immune function by mimicking an evolutionarily conserved efficient search strategy. Additionally, we find that naive T cells migrating in lymph nodes also obey non-Gaussian statistics. Altogether, our work demonstrates how physical
Weinmann, Andreas; Storath, Martin
2014-01-01
Mumford-Shah and Potts functionals are powerful variational models for regularization which are widely used in signal and image processing; typical applications are edge-preserving denoising and segmentation. Being both non-smooth and non-convex, they are computationally challenging even for scalar data. For manifold-valued data, the problem becomes even more involved since typical features of vector spaces are not available. In this paper, we propose algorithms for Mumford-Shah and for Potts regularization of manifold-valued signals and images. For the univariate problems, we derive solvers based on dynamic programming combined with (convex) optimization techniques for manifold-valued data. For the class of Cartan-Hadamard manifolds (which includes the data space in diffusion tensor imaging), we show that our algorithms compute global minimizers for any starting point. For the multivariate Mumford-Shah and Potts problems (for image regularization) we propose a splitting into suitable subproblems which we can...
Exactly solvable cellular automaton traffic jam model.
Kearney, Michael J
2006-12-01
A detailed study is undertaken of the v{max}=1 limit of the cellular automaton traffic model proposed by Nagel and Paczuski [Phys. Rev. E 51, 2909 (1995)]. The model allows one to analyze the behavior of a traffic jam initiated in an otherwise freely flowing stream of traffic. By mapping onto a discrete-time queueing system, itself related to various problems encountered in lattice combinatorics, exact results are presented in relation to the jam lifetime, the maximum jam length, and the jam mass (the space-time cluster size or integrated vehicle waiting time), both in terms of the critical and the off-critical behavior. This sets existing scaling results in their natural context and also provides several other interesting results in addition.
A cellular automata model for ant trails
Indian Academy of Sciences (India)
Sibel Gokce; Ozhan Kayacan
2013-05-01
In this study, the unidirectional ant traffic flow with U-turn in an ant trail was investigated using one-dimensional cellular automata model. It is known that ants communicate with each other by dropping a chemical, called pheromone, on the substrate. Apart from the studies in the literature, it was considered in the model that (i) ant colony consists of two kinds of ants, goodand poor-smelling ants, (ii) ants might make U-turn for some special reasons. For some values of densities of good- and poor-smelling ants, the flux and mean velocity of the colony were studied as a function of density and evaporation rate of pheromone.
Cellular Automata Models for Diffusion of Innovations
Fuks, H; Fuks, Henryk; Boccara, Nino
1997-01-01
We propose a probabilistic cellular automata model for the spread of innovations, rumors, news, etc. in a social system. The local rule used in the model is outertotalistic, and the range of interaction can vary. When the range R of the rule increases, the takeover time for innovation increases and converges toward its mean-field value, which is almost inversely proportional to R when R is large. Exact solutions for R=1 and $R=\\infty$ (mean-field) are presented, as well as simulation results for other values of R. The average local density is found to converge to a certain stationary value, which allows us to obtain a semi-phenomenological solution valid in the vicinity of the fixed point n=1 (for large t).
Cocco, Simona; Monasson, Rémi; Weigt, Martin
2013-12-01
We consider the Hopfield-Potts model for the covariation between residues in protein families recently introduced in Cocco, Monasson, Weigt (2013). The patterns of the model are inferred from the data within a new gauge, more symmetric in the residues. We compute the statistical error bars on the pattern components. Results are illustrated on real data for a response regulator receiver domain (Pfam ID PF00072) family.
Short-Time Dynamics of Random-Bond Potts Ferromagnet with Continuous Self-Dual Quenched Disorders
Institute of Scientific and Technical Information of China (English)
PAN ZhengQuan; YING HePing; CHEN MeL; GU DeWei
2002-01-01
We present our Monte Carlo results of the random-bond Potts ferromagnet with the Olson-Young self-dual distribution of quenched disorders in two dimensions. By exploring the short-time scaling dynamics, we find the universal power-law critical behavior of the magnetization and Binder cumulant at the critical point, and thus obtain estimates of the dynamic exponent z and magnetic exponent η, as well as the exponent θ. Our special attention is paid to the dynamic process for the q = 8 Potts model.
Analytical Modeling of Uplink Cellular Networks
Novlan, Thomas D; Andrews, Jeffrey G
2012-01-01
Cellular uplink analysis has typically been undertaken by either a simple approach that lumps all interference into a single deterministic or random parameter in a Wyner-type model, or via complex system level simulations that often do not provide insight into why various trends are observed. This paper proposes a novel middle way that is both accurate and also results in easy-to-evaluate integral expressions based on the Laplace transform of the interference. We assume mobiles and base stations are randomly placed in the network with each mobile pairing up to its closest base station. The model requires two important changes compared to related recent work on the downlink. First, dependence is introduced between the user and base station point processes to make sure each base station serves a single mobile in the given resource block. Second, per-mobile power control is included, which further couples the locations of the mobiles and their receiving base stations. Nevertheless, we succeed in deriving the cov...
Infinite Time Cellular Automata: A Real Computation Model
Givors, Fabien; Ollinger, Nicolas
2010-01-01
We define a new transfinite time model of computation, infinite time cellular automata. The model is shown to be as powerful than infinite time Turing machines, both on finite and infinite inputs; thus inheriting many of its properties. We then show how to simulate the canonical real computation model, BSS machines, with infinite time cellular automata in exactly \\omega steps.
Multilayer Potts perceptrons with Levenberg-Marquardt learning.
Wu, Jiann-Ming
2008-12-01
This paper presents learning multilayer Potts perceptrons (MLPotts) for data driven function approximation. A Potts perceptron is composed of a receptive field and a K -state transfer function that is generalized from sigmoid-like transfer functions of traditional perceptrons. An MLPotts network is organized to perform translation from a high-dimensional input to the sum of multiple postnonlinear projections, each with its own postnonlinearity realized by a weighted K-state transfer function. MLPotts networks span a function space that theoretically covers network functions of multilayer perceptrons. Compared with traditional perceptrons, weighted Potts perceptrons realize more flexible postnonlinear functions for nonlinear mappings. Numerical simulations show MLPotts learning by the Levenberg-Marquardt (LM) method significantly improves traditional supervised learning of multilayer perceptrons for data driven function approximation.
SEM++: A particle model of cellular growth, signaling and migration
Milde, Florian; Tauriello, Gerardo; Haberkern, Hannah; Koumoutsakos, Petros
2014-06-01
We present a discrete particle method to model biological processes from the sub-cellular to the inter-cellular level. Particles interact through a parametrized force field to model cell mechanical properties, cytoskeleton remodeling, growth and proliferation as well as signaling between cells. We discuss the guiding design principles for the selection of the force field and the validation of the particle model using experimental data. The proposed method is integrated into a multiscale particle framework for the simulation of biological systems.
Schramm Loewner evolution in the three-state Potts model—a numerical study
Gamsa, Adam; Cardy, John
2007-08-01
The scaling limit of the spin cluster boundaries of the Ising model with domain wall boundary conditions is Schramm Loewner evolution (SLE) with κ = 3. We hypothesize that the three-state Potts model with appropriate boundary conditions has spin cluster boundaries which are also SLE in the scaling limit, but with κ = 10/3. To test this, we generate samples using the Wolff algorithm and test them against predictions of SLE: we examine the statistics of the Loewner driving function, estimate the fractal dimension and test against Schramm's formula. The results are in support of our hypothesis.
Cellular modelling using P systems and process algebra
Institute of Scientific and Technical Information of China (English)
Francisco J.Romero-Campero; Marian Gheorghe; Gabriel Ciobanu; John M. Auld; Mario J. Pérez-Jiménez
2007-01-01
In this paper various molecular chemical interactions are modelled under different computational paradigms. P systems and π-calculus are used to describe intra-cellular reactions like protein-protein interactions and gene regulation control.
Modeling In Vitro Cellular Responses to Silver Nanoparticles
Directory of Open Access Journals (Sweden)
Dwaipayan Mukherjee
2014-01-01
Full Text Available Engineered nanoparticles (NPs have been widely demonstrated to induce toxic effects to various cell types. In vitro cell exposure systems have high potential for reliable, high throughput screening of nanoparticle toxicity, allowing focusing on particular pathways while excluding unwanted effects due to other cells or tissue dosimetry. The work presented here involves a detailed biologically based computational model of cellular interactions with NPs; it utilizes measurements performed in human cell culture systems in vitro, to develop a mechanistic mathematical model that can support analysis and prediction of in vivo effects of NPs. The model considers basic cellular mechanisms including proliferation, apoptosis, and production of cytokines in response to NPs. This new model is implemented for macrophages and parameterized using in vitro measurements of changes in cellular viability and mRNA levels of cytokines: TNF, IL-1b, IL-6, IL-8, and IL-10. The model includes in vitro cellular dosimetry due to nanoparticle transport and transformation. Furthermore, the model developed here optimizes the essential cellular parameters based on in vitro measurements, and provides a “stepping stone” for the development of more advanced in vivo models that will incorporate additional cellular and NP interactions.
Oh, Eung Seok; Heo, Chaejeong; Kim, Ji Seon; Lee, Young Hee; Kim, Jong Min
2013-05-01
Parkinson's disease (PD) is characterized by progressive dopaminergic cell loss in the substantianigra (SN) and elevated iron levels demonstrated by autopsy and with 7-Tesla magnetic resonance imaging. Direct visualization of iron with live imaging techniques has not yet been successful. The aim of this study is to visualize and quantify the distribution of cellular iron using an intrinsic iron hyperspectral fluorescence signal. The 1-methyl-4-phenylpyridinium (MPP+)-induced cellular model of PD was established in SHSY5Y cells. The cells were exposed to iron by treatment with ferric ammonium citrate (FAC, 100 μM) for up to 6 hours. The hyperspectral fluorescence imaging signal of iron was examined usinga high- resolution dark-field optical microscope system with signal absorption for the visible/ near infrared (VNIR) spectral range. The 6-hour group showed heavy cellular iron deposition compared with the small amount of iron accumulation in the 1-hour group. The cellular iron was dispersed in a small, particulate form, whereas extracellular iron was detected in an aggregated form. In addition, iron particles were found to be concentrated on the cell membrane/edge of shrunken cells. The cellular iron accumulation readily occurred in MPP+-induced cells, which is consistent with previous studies demonstrating elevated iron levels in the SN in PD. This direct iron imaging methodology could be applied to analyze the physiological role of iron in PD, and its application might be expanded to various neurological disorders involving other metals, such as copper, manganese or zinc.
Cellular automaton for realistic modelling of landslides
Segrè, E; Enrico Segre; Chiara Deangeli
1994-01-01
We develop a numerical model for the simulation of debris flow in landslides over a complex three dimensional topography. The model is based on a lattice, in which debris can be transferred among nearest neighbours according to established empirical relationships for granular flows. The model is validated comparing its results with reported field data. Our model is in fact a realistic elaboration of simpler ``sandpile automata'', which have in recent years been studied as supposedly paradigmatic of ``self organized criticality''. Statistics and scaling properties of the simulation are examined, showing that the model has an intermittent behaviour.
Dalmasso, Giovanni; Marin Zapata, Paula Andrea; Brady, Nathan Ryan; Hamacher-Brady, Anne
2017-01-01
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 amplifying
Minimal model for complex dynamics in cellular processes.
Suguna, C; Chowdhury, K K; Sinha, S
1999-11-01
Cellular functions are controlled and coordinated by the complex circuitry of biochemical pathways regulated by genetic and metabolic feedback processes. This paper aims to show, with the help of a minimal model of a regulated biochemical pathway, that the common nonlinearities and control structures present in biomolecular interactions are capable of eliciting a variety of functional dynamics, such as homeostasis, periodic, complex, and chaotic oscillations, including transients, that are observed in various cellular processes.
Simulation of primary static recrystallization with cellular operator model
Mukhopadhyay, Prantik
2005-01-01
1. Based on the modified cellular automata approach of Reher [60] a cellular operator model has been developed that is capable of accounting for spatial and temporal inhomogeneity on a finer scale. For this a scalable subgrid automaton is introduced that allows for a high spatial resolution on demand and still high computational efficiency. The scalable subgrid permits to track the minute changes of growth front during recrystallization owing to local variations of boundary mobility and net d...
A cellular automata evacuation model considering friction and repulsion
Institute of Scientific and Technical Information of China (English)
SONG Weiguo; YU Yanfei; FAN Weicheng; Zhang Heping
2005-01-01
There exist interactions among pedestrians and between pedestrian and environment in evacuation. These interactions include attraction, repulsion and friction that play key roles in human evacuation behaviors, speed and efficiency. Most former evacuation models focus on the attraction force, while repulsion and friction are not well modeled. As a kind of multi-particle self-driven model, the social force model introduced in recent years can represent those three forces but with low simulation efficiency because it is a continuous model with complex rules. Discrete models such as the cellular automata model and the lattice gas model have simple rules and high simulation efficiency, but are not quite suitable for interactions' simulation. In this paper, a new cellular automata model based on traditional models is introduced in which repulsion and friction are modeled quantitatively. It is indicated that the model can simulate some basic behaviors, e.g.arching and the "faster-is-slower" phenomenon, in evacuation as multi-particle self-driven models, but with high efficiency as the normal cellular automata model and the lattice gas model.
A cellular automaton evacuation model based on mobile robot's behaviors
Institute of Scientific and Technical Information of China (English)
WENG WenGuo; YUAN HongYong; FAN WeiCheng
2007-01-01
The research of evacuation in some emergencies, e.g. fire, is of great benefit to reducing the injuries of persons. In this paper, a cellular automaton evacuation model based on mobile robot's behaviors is presented. Each person is treated as an intelligent mobile robot, and motor schemas, including move-to-goal, avoid-obstacle, swirl-obstacle and nervous-motion, drive persons to interact with their environment. The motor schemas are combined with cellular automaton theory, and an evacuation model is built. Evacuation simulation of persons with different move velocities shows that the presented model can predict accurately the evacuation phenomena in some emergencies.
Modeling diffusion of innovations with probabilistic cellular automata
Boccara, N; Boccara, Nino; Fuks, Henryk
1997-01-01
We present a family of one-dimensional cellular automata modeling the diffusion of an innovation in a population. Starting from simple deterministic rules, we construct models parameterized by the interaction range and exhibiting a second-order phase transition. We show that the number of individuals who eventually keep adopting the innovation strongly depends on connectivity between individuals.
Modeling Integrated Cellular Machinery Using Hybrid Petri-Boolean Networks
Berestovsky, Natalie; Zhou, Wanding; Nagrath, Deepak; Nakhleh, Luay
2013-01-01
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 using such more
Modeling integrated cellular machinery using hybrid Petri-Boolean networks.
Directory of Open Access Journals (Sweden)
Natalie Berestovsky
Full Text Available The behavior and phenotypic changes of cells are governed by a cellular circuitry that represents a set of biochemical reactions. Based on biological functions, this circuitry is divided into three types of networks, each encoding for a major biological process: signal transduction, transcription regulation, and metabolism. This division has generally enabled taming computational complexity dealing with the entire system, allowed for using modeling techniques that are specific to each of the components, and achieved separation of the different time scales at which reactions in each of the three networks occur. Nonetheless, with this division comes loss of information and power needed to elucidate certain cellular phenomena. Within the cell, these three types of networks work in tandem, and each produces signals and/or substances that are used by the others to process information and operate normally. Therefore, computational techniques for modeling integrated cellular machinery are needed. In this work, we propose an integrated hybrid model (IHM that combines Petri nets and Boolean networks to model integrated cellular networks. Coupled with a stochastic simulation mechanism, the model simulates the dynamics of the integrated network, and can be perturbed to generate testable hypotheses. Our model is qualitative and is mostly built upon knowledge from the literature and requires fine-tuning of very few parameters. We validated our model on two systems: the transcriptional regulation of glucose metabolism in human cells, and cellular osmoregulation in S. cerevisiae. The model produced results that are in very good agreement with experimental data, and produces valid hypotheses. The abstract nature of our model and the ease of its construction makes it a very good candidate for modeling integrated networks from qualitative data. The results it produces can guide the practitioner to zoom into components and interconnections and investigate them
WWW Business Applications Based on the Cellular Model
Institute of Scientific and Technical Information of China (English)
Toshio Kodama; Tosiyasu L. Kunii; Yoichi Seki
2008-01-01
A cellular model based on the Incrementally Modular Abstraction Hierarchy (IMAH) is a novel model that can represent the architecture of and changes in cyberworlds, preserving invariants from a general level to a specific one. We have developed a data processing system called the Cellular Data System (CDS). In the development of business applications, you can prevent combinatorial explosion in the process of business design and testing by using CDS. In this paper, we have first designed and implemented wide-use algebra on the presentation level. Next, we have developed and verified the effectiveness of two general business applications using CDS: 1) a customer information management system, and 2) an estimate system.
Modeling evolution and immune system by cellular automata
Energy Technology Data Exchange (ETDEWEB)
Bezzi, M. [Scuola Internazionale Superiore di Studi Avanzati, Trieste (Italy); Istituto Nazionale di Fisica della Materia, Florence (Italy)
2001-07-01
In this review the behavior of two different biological systems is investigated using cellular automata. Starting from this spatially extended approach it is also tried, in some cases, to reduce the complexity of the system introducing mean-field approximation, and solving (or trying to solve) these simplified systems. It is discussed the biological meaning of the results, the comparison with experimental data (if available) and the different features between spatially extended and mean-field versions. The biological systems considered in this review are the following: Darwinian evolution in simple ecosystems and immune system response. In the first section the main features of molecular evolution are introduced, giving a short survey of genetics for physicists and discussing some models for prebiotic systems and simple ecosystems. It is also introduced a cellular automaton model for studying a set of evolving individuals in a general fitness landscape, considering also the effects of co-evolution. In particular the process of species formation (speciation) is described in sect. 5. The second part deals with immune system modeling. The biological features of immune response are discussed, as well as it is introduced the concept of shape space and of idiotypic network. More detailed reviews which deal with immune system models (mainly focused on idiotypic network models) can be found. Other themes here discussed: the applications of CA to immune system modeling, two complex cellular automata for humoral and cellular immune response. Finally, it is discussed the biological data and the general conclusions are drawn in the last section.
A sub-cellular viscoelastic model for cell population mechanics.
Directory of Open Access Journals (Sweden)
Yousef Jamali
Full Text Available Understanding the biomechanical properties and the effect of biomechanical force on epithelial cells is key to understanding how epithelial cells form uniquely shaped structures in two or three-dimensional space. Nevertheless, with the limitations and challenges posed by biological experiments at this scale, it becomes advantageous to use mathematical and 'in silico' (computational models as an alternate solution. This paper introduces a single-cell-based model representing the cross section of a typical tissue. Each cell in this model is an individual unit containing several sub-cellular elements, such as the elastic plasma membrane, enclosed viscoelastic elements that play the role of cytoskeleton, and the viscoelastic elements of the cell nucleus. The cell membrane is divided into segments where each segment (or point incorporates the cell's interaction and communication with other cells and its environment. The model is capable of simulating how cells cooperate and contribute to the overall structure and function of a particular tissue; it mimics many aspects of cellular behavior such as cell growth, division, apoptosis and polarization. The model allows for investigation of the biomechanical properties of cells, cell-cell interactions, effect of environment on cellular clusters, and how individual cells work together and contribute to the structure and function of a particular tissue. To evaluate the current approach in modeling different topologies of growing tissues in distinct biochemical conditions of the surrounding media, we model several key cellular phenomena, namely monolayer cell culture, effects of adhesion intensity, growth of epithelial cell through interaction with extra-cellular matrix (ECM, effects of a gap in the ECM, tensegrity and tissue morphogenesis and formation of hollow epithelial acini. The proposed computational model enables one to isolate the effects of biomechanical properties of individual cells and the
Empirical study on entropy models of cellular manufacturing systems
Institute of Scientific and Technical Information of China (English)
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
Institute of Scientific and Technical Information of China (English)
XUN Jing; NING Bin; LI Ke-Ping
2009-01-01
In this paper, we propose a new cellular automata model to simulate the railway traffic at station.Based on NaSch model, the proposed station model is composed of the main track and the siding track.Two different schemes for trains passing through station are considered.One is the scheme of "pass by the main track, start and stop by the siding track".The other is the scheme of "two tracks play the same role".We simulate the train movement using the proposed model and analyze the traffic flow at station.The simulation results demonstrate that the proposed cellular automata model can be successfully used for the simulations of railway traffic.Some characteristic behaviors of railway traffic flow can be reproduced.Moreover, the simulation values of the minimum headway are close to the theoretical values.This result demonstrates the dependability and availability of the proposed model.
Pott's Puffy Tumor Arising from Frontal Sinusitis
Energy Technology Data Exchange (ETDEWEB)
Lim, Ji Yeon; Kang, Hyun Koo [Seoul Veterans Hospital, Seoul (Korea, Republic of)
2010-02-15
Pott's puffy tumor is an extremely rare and potentially life-threatening complication of frontal sinusitis. We report a case of a 64-year-old man who presented at our emergency department with mild tenderness on the glabellar area and diplopia. Computed Tomography (CT) revealed frontal sinusitis and osteomyelitis of the frontal bone. Following sinus trephination and long-term antibiotic therapy, the patient achieved a complete recovery.
A Modified Cellular Automaton Model for Traffic Flow
Institute of Scientific and Technical Information of China (English)
葛红霞; 董力耘; 雷丽; 戴世强
2004-01-01
A modified cellular automaton model for traffic flow was proposed. A novel concept about the changeable security gap was introduced and a parameter related to the variable security gap was determined. The fundamental diagram obtained by simulation shows that the maximum flow more approaches to the observed data than that of the NaSch model, indicating that the presented model is more reasonable and realistic.
A simplified cellular automation model for city traffic
Energy Technology Data Exchange (ETDEWEB)
Simon, P.M.; Nagel, K. [Los Alamos National Lab., NM (United States)]|[Santa Fe Inst., NM (United States)
1997-12-31
The authors systematically investigate the effect of blockage sites in a cellular automata model for traffic flow. Different scheduling schemes for the blockage sites are considered. None of them returns a linear relationship between the fraction of green time and the throughput. The authors use this information for a fast implementation of traffic in Dallas.
Analytical modeling of bargaining solutions for multicast cellular services
Directory of Open Access Journals (Sweden)
Giuseppe Araniti
2013-07-01
Full Text Available Nowadays, the growing demand for group-oriented services over mobile devices has lead to the definition of new communication standards and multimedia applications in cellular systems. In this article we study the use of game theoretic solutions for these services to model and perform a trade-off analysis between fairness and efficiency in the resources allocation. More precisely, we model bargaining solutions for the multicast data services provisioning and introduce the analytical resolution for the proposed solutions.
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.
Modelling Nonlinear Sequence Generators in terms of Linear Cellular Automata
Fúster-Sabater, Amparo; 10.1016/j.apm.2005.08.013
2010-01-01
In this work, a wide family of LFSR-based sequence generators, the so-called Clock-Controlled Shrinking Generators (CCSGs), has been analyzed and identified with a subset of linear Cellular Automata (CA). In fact, a pair of linear models describing the behavior of the CCSGs can be derived. The algorithm that converts a given CCSG into a CA-based linear model is very simple and can be applied to CCSGs in a range of practical interest. The linearity of these cellular models can be advantageously used in two different ways: (a) for the analysis and/or cryptanalysis of the CCSGs and (b) for the reconstruction of the output sequence obtained from this kind of generators.
Fire Spread Model for Old Towns Based on Cellular Automaton
Institute of Scientific and Technical Information of China (English)
GAO Nan; WENG Wenguo; MA Wei; NI Shunjiang; HUANG Quanyi; YUAN Hongyong
2008-01-01
Old towns like Lijiang have enormous historic,artistic,and architectural value.The buildings in such old towns are usually made of highly combustible materials,such as wood and grass.If a fire breaks out,it will spread to multiple buildings,so fire spreading and controlling in old towns need to be studied.This paper presents a fire spread model for old towns based on cellular automaton.The cellular automaton rules were set according to historical fire data in empirical formulas.The model also considered the effects of climate.The simulation results were visualized in a geography information system.An example of a fire spread in Lijiang was investigated with the results showing that this model provides a realistic tool for predicting fire spread in old towns.Fire brigades can use this tool to predict when and how a fire spreads to minimize the losses.
Multiscale mathematical modeling and simulation of cellular dynamical process.
Nakaoka, Shinji
2014-01-01
Epidermal homeostasis is maintained by dynamic interactions among molecules and cells at different spatiotemporal scales. Mathematical modeling and simulation is expected to provide clear understanding and precise description of multiscaleness in tissue homeostasis under systems perspective. We introduce a stochastic process-based description of multiscale dynamics. Agent-based modeling as a framework of multiscale modeling to achieve consistent integration of definitive subsystems is proposed. A newly developed algorithm that particularly aims to perform stochastic simulations of cellular dynamical process is introduced. Finally we review applications of multiscale modeling and quantitative study to important aspects of epidermal and epithelial homeostasis.
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.
Public Evacuation Process Modeling and Simulatiaon Based on Cellular Automata
Directory of Open Access Journals (Sweden)
Zhikun Wang
2013-11-01
Full Text Available Considering attraction of the nearest exit, repulsive force of the fire, barrier and its display style, effect of fire exit location on escape time in fire hazard, a mathematical model of evacuation process model was build based on cellular automatic theory. The program was developed by JavaScript. The influencing factors of evacuation were obtained through the simulation model by inputting crew size, creating initial positions of crew and fire seat stochastically. The experimental results show that the evacuation simulation model with authenticity and validity, which has guiding significance for people evacuation and public escape system design.
Modeling self-organizing traffic lights with elementary cellular automata
Gershenson, Carlos
2009-01-01
There have been several highway traffic models proposed based on cellular automata. The simplest one is elementary cellular automaton rule 184. We extend this model to city traffic with cellular automata coupled at intersections using only rules 184, 252, and 136. The simplicity of the model offers a clear understanding of the main properties of city traffic and its phase transitions. We use the proposed model to compare two methods for coordinating traffic lights: a green-wave method that tries to optimize phases according to expected flows and a self-organizing method that adapts to the current traffic conditions. The self-organizing method delivers considerable improvements over the green-wave method. For low densities, the self-organizing method promotes the formation and coordination of platoons that flow freely in four directions, i.e. with a maximum velocity and no stops. For medium densities, the method allows a constant usage of the intersections, exploiting their maximum flux capacity. For high dens...
A cellular automata model with probability infection and spatial dispersion
Institute of Scientific and Technical Information of China (English)
Jin Zhen; Liu Quan-Xing; Mainul Haque
2007-01-01
In this article, we have proposed an epidemic model based on the probability cellular automata theory. The essential mathematical features are analysed with the help of stability theory. We have given an alternative modelling approach for the spatiotemporal system which is more realistic from the practical point of view. A discrete and spatiotemporal approach is shown by using cellular automata theory. It is interesting to note that both the size of the endemic equilibrium and the density of the individuals increase with the increase of the neighbourhood size and infection rate, but the infections decrease with the increase of the recovery rate. The stability of the system around the positive interior equilibrium has been shown by using a suitable Lyapunov function. Finally, experimental data simulation for SARS disease in China in 2003 and a brief discussion are given.
A COLLABORATIVE LOCATION MODEL FOR CELLULAR MOBILE POSITION LOCATION
Institute of Scientific and Technical Information of China (English)
Deng Ping; Liu Lin; Fan Pingzhi
2004-01-01
In cellular network, several Time Difference Of Arrival (TDOA) location algorithms can be applied to mobile position estimation. However, each algorithm has its own limitations and none of them is proved to be the most reliable one in different channel environments. In this paper Kleine-Ostmann's data fusion model is modified and a collaborative location model which incorporates position estimate of two TDOA location algorithms is proposed.Analysis and simulation show that more reliable and accurate mobile position estimation can be achieved based on this model.
Microbial Growth Modeling and Simulation Based on Cellular Automata
Directory of Open Access Journals (Sweden)
Hong Men
2013-07-01
Full Text Available In order to simulate the micro-evolutionary process of the microbial growth, [Methods] in this study, we adopt two-dimensional cellular automata as its growth space. Based on evolutionary mechanism of microbial and cell-cell interactions, we adopt Moore neighborhood and make the transition rules. Finally, we construct the microbial growth model. [Results] It can describe the relationships among the cell growth, division and death. And also can effectively reflect spatial inhibition effect and substrate limitation effect. [Conclusions] The simulation results show that CA model is not only consistent with the classic microbial kinetic model, but also be able to simulate the microbial growth and evolution.
Statistical mechanics model for the dynamics of collective epigenetic histone modification.
Zhang, Hang; Tian, Xiao-Jun; Mukhopadhyay, Abhishek; Kim, K S; Xing, Jianhua
2014-02-14
Epigenetic histone modifications play an important role in the maintenance of different cell phenotypes. The exact molecular mechanism for inheritance of the modification patterns over cell generations remains elusive. We construct a Potts-type model based on experimentally observed nearest-neighbor enzyme lateral interactions and nucleosome covalent modification state biased enzyme recruitment. The model can lead to effective nonlocal interactions among nucleosomes suggested in previous theoretical studies, and epigenetic memory is robustly inheritable against stochastic cellular processes.
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.
Xu, Kaixuan; Wang, Jun
2017-02-01
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.
Unstable network fragmentation in co-evolution of Potts spins and system topology
Toruniewska, Joanna; Suchecki, Krzysztof; Hołyst, Janusz A.
2016-10-01
We investigate co-evolution of discrete q-state Potts model and the underlying network topology, where spin changes and link re-wiring follow the same canonical ensemble dynamics in a constant temperature. It means that there are no absorbing, frozen states present in our model. Depending on the temperature T and probability of link dynamics p the system can exist in one of three states: ordered, disordered and ordered clusters (fragmented network), with the last being unstable and slowly relaxing into ordered state. The transition from ordered clusters to globally ordered system is characterized by non-exponential, slow growth of the order parameter. We investigate this process analytically and explain the transition characteristics as the result of the dominance of activity of "surface" nodes in each ordered cluster, as opposed to "bulk" nodes that are inactive.
Pott's Disease in a Pediatric Patient. A Case Report
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Lourdes Marimón Amador
2014-08-01
Full Text Available The case of a four-year old boy with Pott's disease diagnosed by clinical, radiological and laboratory study at the Guido Valladares National Hospital in East Timor is presented. Inquiries about the etiopathogenesis of the disease in relation to the family and personal history were conducted. This is a very complex and clinically important case since a rare and serious complication was observed in the child. It is concluded that early diagnosis of this condition is essential due to its poor prognosis once developed.
Occupant evacuation model based on cellular automata in fire
Institute of Scientific and Technical Information of China (English)
无
2002-01-01
By applying the rules set in traffic flow and pedestrian flow models, a basic cellular automata model is presented to simulate occupant evacuation in fire. Some extended models are introduced to study the special phenomena of evacuation from the fire room. The key of the models is the introduction of the danger grade which makes the route choice convenient and reasonable. Fire not only influences the emotional and behavioral characteristics of an individual but also affects his physical constitution, which reduces his maximal possible velocity. The models consider these influence factors by applying a set of simple but effective rules. It is needed to emphasize that all rules are established according to the essential phenomenon in fire evacuation, that is, all the occupants would try to move to the safest place as fast as possible. Some simulation examples are also presented to validate the applicability of the models.
Infinity computations in cellular automaton forest-fire model
Iudin, D. I.; Sergeyev, Ya. D.; Hayakawa, M.
2015-03-01
Recently a number of traditional models related to the percolation theory has been considered by means of a new computational methodology that does not use Cantor's ideas and describes infinite and infinitesimal numbers in accordance with the principle 'The whole is greater than the part' (Euclid's Common Notion 5). Here we apply the new arithmetic to a cellular automaton forest-fire model which is connected with the percolation methodology and in some sense combines the dynamic and the static percolation problems and under certain conditions exhibits critical fluctuations. It is well known that there exist two versions of the model: real forest-fire model where fire catches adjacent trees in the forest in the step by step manner and simplified version with instantaneous combustion. Using new approach we observe that in both situations we deal with the same model but with different time resolution. We show that depending on the "microscope" we use the same cellular automaton forest-fire model reveals either instantaneous forest combustion or step by step firing. By means of the new approach it was also observed that as far as we choose an infinitesimal tree growing rate and infinitesimal ratio between the ignition probability and the growth probability we determine the measure or extent of the system size infinity that provides the criticality of the system dynamics. Correspondent inequalities for grosspowers are derived.
Cellular automata modelling of phase-change memories
Institute of Scientific and Technical Information of China (English)
Wanhua Yu; David Wright
2008-01-01
A novel approach to modelling phase-transition processes in phase change materials used for optical and electrical data storage applications is presented. The model is based on a cellular automaton (CA) approach to predict crystallization behaviour that is linked to thermal and electrical simulations to enable the study of the data writing and erasing processes. The CA approach is shown to be able to predict the evolution of the microstructure during the rapid heating and cooling cycles pertinent to data storage technology, and maps crystallization behaviour on the nanoscale. A simple example based on possible future nonvolatile phase-change random access solid-state memory is presented.
Modeling cellular lysis in skeletal muscle due to electric shock.
Cela, Carlos J; Lee, Raphael C; Lazzi, Gianluca
2011-05-01
High-voltage electrical trauma frequently results in injury patterns that cannot be completely attributed to Joule heating. An electrical-injury model describing cellular lysis damage caused by supraphysiological electric fields is introduced, and used to evaluate the effects of high-voltage electric shock on the skeletal muscle of a human upper limb in a configuration that simulates hand-to-hand contact. A novel multiresolution admittance method, capable of efficiently handling large computational models while maintaining excellent accuracy, was used to perform the numerical computations. Values for the computed current through the arm and the upper limb impedance are reported.
A Realistic Cellular Automaton Model for Synchronized Traffic Flow
Institute of Scientific and Technical Information of China (English)
ZHAO Bo-Han; HU Mao-Bin; JIANG Rui; WU Qing-Song
2009-01-01
A cellular automaton model is proposed to consider the anticipation effect in drivers' behavior. It is shown that the anticipation effect can be one of the origins of synchronized traffic flow. With anticipation effect, the congested traffic flow simulated by the model exhibits the features of synchronized flow. The spatiotemporal patterns induced by an on-ramp are also consistent with the three-phaee traffic theory. Since the origin of synchronized flow is still controversial, our work can shed some light on the mechanism of synchronized flow.
A cellular automaton model for a bridge traffic bottleneck
Institute of Scientific and Technical Information of China (English)
Shifa Xiao; Lingjiang Kong; Muren Liu
2005-01-01
A cellular automaton (CA) model is proposed in this paper to analyze a bridge traffic bottleneck. The simulation results with this model show that there are several phase transitions in the traffic average density, velocity and flow for each lane under a periodic boundary condition. An unstable phase in the traffic average density and velocity for the upstream and downstream lanes of the bridge is shown in a range of initial traffic densities. The critical points of the phase transitions and the phenomenon of the unstable phase found in the simulation are also explained with the mean-field theory.
Modeling and simulation for train control system using cellular automata
Institute of Scientific and Technical Information of China (English)
LI; KePing; GAO; ZiYou; YANG; LiXing
2007-01-01
Train control system plays a key role in railway traffic. Its function is to manage and control the train movement on railway networks. In our previous works, based on the cellular automata (CA) model, we proposed several models and algorithms for simulating the train movement under different control system conditions. However, these models are only suitable for some simple traffic conditions. Some basic factors, which are important for train movement, are not considered. In this paper, we extend these models and algorithms and give a unified formula. Using the proposed method, we analyze and discuss the space-time diagram of railway traffic flow and the trajectories of the train movement. The numerical simulation and analytical results demonstrate that the unified CA model is an effective tool for simulating the train control system.
Cancer models, genomic instability and somatic cellular Darwinian evolution
Directory of Open Access Journals (Sweden)
Little Mark P
2010-04-01
Full Text Available Abstract The biology of cancer is critically reviewed and evidence adduced that its development can be modelled as a somatic cellular Darwinian evolutionary process. The evidence for involvement of genomic instability (GI is also reviewed. A variety of quasi-mechanistic models of carcinogenesis are reviewed, all based on this somatic Darwinian evolutionary hypothesis; in particular, the multi-stage model of Armitage and Doll (Br. J. Cancer 1954:8;1-12, the two-mutation model of Moolgavkar, Venzon, and Knudson (MVK (Math. Biosci. 1979:47;55-77, the generalized MVK model of Little (Biometrics 1995:51;1278-1291 and various generalizations of these incorporating effects of GI (Little and Wright Math. Biosci. 2003:183;111-134; Little et al. J. Theoret. Biol. 2008:254;229-238. Reviewers This article was reviewed by RA Gatenby and M Kimmel.
Cellular automaton model considering headway-distance effect
Institute of Scientific and Technical Information of China (English)
Hu Shou-Xin; Gao Kun; Wang Bing-Hong; Lu Yu-Feng
2008-01-01
This paper presents a cellular automaton model for single-lane traffic flow.On the basis of the Nagel-Schreckenberg (NS) model,it further considers the effect of headway-distance between two successive cars on the randomization of the latter one.In numerical simulations,this model shows the following characteristics.(1) With a simple structure,this model succeeds in reproducing the hysteresis effect,which is absent in the NS model.(2) Compared with the slow-tostart models,this model exhibits a local fundamental diagram which is more consistent to empirical observations.(3)This model has much higher efficiency in dissolving congestions compared with the so-called NS model with velocitydependent randomization (VDR model).(4) This model is more robust when facing traffic obstructions.It can resist much longer shock times and has much shorter relaxation times on the other hand.To summarize,compared with the existing models,this model is quite simple in structure,but has good characteristics.
Tight Bounds for Mixing of the Swendsen-Wang Algorithm at the Potts Transition Point
Borgs, Christian; Tetali, Prasad
2010-01-01
We study two widely used algorithms for the Potts model on rectangular subsets of the hypercubic lattice Z^d - heat bath dynamics and the Swendsen-Wang algorithm - and prove that, under certain circumstances, the mixing in these algorithms is torpid or slow. In particular, we show that for heat bath dynamics throughout the region of phase coexistence, and for the Swendsen-Wang algorithm at the transition point, the mixing time in a box of side length L with periodic boundary conditions has upper and lower bounds which are exponential in L^{d-1}. This work provides the first upper bound of this form for the Swendsen-Wang algorithm, and gives lower bounds for both algorithms which significantly improve the previous lower bounds that were exponential in L/(log L)^2.
Structural modeling of sandwich structures with lightweight cellular cores
Institute of Scientific and Technical Information of China (English)
T. Liu; Z. C. Deng; T. J. Lu
2007-01-01
An effective single layered finite element (FE) computational model is proposed to predict the structural behavior of lightweight sandwich panels having two dimensional (2D) prismatic or three dimensional (3D) truss cores.Three different types of cellular core topology are considered: pyramidal truss core (3D), Kagome truss core (3D) and corrugated core (2D), representing three kinds of material anisotropy: orthotropic, monoclinic and general anisotropic. A homogenization technique is developed to obtain the homogenized macroscopic stiffness properties of the cellular core. In comparison with the results obtained by using detailed FE model, the single layered computational model cangive acceptable predictions for both the static and dynamic behaviors of orthotropic truss core sandwich panels. However, for non-orthotropic 3D truss cores, the predictions are not so well. For both static and dynamic behaviors of a 2D corrugated core sandwich panel, the predictions derived by the single layered computational model is generally acceptable when the size of the unit cell varies within a certain range, with the predictions for moderately strong or strong corrugated cores more accurate than those for weak cores.
Integrating cellular metabolism into a multiscale whole-body model.
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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.
A Fluid Model for Performance Analysis in Cellular Networks
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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.
Structural modeling of sandwich structures with lightweight cellular cores
Liu, T.; Deng, Z. C.; Lu, T. J.
2007-10-01
An effective single layered finite element (FE) computational model is proposed to predict the structural behavior of lightweight sandwich panels having two dimensional (2D) prismatic or three dimensional (3D) truss cores. Three different types of cellular core topology are considered: pyramidal truss core (3D), Kagome truss core (3D) and corrugated core (2D), representing three kinds of material anisotropy: orthotropic, monoclinic and general anisotropic. A homogenization technique is developed to obtain the homogenized macroscopic stiffness properties of the cellular core. In comparison with the results obtained by using detailed FE model, the single layered computational model can give acceptable predictions for both the static and dynamic behaviors of orthotropic truss core sandwich panels. However, for non-orthotropic 3D truss cores, the predictions are not so well. For both static and dynamic behaviors of a 2D corrugated core sandwich panel, the predictions derived by the single layered computational model is generally acceptable when the size of the unit cell varies within a certain range, with the predictions for moderately strong or strong corrugated cores more accurate than those for weak cores.
Robustness of a Cellular Automata Model for the HIV Infection
Figueirêdo, P H; Santos, R M Zorzenon dos
2008-01-01
An investigation was conducted to study the robustness of the results obtained from the cellular automata model which describes the spread of the HIV infection within lymphoid tissues [R. M. Zorzenon dos Santos and S. Coutinho, Phys. Rev. Lett. 87, 168102 (2001)]. The analysis focussed on the dynamic behavior of the model when defined in lattices with different symmetries and dimensionalities. The results illustrated that the three-phase dynamics of the planar models suffered minor changes in relation to lattice symmetry variations and, while differences were observed regarding dimensionality changes, qualitative behavior was preserved. A further investigation was conducted into primary infection and sensitiveness of the latency period to variations of the model's stochastic parameters over wide ranging values. The variables characterizing primary infection and the latency period exhibited power-law behavior when the stochastic parameters varied over a few orders of magnitude. The power-law exponents were app...
A modified weighted probabilistic cellular automaton traffic flow model
Institute of Scientific and Technical Information of China (English)
Zhuang Qian; Jia Bin; Li Xin-Gang
2009-01-01
This paper modifies the weighted probabilistic cellular automaton model (Li X L,Kuang H,Song T,et al 2008Chin.Phys.B 17 2366) which considered a diversity of traffic behaviors under real traffic situations induced by various driving characters and habits.In the new model,the effects of the velocity at the last time step and drivers' desire for acceleration are taken into account.The fundamental diagram,spatial-temporal diagram,and the time series of one-minute data axe analyzed.The results show that this model reproduces synchronized flow.Finally,it simulates the on-ramp system with the proposed model.Some characteristics including the phase diagram are studied.
Network modeling of membrane-based artificial cellular systems
Freeman, Eric C.; Philen, Michael K.; Leo, Donald J.
2013-04-01
Computational models are derived for predicting the behavior of artificial cellular networks for engineering applications. The systems simulated involve the use of a biomolecular unit cell, a multiphase material that incorporates a lipid bilayer between two hydrophilic compartments. These unit cells may be considered building blocks that enable the fabrication of complex electrochemical networks. These networks can incorporate a variety of stimuli-responsive biomolecules to enable a diverse range of multifunctional behavior. Through the collective properties of these biomolecules, the system demonstrates abilities that recreate natural cellular phenomena such as mechanotransduction, optoelectronic response, and response to chemical gradients. A crucial step to increase the utility of these biomolecular networks is to develop mathematical models of their stimuli-responsive behavior. While models have been constructed deriving from the classical Hodgkin-Huxley model focusing on describing the system as a combination of traditional electrical components (capacitors and resistors), these electrical elements do not sufficiently describe the phenomena seen in experiment as they are not linked to the molecular scale processes. From this realization an advanced model is proposed that links the traditional unit cell parameters such as conductance and capacitance to the molecular structure of the system. Rather than approaching the membrane as an isolated parallel plate capacitor, the model seeks to link the electrical properties to the underlying chemical characteristics. This model is then applied towards experimental cases in order that a more complete picture of the underlying phenomena responsible for the desired sensing mechanisms may be constructed. In this way the stimuli-responsive characteristics may be understood and optimized.
Simulation of root forms using cellular automata model
Energy Technology Data Exchange (ETDEWEB)
Winarno, Nanang, E-mail: nanang-winarno@upi.edu; Prima, Eka Cahya [International Program on Science Education, Universitas Pendidikan Indonesia, Jl. Dr. Setiabudi no 229, Bandung40154 (Indonesia); Afifah, Ratih Mega Ayu [Department of Physics Education, Post Graduate School, Universitas Pendidikan Indonesia, Jl. Dr. Setiabudi no 229, Bandung40154 (Indonesia)
2016-02-08
This research aims to produce a simulation program for root forms using cellular automata model. Stephen Wolfram in his book entitled “A New Kind of Science” discusses the formation rules based on the statistical analysis. In accordance with Stephen Wolfram’s investigation, the research will develop a basic idea of computer program using Delphi 7 programming language. To best of our knowledge, there is no previous research developing a simulation describing root forms using the cellular automata model compared to the natural root form with the presence of stone addition as the disturbance. The result shows that (1) the simulation used four rules comparing results of the program towards the natural photographs and each rule had shown different root forms; (2) the stone disturbances prevent the root growth and the multiplication of root forms had been successfully modeled. Therefore, this research had added some stones, which have size of 120 cells placed randomly in the soil. Like in nature, stones cannot be penetrated by plant roots. The result showed that it is very likely to further develop the program of simulating root forms by 50 variations.
A cellular automaton model for ship traffic flow in waterways
Qi, Le; Zheng, Zhongyi; Gang, Longhui
2017-04-01
With the development of marine traffic, waterways become congested and more complicated traffic phenomena in ship traffic flow are observed. It is important and necessary to build a ship traffic flow model based on cellular automata (CAs) to study the phenomena and improve marine transportation efficiency and safety. Spatial discretization rules for waterways and update rules for ship movement are two important issues that are very different from vehicle traffic. To solve these issues, a CA model for ship traffic flow, called a spatial-logical mapping (SLM) model, is presented. In this model, the spatial discretization rules are improved by adding a mapping rule. And the dynamic ship domain model is considered in the update rules to describe ships' interaction more exactly. Take the ship traffic flow in the Singapore Strait for example, some simulations were carried out and compared. The simulations show that the SLM model could avoid ship pseudo lane-change efficiently, which is caused by traditional spatial discretization rules. The ship velocity change in the SLM model is consistent with the measured data. At finally, from the fundamental diagram, the relationship between traffic ability and the lengths of ships is explored. The number of ships in the waterway declines when the proportion of large ships increases.
Motor Schema-Based Cellular Automaton Model for Pedestrian Dynamics
Weng, Wenguo; Hasemi, Yuji; Fan, Weicheng
A new cellular automaton model for pedestrian dynamics based on motor schema is presented. Each pedestrian is treated as an intelligent mobile robot, and motor schemas including move-to-goal, avoid-away and avoid-around drive pedestrians to interact with their environment. We investigate the phenomenon of many pedestrians with different move velocities escaping from a room. The results show that the pedestrian with high velocity have predominance in competitive evacuation, if we only consider repulsion from or avoiding around other pedestrians, and interaction with each other leads to disordered evacuation, i.e., decreased evacuation efficiency. Extensions of the model using learning algorithms for controlling pedestrians, i.e., reinforcement learning, neural network and genetic algorithms, etc. are noted.
Critical Behavior in a Cellular Automata Animal Disease Transmission Model
Morley, P D; Chang, Julius
2003-01-01
Using a cellular automata model, we simulate the British Government Policy (BGP) in the 2001 foot and mouth epidemic in Great Britain. When clinical symptoms of the disease appeared on a farm, there is mandatory slaughter (culling) of all livestock on an infected premise (IP). Those farms that neighbor an IP (contiguous premise, CP), are also culled, aka nearest neighbor interaction. Farms where the disease may be prevalent from animal, human, vehicle or airborne transmission (dangerous contact, DC), are additionally culled, aka next-to-nearest neighbor iteractions and lightning factor. The resulting mathematical model possesses a phase transition, whereupon if the physical disease transmission kernel exceeds a critical value, catastrophic loss of animals ensues. The non-local disease transport probability can be as low as .01% per day and the disease can still be in the high mortality phase. We show that the fundamental equation for sustainable disease transport is the criticality equation for neutron fissio...
A dynamic cellular vertex model of growing epithelial tissues
Lin, Shao-Zhen; Li, Bo; Feng, Xi-Qiao
2017-03-01
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.
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Patricia Campos
1989-09-01
Full Text Available Se presentan 27 casos de mal de Pott en niños entre 6 meses y 14 años de edad vistos durante un período de 2 años con tiempo de seguimiento hasta de 18 meses, 67% menores de 6 años y de ellos 2 pacientes menores de 1 año. Hubo predominio de pacientes de sexo masculino. El síntoma "jiba" fue el mas frecuente. La localización mas frecuente de la lesión fue el nivel dorsal. Todos recibieron tratamiento médico con 4 drogas, 14 de ellos necesitaron de métodos ortopédicos y solo 6 fueron sometidos a corrección quirúrgica. En mas del 50% hubo una evolución favorable hacia la curación o la mejoría con secuelas.
Patricia Campos; Eduardo Chaparro; Federico Valença; Alfredo Fuentes-Davila
1989-01-01
Se presentan 27 casos de mal de Pott en niños entre 6 meses y 14 años de edad vistos durante un período de 2 años con tiempo de seguimiento hasta de 18 meses, 67% menores de 6 años y de ellos 2 pacientes menores de 1 año. Hubo predominio de pacientes de sexo masculino. El síntoma "jiba" fue el mas frecuente. La localización mas frecuente de la lesión fue el nivel dorsal. Todos recibieron tratamiento médico con 4 drogas, 14 de ellos necesitaron de métodos ortopédicos y solo 6 fueron sometidos ...
Case report: a student of Asian origin with Pott's disease.
Roggeman, Stijn; Buyck, Griet; Petrovic, Mirko; Callens, Steven; Van Braeckel, Eva
2016-05-03
We describe a case report of a student of Asian origin who presented with fever of unknown origin, cough, recent onset low back pain and weight loss. Initial physical examination was unremarkable. Laboratory results showed inflammation, but extensive testing for bacteriological and viral serology was negative. While the chest Computed Tomography (CT) scan did not show any abnormal findings, pelvic CT scan revealed an osteolytic sacral mass, with extension to the soft tissues and muscles, and concomitant nerve compression. An ultrasonography-guided puncture of the lesion eventually showed Mycobacterium tuberculosis, leading to the diagnosis of tuberculous spondylitis or Pott's disease. The standard tuberculostatic treatment was applied during 9 months with a good clinical result. Skeletal tuberculosis is not common in Western countries and it can be overlooked in foreign patients with fever of unknown origin.
Load-Aware Modeling and Analysis of Heterogeneous Cellular Networks
Dhillon, Harpreet S; Andrews, Jeffrey G
2012-01-01
Random spatial models are attractive for modeling heterogeneous cellular networks (HCNs) due to their realism, tractability, and scalability. A major limitation of such models to date in the context of HCNs is the neglect of network traffic and load: all base stations (BSs) have typically been assumed to always be transmitting. Small cells in particular will have a lighter load than macrocells, and so their contribution to the network interference may be significantly overstated in a fully loaded model. This paper incorporates a flexible notion of BS load by introducing a new idea of conditionally thinning the interference field. For a $K$-tier HCN where BSs across tiers differ in terms of transmit power, supported data rate, deployment density, and now load, we derive the coverage probability for a typical mobile, which connects to the strongest BS signal. Conditioned on this connection, the interfering BSs of the $i^{th}$ tier are assumed to transmit independently with probability $p_i$, which models the lo...
A cellular automaton model for evacuation flow using game theory
Guan, Junbiao; Wang, Kaihua; Chen, Fangyue
2016-11-01
Game theory serves as a good tool to explore crowd dynamic conflicts during evacuation processes. The purpose of this study is to simulate the complicated interaction behavior among the conflicting pedestrians in an evacuation flow. Two types of pedestrians, namely, defectors and cooperators, are considered, and two important factors including fear index and cost coefficient are taken into account. By combining the snowdrift game theory with a cellular automaton (CA) model, it is shown that the increase of fear index and cost coefficient will lengthen the evacuation time, which is more apparent for large values of cost coefficient. Meanwhile, it is found that the defectors to cooperators ratio could always tend to consistent states despite different values of parameters, largely owing to self-organization effects.
A cellular automaton model for neurogenesis in Drosophila
Luthi, Pascal O.; Chopard, Bastien; Preiss, Anette; Ramsden, Jeremy J.
1998-07-01
A cellular automaton (CA) is constructed for the formation of the central nervous system of the Drosophila embryo. This is an experimentally well-studied system in which complex interactions between neighbouring cells appear to drive their differentiation into different types. It appears that all the cells initially have the potential to become neuroblasts, and all strive to this end, but those which differentiate first block their as yet undifferentiated neighbours from doing so. The CA makes use of observational evidence for a lateral inhibition mechanism involving signalling products S of the ‘proneural’ or neuralizing genes. The key concept of the model is that cells are continuously producing S, but the production rate is lowered by inhibitory signals received from neighbouring cells which have advanced further along the developmental pathway. Comparison with experimental data shows that it well accounts for the observed proportion of neuroectodermal cells delaminating as neuroblasts.
Two dimensional cellular automaton for evacuation modeling: hybrid shuffle update
Arita, Chikashi; Appert-Rolland, Cécile
2015-01-01
We consider a cellular automaton model with a static floor field for pedestrians evacuating a room. After identifying some properties of real pedestrian flows, we discuss various update schemes, and we introduce a new one, the hybrid shuffle update. The properties specific to pedestrians are incorporated in variables associated to particles called phases, that represent their step cycles. The dynamics of the phases gives naturally raise to some friction, and allows to reproduce several features observed in experiments. We study in particular the crossover between a low- and a high-density regime that occurs when the density of pedestrian increases, the dependency of the outflow in the strength of the floor field, and the shape of the queue in front of the exit.
The importance of volume exclusion in modelling cellular migration.
Dyson, Louise; Baker, Ruth E
2015-09-01
The modelling of collective migration has traditionally been undertaken in a continuous framework, with little reference to the individual-level mechanisms that give rise to such a concerted movement. One factor whose importance is now coming to light is that the individuals themselves occupy space in the domain, thus obstructing others from moving past them (volume exclusion). In this work, we systematically derive continuous descriptions of cellular migration with volume exclusion for a wide range of individual-based mechanisms and in one, two and three dimensions. We also consider subpopulations of migrating individuals, which may have different characteristics, such as differing sizes and speeds of migration. We demonstrate that volume exclusion is of particular importance when biased movement is included, and thus conclude that volume exclusion may have its greatest effect when considering directed migratory mechanisms such as chemotaxis.
Predictability of the large relaxations in a cellular automaton model
Energy Technology Data Exchange (ETDEWEB)
Tejedor, Alejandro; Ambroj, Samuel; Gomez, Javier B; Pacheco, Amalio F [Faculty of Sciences, University of Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza (Spain)
2008-09-19
A simple one-dimensional cellular automaton model with threshold dynamics is introduced. It is loaded at a uniform rate and unloaded by abrupt relaxations. The cumulative distribution of the size of the relaxations is analytically computed and behaves as a power law with an exponent equal to -1. This coincides with the phenomenological Gutenberg-Richter behavior observed in seismology for the cumulative statistics of earthquakes at the regional or global scale. The key point of the model is the zero-load state of the system after the occurrence of any relaxation, no matter what its size. This leads to an equipartition of probability between all possible load configurations in the system during the successive loading cycles. Each cycle ends with the occurrence of the greatest-or characteristic-relaxation in the system. The duration of the cycles in the model is statistically distributed with a coefficient of variation ranging from 0.5 to 1. The predictability of the characteristic relaxations is evaluated by means of error diagrams. This model illustrates the value taking into account the refractory periods to obtain a considerable gain in the quality of the predictions.
Modeling dynamics of HIV infected cells using stochastic cellular automaton
Precharattana, Monamorn; Triampo, Wannapong
2014-08-01
Ever since HIV was first diagnosed in human, a great number of scientific works have been undertaken to explore the biological mechanisms involved in the infection and progression of the disease. Several cellular automata (CA) models have been introduced to gain insights into the dynamics of the disease progression but none of them has taken into account effects of certain immune cells such as the dendritic cells (DCs) and the CD8+ T lymphocytes (CD8+ T cells). In this work, we present a CA model, which incorporates effects of the HIV specific immune response focusing on the cell-mediated immunities, and investigate the interaction between the host immune response and the HIV infected cells in the lymph nodes. The aim of our work is to propose a model more realistic than the one in Precharattana et al. (2010) [10], by incorporating roles of the DCs, the CD4+ T cells, and the CD8+ T cells into the model so that it would reproduce the HIV infection dynamics during the primary phase of HIV infection.
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
A cellular automata model of epidemics of a heterogeneous susceptibility
Institute of Scientific and Technical Information of China (English)
Jin Zhen; Liu Quan-Xing
2006-01-01
In this paper we present a model with spatial heterogeneity based on cellular automata (CA). In the model we consider the relevant heterogeneity of host (susceptible) mixing and the natural birth rate. We divide the susceptible population into three groups according to the immunity of each individual based on the classical susceptible-infectedremoved (SIR) epidemic models, and consider the spread of an infectious disease transmitted by direct contact among humans and vectors that have not an incubation period to become infectious. We test the local stability and instability of the disease-free equilibrium by the spectrum radii of Jacobian. The simulation shows that the structure of the nearest neighbour size of the cell (or the degree of the scale-free networks) plays a very important role in the spread properties of infectious disease. The positive equilibrium of the infections versus the neighbour size follows the third power law if an endemic equilibrium point exists. Finally, we analyse the feature of the infection waves for the homogeneity and heterogeneous cases respectively.
Modeling psychiatric disorders: from genomic findings to cellular phenotypes
Falk, A; Heine, V M; Harwood, A J; Sullivan, P F; Peitz, M; Brüstle, O; Shen, S; Sun, Y-M; Glover, J C; Posthuma, D; Djurovic, S
2016-01-01
Major programs in psychiatric genetics have identified >150 risk loci for psychiatric disorders. These loci converge on a small number of functional pathways, which span conventional diagnostic criteria, suggesting a partly common biology underlying schizophrenia, autism and other psychiatric disorders. Nevertheless, the cellular phenotypes that capture the fundamental features of psychiatric disorders have not yet been determined. Recent advances in genetics and stem cell biology offer new prospects for cell-based modeling of psychiatric disorders. The advent of cell reprogramming and induced pluripotent stem cells (iPSC) provides an opportunity to translate genetic findings into patient-specific in vitro models. iPSC technology is less than a decade old but holds great promise for bridging the gaps between patients, genetics and biology. Despite many obvious advantages, iPSC studies still present multiple challenges. In this expert review, we critically review the challenges for modeling of psychiatric disorders, potential solutions and how iPSC technology can be used to develop an analytical framework for the evaluation and therapeutic manipulation of fundamental disease processes. PMID:27240529
A Computational model for compressed sensing RNAi cellular screening
2012-01-01
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 screening experiments which
Stochastic cellular automata model for stock market dynamics
Bartolozzi, M.; Thomas, A. W.
2004-04-01
In the present work we introduce a stochastic cellular automata model in order to simulate the dynamics of the stock market. A direct percolation method is used to create a hierarchy of clusters of active traders on a two-dimensional grid. Active traders are characterized by the decision to buy, σi (t)=+1 , or sell, σi (t)=-1 , a stock at a certain discrete time step. The remaining cells are inactive, σi (t)=0 . The trading dynamics is then determined by the stochastic interaction between traders belonging to the same cluster. Extreme, intermittent events, such as crashes or bubbles, are triggered by a phase transition in the state of the bigger clusters present on the grid, where almost all the active traders come to share the same spin orientation. Most of the stylized aspects of the financial market time series, including multifractal proprieties, are reproduced by the model. A direct comparison is made with the daily closures of the S&P500 index.
A Computational Model of Cellular Engraftment on Lung Scaffolds
Directory of Open Access Journals (Sweden)
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
Cortical factor feedback model for cellular locomotion and cytofission.
Directory of Open Access Journals (Sweden)
Shin I Nishimura
2009-03-01
Full Text Available Eukaryotic cells can move spontaneously without being guided by external cues. For such spontaneous movements, a variety of different modes have been observed, including the amoeboid-like locomotion with protrusion of multiple pseudopods, the keratocyte-like locomotion with a widely spread lamellipodium, cell division with two daughter cells crawling in opposite directions, and fragmentations of a cell to multiple pieces. Mutagenesis studies have revealed that cells exhibit these modes depending on which genes are deficient, suggesting that seemingly different modes are the manifestation of a common mechanism to regulate cell motion. In this paper, we propose a hypothesis that the positive feedback mechanism working through the inhomogeneous distribution of regulatory proteins underlies this variety of cell locomotion and cytofission. In this hypothesis, a set of regulatory proteins, which we call cortical factors, suppress actin polymerization. These suppressing factors are diluted at the extending front and accumulated at the retracting rear of cell, which establishes a cellular polarity and enhances the cell motility, leading to the further accumulation of cortical factors at the rear. Stochastic simulation of cell movement shows that the positive feedback mechanism of cortical factors stabilizes or destabilizes modes of movement and determines the cell migration pattern. The model predicts that the pattern is selected by changing the rate of formation of the actin-filament network or the threshold to initiate the network formation.
Directory of Open Access Journals (Sweden)
Chang-Hua Zou
2009-01-01
Full Text Available Problem statement: Cardiovascular Diseases (CVD continued to be the leading cause of death. Failure or abnormal cardiac cellular or sub-cellular vibrations (oscillations could lead failure or abnormal heart beats that could cause CVD. Understanding the mechanisms of the vibrations (oscillations could help to prevent or to treat the diseases. Scientists have studied the mechanisms for more than 100 years. To our knowledge, the mechanisms are still unclear today. In this investigation, based on published data or results, conservation laws of the momentum as well as the energy, in views of biology, biochemistry, informatics and physics (BioChemInfoPhysics, we proposed our models of cardiac cellular and sub-cellular vibrations (oscillations of biological components, such as free ions in Biological Fluids (BF, Biological Membranes (BM, Ca++H+ (Ca++ and Na+K+ ATPases, Na+Ca++ exchangers (NCX, Ca++ carriers and myosin heads. Approach: Our models were described with 4-D (x, y, z, t or r, ?, z, t momentum transfer equations in mathematical physics. Results: The momentum transfer equations were solved with free and forced, damped, un-damped and over-damped, vibrations (oscillations. The biological components could be modeled as resonators or vibrators (oscillators, such as liquid plasmas, membranes, active springs, passive springs and active swings. Conclusion: We systematically provided new insights of automation (ignition and maintain, transportation, propagation and orientation of the cardiac cellular and sub-cellular vibrations (oscillations and resonances, with our BioChemInfoPhysics models of 4-D momentum transfer equations. Our modeling results implied: Auto-rhythmic cells (Sinoatrial Node Cells (SANC, Atrioventricular Node Cells (AVNC, Purkinje fibers, non-Auto-rhythmic ventricular myocytes and their Sarcoplasmic Reticulums (SR work as Biological Liquid Plasma Resonators (BLPR. The resonators were
Weak confinement in the three-state Potts Field Theory
Rutkevich, Sergei
Kink topological excitations are quite common in one-dimensional quantum ferromagnetic systems with the spontaneously broken discrete symmetry. Application of the external magnetic field h induces the long-range attractive force between kinks leading to their confinement. While in the Ising Field Theory the particle sector in the confinement regime contains only the two-kink bound states (''the mesons''), in the three-state Potts Field Theory (PFT) the three-kink bound states (''the baryons'') can exist as well. In the weak confinement regime, which is realized at small external magnetic fields, the meson masses in the PFT can be determined analytically in the leading order in h by means of the solution of a quantum-mechanical problem for two non-relativistic particles interacting with a linear attractive potential, and my means of the WKB method. The masses of lightest baryons in the three-state PFT were calculated by the numerical solution of a three-particle quantum-mechanical problem. The obtained mass spectra for the PFT mesons and baryons were confirmed recently by Lencés and Takács in numerical calculations based on the truncated conformal space approach.
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
Quantum loop subalgebra and eigenvectors of the superintegrable chiral Potts transfer matrices
Energy Technology Data Exchange (ETDEWEB)
Au-Yang, Helen; Perk, Jacques H H, E-mail: perk@okstate.edu, E-mail: helenperk@yahoo.com [Department of Physics, Oklahoma State University, 145 Physical Sciences, Stillwater, OK 74078-3072 (United States)
2011-01-14
It has been shown in earlier works that for Q = 0 and L a multiple of N, the ground state sector eigenspace of the superintegrable {tau}{sub 2}(t{sub q}) model is highly degenerate and is generated by a quantum loop algebra L(sl{sub 2}). Furthermore, this loop algebra can be decomposed into r = (N - 1)L/N simple sl{sub 2} algebras. For Q {ne} 0, we shall show here that the corresponding eigenspace of {tau}{sub 2}(t{sub q}) is still highly degenerate, but splits into two spaces, each containing 2{sup r-1} independent eigenvectors. The generators for the sl{sub 2} subalgebras, and also for the quantum loop subalgebra, are given generalizing those in the Q = 0 case. However, the Serre relations for the generators of the loop subalgebra are only proven for some states, tested on small systems and conjectured otherwise. Assuming their validity we construct the eigenvectors of the Q {ne} 0 ground state sectors for the transfer matrix of the superintegrable chiral Potts model.
Ishimoto, Yukitaka
2014-01-01
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, the cellular Potts model. So far, in any case, pressures have not neatly been dealt with and curvatures of the cell boundaries have been even omitted through their approximations. We focus on these quantities and formulate them on the vertex model. Thus, a model with the curvatures is constructed and its algorithm is given for simulation. Its possible extensions and applications will also be discussed.
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.
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.
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…
Simple Cellular Automata-Based Linear Models for the Shrinking Generator
Fúster-Sabater, Amparo
2010-01-01
Structural properties of two well-known families of keystream generators, Shrinking Generators and Cellular Automata, have been analyzed. Emphasis is on the equivalence of the binary sequences obtained from both kinds of generators. In fact, Shrinking Generators (SG) can be identified with a subset of linear Cellular Automata (mainly rule 90, rule 150 or a hybrid combination of both rules). The linearity of these cellular models can be advantageously used in the cryptanalysis of those keystream generators.
Stochastic Models of Vesicular Sorting in Cellular Organelles
Vagne, Quentin
2016-01-01
The proper sorting of membrane components by regulated exchange between cellular organelles is crucial to intra-cellular organization. This process relies on the budding and fusion of transport vesicles, and should be strongly influenced by stochastic fluctuations considering the relatively small size of many organelles. We identify the perfect sorting of two membrane components initially mixed in a single compartment as a first passage process, and we show that the mean sorting time exhibits two distinct regimes as a function of the ratio of vesicle fusion to budding rates. Low ratio values leads to fast sorting, but results in a broad size distribution of sorted compartments dominated by small entities. High ratio values result in two well defined sorted compartments but is exponentially slow. Our results suggests an optimal balance between vesicle budding and fusion for the rapid and efficient sorting of membrane components, and highlight the importance of stochastic effects for the steady-state organizati...
A Large Deformation Model for the Elastic Moduli of Two-dimensional Cellular Materials
Institute of Scientific and Technical Information of China (English)
HU Guoming; WAN Hui; ZHANG Youlin; BAO Wujun
2006-01-01
We developed a large deformation model for predicting the elastic moduli of two-dimensional cellular materials. This large deformation model was based on the large deflection of the inclined members of the cells of cellular materials. The deflection of the inclined member, the strain of the representative structure and the elastic moduli of two-dimensional cellular materials were expressed using incomplete elliptic integrals. The experimental results show that these elastic moduli are no longer constant at large deformation, but vary significantly with the strain. A comparison was made between this large deformation model and the small deformation model proposed by Gibson and Ashby.
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.
Predictive model to describe water migration in cellular solid foods during storage
Voogt, J.A.; Hirte, A.; Meinders, M.B.J.
2011-01-01
BACKGROUND: Water migration in cellular solid foods during storage causes loss of crispness. To improve crispness retention, physical understanding of this process is needed. Mathematical models are suitable tools to gain this physical knowledge. RESULTS: Water migration in cellular solid foods invo
Predictive model to describe water migration in cellular solid foods during storage
Voogt, J.A.; Hirte, A.; Meinders, M.B.J.
2011-01-01
Background: Water migration in cellular solid foods during storage causes loss of crispness. To improve crispness retention, physical understanding of this process is needed. Mathematical models are suitable tools to gain this physical knowledge. Results: Water migration in cellular solid foods invo
A mathematical model of amphibian skin epithelium with two types of transporting cellular units
DEFF Research Database (Denmark)
Larsen, Erik Hviid; Rasmussen, B E
1985-01-01
A computer model of ion transport across amphibian skin epithelium containing two types of cellular units, their relative number and sizes, and a paracellular pathway has been developed. The two cellular units are, a large Na+ transporting compartment representing the major epithelium from stratum...
Dynamic modeling of cellular response to DNA damage based on p53 stress response networks
Institute of Scientific and Technical Information of China (English)
Jinpeng Qi; Yongsheng Ding; Shihuang Shao
2009-01-01
Under acute perturbations from the outside, cells can trigger self-defensive mechanisms to fight against genome stress. To investigate the cellular response to continuous ion radiation (IR), a dynamic model for p53 stress response networks at the cellular level is proposed. The model can successfully be used to simulate the dynamic processes of double-strand breaks (DSBs) generation and their repair, switch-like ataxia telangiectasia mutated (ATM) activation, oscillations occurring in the p53-MDM2 feedback loop, as well as toxins elimination triggered by p53 stress response networks. Especially, the model can predict the plausible outcomes of cellular response under different IR dose regimes.
An 8-year-old boy with a Pott's puffy tumor
Huijssoon, E; Woerdeman, PA; van Diemen-Steenvoorde, RAAM; Hanlo, PW; Plotz, FB
2003-01-01
An 8-year old boy with a history of trauma, sinusitis and a swelling of the frontal. bone with somnolence was diagnosed with a Pott's puffy tumor (PPT). Minimal invasive surgical intervention was performed together with a strict regimen of antibiotic therapy. In this case debridement of the frontal
Modeling collective & intelligent decision making of multi-cellular populations.
Shin, Yong-Jun; Mahrou, Bahareh
2014-01-01
In the presence of unpredictable disturbances and uncertainties, cells intelligently achieve their goals by sharing information via cell-cell communication and making collective decisions, which are more reliable compared to individual decisions. Inspired by adaptive sensor network algorithms studied in communication engineering, we propose that a multi-cellular adaptive network can convert unreliable decisions by individual cells into a more reliable cell-population decision. It is demonstrated using the effector T helper (a type of immune cell) population, which plays a critical role in initiating immune reactions in response to invading foreign agents (e.g., viruses, bacteria, etc.). While each individual cell follows a simple adaptation rule, it is the combined coordination among multiple cells that leads to the manifestation of "self-organizing" decision making via cell-cell communication.
A cellular automata traffic flow modeling of desired speed variability
Institute of Scientific and Technical Information of China (English)
K.Bentaleb; K.Jetto; H.Ez-Zahraouy; A.Benyoussef
2013-01-01
The satisfaction rate of desired velocity in the case of a mixture of fast and slow vehicles is studied by using a cellular automaton method.It is found that at low density the satisfaction rate depends on the maximal velocity.However,the behavior of the satisfaction rate as a function of the coefficient of variance is independent of the maximal velocity.This is in good agreement with empirical results obtained by Lipshtat [Phys.Rev.E 79 066110 (2009)].Furthermore,our numerical result demonstrates that at low density the satisfaction rate takes higher values,whereas the coefficient of variance is close to zero.The coefficient of variance increases with increasing density,while the satisfaction rate decreases to zero.Moreover,we have also shown that,at low density the coefficient variance depends strongly on the probability of overtaking.
Cellular Automation Model of Traffic Flow Based on the Car-Following Model
Institute of Scientific and Technical Information of China (English)
LI Ke-Ping; GAO Zi-You
2004-01-01
@@ We propose a new cellular automation (CA) traffic model that is based on the car-following model. A class of driving strategies is used in the car-following model instead of the acceleration in the NaSch traffic model. In our model, some realistic driver behaviour and detailed vehicle characteristics have been taken into account, such as distance-headway and safe distance, etc. The simulation results show that our model can exhibit some traffic flow states that have been observed in the real traffic, and both of the maximum flux and the critical density are very close to the real measurement. Moreover, it is easy to extend our method to multi-lane traffic.
A multiscale theoretical model for diffusive mass transfer in cellular biological media.
Kapellos, George E; Alexiou, Terpsichori S; Payatakes, Alkiviades C
2007-11-01
An integrated methodology is developed for the theoretical analysis of solute transport and reaction in cellular biological media, such as tissues, microbial flocs, and biofilms. First, the method of local spatial averaging with a weight function is used to establish the equation which describes solute conservation at the cellular biological medium scale, starting with a continuum-based formulation of solute transport at finer spatial scales. Second, an effective-medium model is developed for the self-consistent calculation of the local diffusion coefficient in the cellular biological medium, including the effects of the structural heterogeneity of the extra-cellular space and the reversible adsorption to extra-cellular polymers. The final expression for the local effective diffusion coefficient is: D(Abeta)=lambda(beta)D(Aupsilon), where D(Aupsilon) is the diffusion coefficient in water, and lambda(beta) is a function of the composition and fundamental geometric and physicochemical system properties, including the size of solute molecules, the size of extra-cellular polymer fibers, and the mass permeability of the cell membrane. Furthermore, the analysis sheds some light on the function of the extra-cellular hydrogel as a diffusive barrier to solute molecules approaching the cell membrane, and its implications on the transport of chemotherapeutic agents within a cellular biological medium. Finally, the model predicts the qualitative trend as well as the quantitative variability of a large number of published experimental data on the diffusion coefficient of oxygen in cell-entrapping gels, microbial flocs, biofilms, and mammalian tissues.
Simulation Modeling by Classification of Problems: A Case of Cellular Manufacturing
Afiqah, K. N.; Mahayuddin, Z. R.
2016-02-01
Cellular manufacturing provides good solution approach to manufacturing area by applying Group Technology concept. The evolution of cellular manufacturing can enhance performance of the cell and to increase the quality of the product manufactured but it triggers other problem. Generally, this paper highlights factors and problems which emerge commonly in cellular manufacturing. The aim of the research is to develop a thorough understanding of common problems in cellular manufacturing. A part from that, in order to find a solution to the problems exist using simulation technique, this classification framework is very useful to be adapted during model building. Biology evolution tool was used in the research in order to classify the problems emerge. The result reveals 22 problems and 25 factors using cladistic technique. In this research, the expected result is the cladogram established based on the problems in cellular manufacturing gathered.
Modelling lava flows by Cellular Nonlinear Networks (CNN: preliminary results
Directory of Open Access Journals (Sweden)
C. Del Negro
2005-01-01
Full Text Available The forecasting of lava flow paths is a complex problem in which temperature, rheology and flux-rate all vary with space and time. The problem is more difficult to solve when lava runs down a real topography, considering that the relations between characteristic parameters of flow are typically nonlinear. An alternative approach to this problem that does not use standard differential equation methods is Cellular Nonlinear Networks (CNNs. The CNN paradigm is a natural and flexible framework for describing locally interconnected, simple, dynamic systems that have a lattice-like structure. They consist of arrays of essentially simple, nonlinearly coupled dynamic circuits containing linear and non-linear elements able to process large amounts of information in real time. Two different approaches have been implemented in simulating some lava flows. Firstly, a typical technique of the CNNs to analyze spatio-temporal phenomena (as Autowaves in 2-D and in 3-D has been utilized. Secondly, the CNNs have been used as solvers of partial differential equations of the Navier-Stokes treatment of Newtonian flow.
Establishment of a novel cellular model for myxofibrosarcoma heterogeneity
Lohberger, Birgit; Stuendl, Nicole; Leithner, Andreas; Rinner, Beate; Sauer, Stefan; Kashofer, Karl; Liegl-Atzwanger, Bernadette
2017-01-01
Human cancers frequently display substantial intra-tumoural heterogeneity in virtually all distinguishable phenotypic features, such as cellular morphology, gene expression, and metastatic potential. In order to investigate tumour heterogeneity in myxofibrosarcoma, we established a novel myxofibrosarcoma cell line with two well defined sub-clones named MUG-Myx2a and MUG-Myx2b. The parental tumour tissue and both MUG-Myx2 cell lines showed the same STR profile. The fact that MUG-Myx2a showed higher proliferation activity, faster migration and enhanced tumourigenicity was of particular interest. NGS mutation analysis revealed corresponding mutations in the FGFR3, KIT, KDR and TP53 genes. In contrast, the MUG-Myx2a cell lines showed an additional PTEN mutation. Analysis of CNV uncovered a highly aberrant karyotype with frequent losses and gains in the tumour sample. The two MUG-Myx2 cell lines share several CNV features of the tumour tissue, while some CNVs are present only in the two cell lines. Furthermore, certain CNV gains and losses that are exclusive to either MUG-Myx2a or MUG-Myx2b, distinguish the two cell lines. As it is currently not possible to purchase two different sarcoma cell lines derived from the same patient, the novel myxofibrosarcoma cell lines MUG-Myx2a and MUG-Myx2b will be useful tools to study pathogenesis, tumour heterogeneity and treatment options. PMID:28304377
Logical Modeling and Dynamical Analysis of Cellular Networks.
Abou-Jaoudé, Wassim; Traynard, Pauline; Monteiro, Pedro T; Saez-Rodriguez, Julio; Helikar, Tomáš; Thieffry, Denis; Chaouiya, Claudine
2016-01-01
The logical (or logic) formalism is increasingly used to model regulatory and signaling networks. Complementing these applications, several groups contributed various methods and tools to support the definition and analysis of logical models. After an introduction to the logical modeling framework and to several of its variants, we review here a number of recent methodological advances to ease the analysis of large and intricate networks. In particular, we survey approaches to determine model attractors and their reachability properties, to assess the dynamical impact of variations of external signals, and to consistently reduce large models. To illustrate these developments, we further consider several published logical models for two important biological processes, namely the differentiation of T helper cells and the control of mammalian cell cycle.
Jeans type instability for a chemotactic model of cellular aggregation
Chavanis, Pierre-Henri
2008-01-01
We consider an inertial model of chemotactic aggregation generalizing the Keller-Segel model and we study the linear dynamical stability of an infinite and homogeneous distribution of cells (bacteria, amoebae, endothelial cells,...) when inertial effects are accounted for. These inertial terms model cells directional persistance. We determine the condition of instability and the growth rate of the perturbation as a function of the cell density and the wavelength of the perturbation. We discuss the differences between overdamped (Keller-Segel) and inertial models. Finally, we show the analogy between the instability criterion for biological populations and the Jeans instability criterion in astrophysics.
Boolean network models of cellular regulation: prospects and limitations.
Bornholdt, Stefan
2008-08-06
Computer models are valuable tools towards an understanding of the cell's biochemical regulatory machinery. Possible levels of description of such models range from modelling the underlying biochemical details to top-down approaches, using tools from the theory of complex networks. The latter, coarse-grained approach is taken where regulatory circuits are classified in graph-theoretical terms, with the elements of the regulatory networks being reduced to simply nodes and links, in order to obtain architectural information about the network. Further, considering dynamics on networks at such an abstract level seems rather unlikely to match dynamical regulatory activity of biological cells. Therefore, it came as a surprise when recently examples of discrete dynamical network models based on very simplistic dynamical elements emerged which in fact do match sequences of regulatory patterns of their biological counterparts. Here I will review such discrete dynamical network models, or Boolean networks, of biological regulatory networks. Further, we will take a look at such models extended with stochastic noise, which allow studying the role of network topology in providing robustness against noise. In the end, we will discuss the interesting question of why at all such simple models can describe aspects of biology despite their simplicity. Finally, prospects of Boolean models in exploratory dynamical models for biological circuits and their mutants will be discussed.
Le mal de Pott: à propos de 82 cas
Directory of Open Access Journals (Sweden)
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.
Cellular cardiac electrophysiology modeling with Chaste and CellML.
Cooper, Jonathan; Spiteri, Raymond J; Mirams, Gary R
2014-01-01
Chaste is an open-source C++ library for computational biology that has well-developed cardiac electrophysiology tissue simulation support. In this paper, we introduce the features available for performing cardiac electrophysiology action potential simulations using a wide range of models from the Physiome repository. The mathematics of the models are described in CellML, with units for all quantities. The primary idea is that the model is defined in one place (the CellML file), and all model code is auto-generated at compile or run time; it never has to be manually edited. We use ontological annotation to identify model variables describing certain biological quantities (membrane voltage, capacitance, etc.) to allow us to import any relevant CellML models into the Chaste framework in consistent units and to interact with them via consistent interfaces. This approach provides a great deal of flexibility for analysing different models of the same system. Chaste provides a wide choice of numerical methods for solving the ordinary differential equations that describe the models. Fixed-timestep explicit and implicit solvers are provided, as discussed in previous work. Here we introduce the Rush-Larsen and Generalized Rush-Larsen integration techniques, made available via symbolic manipulation of the model equations, which are automatically rearranged into the forms required by these approaches. We have also integrated the CVODE solvers, a 'gold standard' for stiff systems, and we have developed support for symbolic computation of the Jacobian matrix, yielding further increases in the performance and accuracy of CVODE. We discuss some of the technical details of this work and compare the performance of the available numerical methods. Finally, we discuss how this is generalized in our functional curation framework, which uses a domain-specific language for defining complex experiments as a basis for comparison of model behavior.
Propagation Path Loss Models for 5G Urban Micro- and Macro-Cellular Scenarios
DEFF Research Database (Denmark)
Sun, Shu; Rappaport, Theodore S.; Rangan, Sundeep
2016-01-01
This paper presents and compares two candidate large-scale propagation path loss models, the alpha-beta-gamma (ABG) model and the close-in (CI) free space reference distance model, for the design of fifth generation (5G) wireless communication systems in urban micro- and macro-cellular scenarios....
A study of a main-road cellular automata traffic flow model
Institute of Scientific and Technical Information of China (English)
黄乒花; 孔令江; 刘慕仁
2002-01-01
A main-road cellular automata traffic flow model on two dimensions is presented based on the Biham-Middleton-Levine traffic model. Its evolution equations are given and the self-organization and organization cooperation phenomenain this model are also studied by using computer simulation.
Individual Subjective Initiative Merge Model Based on Cellular Automaton
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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.
Macromolecular Chain at a Cellular Surface: a Computer Simulation Model
Xie, Jun; Pandey, Ras
2001-06-01
Computer simulations are performed to study conformation and dynamics of relatively large chain macromolecule at the surface of a model cell membrane - a preliminary attempt to ultimately realistic model for protein on a cell membrane. We use a discrete lattice of size Lx × L × L. The chain molecule of length Lc is modelled by consecutive nodes connected by bonds on the trail of a random walk with appropriate constraints such as excluded volume, energy dependent configurational bias, etc. Monte Carlo method is used to move chains via segmental dynamics, i.e., end-move, kink-jump, crank-shaft, reptation, etc. Membrane substrate is designed by an ensemble of short chains on a flat surface. Large chain molecule is then driven toward the membrane by a field. We plan to examine the dynamics of chain macromolecule, spread of its density, and its conformation.
Dynamical modeling and analysis of large cellular regulatory networks
Bérenguier, D.; Chaouiya, C.; Monteiro, P. T.; Naldi, A.; Remy, E.; Thieffry, D.; Tichit, L.
2013-06-01
The dynamical analysis of large biological regulatory networks requires the development of scalable methods for mathematical modeling. Following the approach initially introduced by Thomas, we formalize the interactions between the components of a network in terms of discrete variables, functions, and parameters. Model simulations result in directed graphs, called state transition graphs. We are particularly interested in reachability properties and asymptotic behaviors, which correspond to terminal strongly connected components (or "attractors") in the state transition graph. A well-known problem is the exponential increase of the size of state transition graphs with the number of network components, in particular when using the biologically realistic asynchronous updating assumption. To address this problem, we have developed several complementary methods enabling the analysis of the behavior of large and complex logical models: (i) the definition of transition priority classes to simplify the dynamics; (ii) a model reduction method preserving essential dynamical properties, (iii) a novel algorithm to compact state transition graphs and directly generate compressed representations, emphasizing relevant transient and asymptotic dynamical properties. The power of an approach combining these different methods is demonstrated by applying them to a recent multilevel logical model for the network controlling CD4+ T helper cell response to antigen presentation and to a dozen cytokines. This model accounts for the differentiation of canonical Th1 and Th2 lymphocytes, as well as of inflammatory Th17 and regulatory T cells, along with many hybrid subtypes. All these methods have been implemented into the software GINsim, which enables the definition, the analysis, and the simulation of logical regulatory graphs.
Mechanism involved in the UCB neurotoxicity on cellular models
Giraudi, Pablo Jose'
2009-01-01
Summary This doctoral thesis covers three years period (2006-2008) during which I have investigated the bilirubin neurotoxicity in the neuroblastoma SH-SY5Y cell line, a neuronal cell model widely used in the study of the pathogenesis and in the development of new therapeutic compounds for neurodegenerative diseases. In the first chapter is summarized the current knowledge about bilirubin chemistry and metabolism including disorders of bilirubin metabolism and the neuronal disturbanc...
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.
A cellular automata model for simulating fed-batch penicillin fermentation process
Institute of Scientific and Technical Information of China (English)
Yu Naigong; Ruan Xiaogang
2006-01-01
A cellular automata model to simulate penicillin fed-batch fermentation process(CAPFM)was established in this study,based on a morphologically structured dynamic penicillin production model,that is in turn based on the growth mechanism of penicillin producing microorganisms and the characteristics of penicillin fed-batch fermentation.CAPFM uses the three-dimensional cellular automata as a growth space,and a Moore-type neighborhood as the cellular neighborhood.The transition roles of CAPFM are designed based on mechanical and structural kinetic models of penicillin batch-fed fermentation processes.Every cell of CAPFM represents a single or specific number of penicillin producing microorganisms,and has various state.The simulation experimental results show that CAPFM replicates the evolutionary behavior of penicillin batch-fed fermentation processes described by the structured penicillin production kinetic model accordingly.
Stochastic Model of Maturation and Vesicular Exchange in Cellular Organelles
Vagne, Quentin
2016-01-01
The dynamical organization of membrane-bound organelles along intracellular transport pathways relies on vesicular exchange between organelles and on biochemical maturation of the organelle content by specific enzymes. The relative importance of each mechanism in controlling organelle dynamics remains controversial, in particular for transport through the Golgi apparatus. Using a stochastic model, we show that full maturation of membrane-bound compartments can be seen as the stochastic escape from a steady-state in which export is dominated by vesicular exchange. We show that full maturation can contribute a significant fraction of the total out-flux for small organelles such as endosomes and Golgi cisternae.
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
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 pri
Designing and implementing a regional urban modeling system using the SLEUTH cellular urban model
Jantz, C.A.; Goetz, S.J.; Donato, D.; Claggett, P.
2010-01-01
This paper presents a fine-scale (30 meter resolution) regional land cover modeling system, based on the SLEUTH cellular automata model, that was developed for a 257000 km2 area comprising the Chesapeake Bay drainage basin in the eastern United States. As part of this effort, we developed a new version of the SLEUTH model (SLEUTH-3r), which introduces new functionality and fit metrics that substantially increase the performance and applicability of the model. In addition, we developed methods that expand the capability of SLEUTH to incorporate economic, cultural and policy information, opening up new avenues for the integration of SLEUTH with other land-change models. SLEUTH-3r is also more computationally efficient (by a factor of 5) and uses less memory (reduced 65%) than the original software. With the new version of SLEUTH, we were able to achieve high accuracies at both the aggregate level of 15 sub-regional modeling units and at finer scales. We present forecasts to 2030 of urban development under a current trends scenario across the entire Chesapeake Bay drainage basin, and three alternative scenarios for a sub-region within the Chesapeake Bay watershed to illustrate the new ability of SLEUTH-3r to generate forecasts across a broad range of conditions. ?? 2009 Elsevier Ltd.
Quantitative model of cell cycle arrest and cellular senescence in primary human fibroblasts.
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Sascha Schäuble
Full Text Available Primary human fibroblasts in tissue culture undergo a limited number of cell divisions before entering a non-replicative "senescent" state. At early population doublings (PD, fibroblasts are proliferation-competent displaying exponential growth. During further cell passaging, an increasing number of cells become cell cycle arrested and finally senescent. This transition from proliferating to senescent cells is driven by a number of endogenous and exogenous stress factors. Here, we have developed a new quantitative model for the stepwise transition from proliferating human fibroblasts (P via reversibly cell cycle arrested (C to irreversibly arrested senescent cells (S. In this model, the transition from P to C and to S is driven by a stress function γ and a cellular stress response function F which describes the time-delayed cellular response to experimentally induced irradiation stress. The application of this model based on senescence marker quantification at the single-cell level allowed to discriminate between the cellular states P, C, and S and delivers the transition rates between the P, C and S states for different human fibroblast cell types. Model-derived quantification unexpectedly revealed significant differences in the stress response of different fibroblast cell lines. Evaluating marker specificity, we found that SA-β-Gal is a good quantitative marker for cellular senescence in WI-38 and BJ cells, however much less so in MRC-5 cells. Furthermore we found that WI-38 cells are more sensitive to stress than BJ and MRC-5 cells. Thus, the explicit separation of stress induction from the cellular stress response, and the differentiation between three cellular states P, C and S allows for the first time to quantitatively assess the response of primary human fibroblasts towards endogenous and exogenous stress during cellular ageing.
Interaction of tea tree oil with model and cellular membranes.
Giordani, Cristiano; Molinari, Agnese; Toccacieli, Laura; Calcabrini, Annarica; Stringaro, Annarita; Chistolini, Pietro; Arancia, Giuseppe; Diociaiuti, Marco
2006-07-27
Tea tree oil (TTO) is the essential oil steam-distilled from Melaleuca alternifolia, a species of northern New South Wales, Australia. It exhibits a broad-spectrum antimicrobial activity and an antifungal activity. Only recently has TTO been shown to inhibit the in vitro growth of multidrug resistant (MDR) human melanoma cells. It has been suggested that the effect of TTO on tumor cells could be mediated by its interaction with the plasma membrane, most likely by inducing a reorganization of lipid architecture. In this paper we report biophysical and structural results obtained using simplified planar model membranes (Langmuir films) mimicking lipid "rafts". We also used flow cytometry analysis (FCA) and freeze-fracturing transmission electron microscopy to investigate the effects of TTO on actual MDR melanoma cell membranes. Thermodynamic (compression isotherms and adsorption kinetics) and structural (Brewster angle microscopy) investigation of the lipid monolayers clearly indicates that TTO interacts preferentially with the less ordered DPPC "sea" and that it does not alter the more ordered lipid "rafts". Structural observations, performed by freeze fracturing, confirm that TTO interacts with the MDR melanoma cell plasma membrane. Moreover, experiments performed by FCA demonstrate that TTO does not interfere with the function of the MDR drug transporter P-gp. We therefore propose that the effect exerted on MDR melanoma cells is mediated by the interaction with the fluid DPPC phase, rather than with the more organized "rafts" and that this interaction preferentially influences the ATP-independent antiapoptotic activity of P-gp likely localized outside "rafts".
Reverse engineering cellular decisions for hybrid reconfigurable network modeling
Blair, Howard A.; Saranak, Jureepan; Foster, Kenneth W.
2011-06-01
Cells as microorganisms and within multicellular organisms make robust decisions. Knowing how these complex cells make decisions is essential to explain, predict or mimic their behavior. The discovery of multi-layer multiple feedback loops in the signaling pathways of these modular hybrid systems suggests their decision making is sophisticated. Hybrid systems coordinate and integrate signals of various kinds: discrete on/off signals, continuous sensory signals, and stochastic and continuous fluctuations to regulate chemical concentrations. Such signaling networks can form reconfigurable networks of attractors and repellors giving them an extra level of organization that has resilient decision making built in. Work on generic attractor and repellor networks and on the already identified feedback networks and dynamic reconfigurable regulatory topologies in biological cells suggests that biological systems probably exploit such dynamic capabilities. We present a simple behavior of the swimming unicellular alga Chlamydomonas that involves interdependent discrete and continuous signals in feedback loops. We show how to rigorously verify a hybrid dynamical model of a biological system with respect to a declarative description of a cell's behavior. The hybrid dynamical systems we use are based on a unification of discrete structures and continuous topologies developed in prior work on convergence spaces. They involve variables of discrete and continuous types, in the sense of type theory in mathematical logic. A unification such as afforded by convergence spaces is necessary if one wants to take account of the affect of the structural relationships within each type on the dynamics of the system.
The natural alternative: protozoa as cellular models for Legionella infection.
Hoffmann, Christine; Harrison, Christopher F; Hilbi, Hubert
2014-01-01
The severe pneumonia known as Legionnaires' disease occurs following infection by the Gram-negative bacterium Legionella pneumophila. Normally resident in fresh-water sources, Legionella are subject to predation by eukaryotic phagocytes such as amoeba and ciliates. To counter this, L. pneumophila has evolved a complex system of effector proteins which allow the bacteria to hijack the phagocytic vacuole, hiding and replicating within their erstwhile killers. These same mechanisms allow L. pneumophila to hijack another phagocyte, lung-based macrophages, which thus avoids a vital part of the immune system and leads to infection. The course of infection can be divided into five main categories: pathogen uptake, formation of the replication-permissive vacuole, intracellular replication, host cell response, and bacterial exit. L. pneumophila effector proteins target every stage of this process, interacting with secretory, endosomal, lysosomal, retrograde and autophagy pathways, as well as with mitochondria. Each of these steps can be studied in protozoa or mammalian cells, and the knowledge gained can be readily applied to human pathogenicity. Here we describe the manner whereby L. pneumophila infects host protozoa, the various techniques which are available to analyse these processes and the implications of this model for Legionella virulence and the pathogenesis of Legionnaires' disease.
Evaluation of BACE1 Silencing in Cellular Models
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Malgorzata Sierant
2009-01-01
Full Text Available Beta-secretase (BACE1 is the major enzyme participating in generation of toxic amyloid-beta (Aβ peptides, identified in amyloid plaques of Alzheimer's disease (AD brains. Its downregulation results in decreasing secretion of Aβ. Thus, BACE1 silencing by RNAi represents possible strategy for antiamyloid therapy in the treatment of AD. In this study, a series of newly designed sequences of synthetic and vector-encoded siRNAs (pSilencer, pcPURhU6, and lentivirus were tested against overexpressed and endogenous BACE1 in several cell lines and in adult neural progenitor cells, derived from rat hippocampus. SiRNAs active in human, mouse, and rat cell models were shown to diminish the level of BACE1. In HCN A94 cells, two BACE1-specific siRNAs did not alter the expression of genes of BACE2 and several selected genes involved in neurogenesis (Synapsin I, βIII-Tubulin, Calbidin, NeuroD1, GluR2, CREB, MeCP2, PKR, however, remarkable lowering of SCG10 mRNA, coding protein of stathmin family, important in the development of nervous system, was observed.
Tools and Models for Integrating Multiple Cellular Networks
Energy Technology Data Exchange (ETDEWEB)
Gerstein, Mark [Yale Univ., New Haven, CT (United States). Gerstein Lab.
2015-11-06
CRIT for correlation analysis in systems biology [5]. For Aim 3, we have further investigated the scaling relationship that the number of Transcription Factors (TFs) in a genome is proportional to the square of the total number of genes. We have extended the analysis from transcription factors to various classes of functional categories, and from individual categories to joint distribution [6]. By introducing a new analytical framework, we have generalized the original toolbox model to take into account of metabolic network with arbitrary network topology [7].
Kinetic theory approach to modeling of cellular repair mechanisms under genome stress.
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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.
Aristotelous, Andreas C; Haider, Mansoor A
2014-08-01
Macroscopic models accounting for cellular effects in natural or engineered tissues may involve unknown constitutive terms that are highly dependent on interactions at the scale of individual cells. Hybrid discrete models, which represent cells individually, were used to develop and apply techniques for modeling diffusive nutrient transport and cellular uptake to identify a nonlinear nutrient loss term in a macroscopic reaction-diffusion model of the system. Flexible and robust numerical methods were used, based on discontinuous Galerkin finite elements in space and a Crank-Nicolson temporal discretization. Scales were bridged via averaging operations over a complete set of subdomains yielding data for identification of a macroscopic nutrient loss term that was accurately captured via a fifth-order polynomial. Accuracy of the identified macroscopic model was demonstrated by direct, quantitative comparisons of the tissue and cellular scale models in terms of three error norms computed on a mesoscale mesh.
Directory of Open Access Journals (Sweden)
Wimol San-Um
2015-12-01
Full Text Available This paper presents a robust cellular associative memory for pattern recognitions using composite trigonometric chaotic neuron models. Robust chaotic neurons are designed through a scan of positive Lyapunov Exponent (LE bifurcation structures, which indicate the quantitative measure of chaoticity for one-dimensional discrete-time dynamical systems. The proposed chaotic neuron model is a composite of sine and cosine chaotic maps, which are independent from the output activation function. Dynamics behaviors are demonstrated through bifurcation diagrams and LE-based bifurcation structures. An application to associative memories of binary patterns in Cellular Neural Networks (CNN topology is demonstrated using a signum output activation function. Examples of English alphabets are stored using symmetric auto-associative matrix of n-binary patterns. Simulation results have demonstrated that the cellular neural network can quickly and effectively restore the distorted pattern to expected information.
Lovreglio, Ruggiero; Ronchi, Enrico; Nilsson, Daniel
2015-11-01
The formulation of pedestrian floor field cellular automaton models is generally based on hypothetical assumptions to represent reality. This paper proposes a novel methodology to calibrate these models using experimental trajectories. The methodology is based on likelihood function optimization and allows verifying whether the parameters defining a model statistically affect pedestrian navigation. Moreover, it allows comparing different model specifications or the parameters of the same model estimated using different data collection techniques, e.g. virtual reality experiment, real data, etc. The methodology is here implemented using navigation data collected in a Virtual Reality tunnel evacuation experiment including 96 participants. A trajectory dataset in the proximity of an emergency exit is used to test and compare different metrics, i.e. Euclidean and modified Euclidean distance, for the static floor field. In the present case study, modified Euclidean metrics provide better fitting with the data. A new formulation using random parameters for pedestrian cellular automaton models is also defined and tested.
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
A coarse-grained model for the simulations of biomolecular interactions in cellular environments
Energy Technology Data Exchange (ETDEWEB)
Xie, Zhong-Ru; Chen, Jiawen; Wu, Yinghao, E-mail: yinghao.wu@einstein.yu.edu [Department of Systems and Computational Biology, Albert Einstein College of Medicine of Yeshiva University, 1300 Morris Park Avenue, Bronx, New York 10461 (United States)
2014-02-07
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.
Caracciolo, Domenico; Istanbulluoglu, Erkan; Noto, Leonardo V.
2014-05-01
Arid grasslands of southwestern North America have changed dramatically over the last 150 years as a result of the shrub encroachment, i.e. the increase in density and biomass of indigenous shrubby plants in grasslands. Numerous studies have documented the expansion of shrublands in the southwestern America Grasslands; in particular the encroachment of shrubs in american deserts has strongly occurred in the Chihuahuan deserts from 1860. The Sevilleta National Wildlife Refuge (SNWR), located in the northern Chihuahuan desert shows a dramatic encroachment front of creosote bush (i.e., shrub) into native desert grassland. This encroachment has been here simulated using an Ecohydrological Cellular Automata Model, CATGraSS. CATGraSS is a spatially distributed model driven by spatially explicit irradiance and runs on a fine-resolution gridded domain. In the model, each cell can hold a single plant type or can represent bare soil. Plant competition is modeled by keeping track of mortality and establishment of plants, both calculated probabilistically based on soil moisture stress. For this study, the model is improved with a stochastic fire and a grazing function, and its plant establishment algorithm is modified. CATGraSS is implemented in a small area (7.3 km2) in SNWR, characterized by two vegetation types: grass savanna and creosote bush. The causes that have been considered for the encroachment in this case study are: the fire return period increase, the grazing increase, the seed dispersal caused by animals, the role of wind direction and the shrub-grass inhibition effect. The model is able to reproduce the encroachment occurred in the SNWR basin, simulating an increasing of the shrub from 2% in 1860 to 42% (i.e., current shrub percentage) in 2010 highlighting as more influent factors the reduced fire frequency and the increased grazing intensity. For the future management and encroachment control, the reduction of the fire return period and the grazing removal
An agent-based model of cellular dynamics and circadian variability in human endotoxemia.
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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.
Two-dimensional cellular automaton model of traffic flow with open boundaries
Tadaki, S I
1996-01-01
A two-dimensional cellular automaton model of traffic flow with open boundaries are investigated by computer simulations. The outflow of cars from the system and the average velocity are investigated. The time sequences of the outflow and average velocity have flicker noises in a jamming phase. The low density behavior are discussed with simple jam-free approximation.
Schokker, D.; Bannink, A.; Smits, M.A.; Rebel, J.M.J.
2013-01-01
The aim of this study was to create a dynamic mathematical model of the development of the cellular branch of the intestinal immune system of poultry during the first 42 days of life and of its response towards an oral infection with Salmonella enterica serovar Enteritidis. The system elements were
Embryonic stem cells as an ectodermal cellular model of human p63-related dysplasia syndromes.
Rostagno, P.; Wolchinsky, Z.; Vigano, A.M.; Shivtiel, S.; Zhou, H.; Bokhoven, J.H.L.M. van; Ferone, G.; Missero, C.; Mantovani, R.; Aberdam, D.; Virolle, T.
2010-01-01
Heterozygous mutations in the TP63 transcription factor underlie the molecular basis of several similar autosomal dominant ectodermal dysplasia (ED) syndromes. Here we provide a novel cellular model derived from embryonic stem (ES) cells that recapitulates in vitro the main steps of embryonic skin d
Performance Evaluation of Road Traffic Control Using a Fuzzy Cellular Model
Płaczek, Bartłomiej
2011-01-01
In this paper a method is proposed for performance evaluation of road traffic control systems. The method is designed to be implemented in an on-line simulation environment, which enables optimisation of adaptive traffic control strategies. Performance measures are computed using a fuzzy cellular traffic model, formulated as a hybrid system combining cellular automata and fuzzy calculus. Experimental results show that the introduced method allows the performance to be evaluated using imprecise traffic measurements. Moreover, the fuzzy definitions of performance measures are convenient for uncertainty determination in traffic control decisions.
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.
Modeling of aluminum-silicon irregular eutectic growth by cellular automaton model
Directory of Open Access Journals (Sweden)
Rui Chen
2016-03-01
Full Text Available Due to the extensive application of Al-Si alloys in the automotive and aerospace industries as structural components, an understanding of their microstructural formation, such as dendrite and (Al+Si eutectic, is of great importance to control the desirable microstructure, so as to modify the performance of castings. Since previous major themes of microstructural simulation are dendrite and regular eutectic growth, few efforts have been paid to simulate the irregular eutectic growth. Therefore, a multiphase cellular automaton (CA model is developed and applied to simulate the time-dependent Al-Si irregular eutectic growth. Prior to model establishment, related experiments were carried out to investigate the influence of cooling rate and Sr modification on the growth of eutectic Si. This CA model incorporates several aspects, including growth algorithms and nucleation criterion, to achieve the competitive and cooperative growth mechanism for nonfaceted-faceted Al-Si irregular eutectic. The growth kinetics considers thermal undercooling, constitutional undercooling, and curvature undercooling, as well as the anisotropic characteristic of eutectic Si growth. The capturing rule takes into account the effects of modification on the silicon growth behaviors. The simulated results indicate that for unmodified alloy, the higher eutectic undercooling results in the higher eutectic growth velocity, and a more refined eutectic microstructure as well as narrower eutectic lamellar spacing. For modified alloy, the eutectic silicon tends to be obvious fibrous morphology and the morphology of eutectic Si is determined by both chemical modifier and cooling rate. The predicted microstructure of Al-7Si alloy under different solidification conditions shows that this proposed model can successfully reproduce both dendrite and eutectic microstructures.
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
Wei, Jianshe; Fujita, Masayo; Nakai, Masaaki; Waragai, Masaaki; Sekigawa, Akio; Sugama, Shuei; Takenouchi, Takato; Masliah, Eliezer; Hashimoto,Makoto
2009-01-01
Gangliosides may be involved in the pathogenesis of Parkinson’s disease and related disorders, although the precise mechanisms governing this involvement remain unknown. In this study, we determined whether changes in endogenous ganglioside levels affect lysosomal pathology in a cellular model of synucleinopathy. For this purpose, dementia with Lewy body-linked P123H β-synuclein (β-syn) neuroblastoma cells transfected with α-synuclein were used as a model system because these cells were chara...
Modeling Recrystallization of Austenite for C-Mn Steels during Hot Deformation by Cellular Automaton
Institute of Scientific and Technical Information of China (English)
无
2002-01-01
By using a cellular automaton method, microstructure evolution of recrystallization in austenite during hot deformation was simulated for C-Mn steels. A model takes into account the influence of deformation temperature, strain, and strain rate on the dynamic recrystallization fraction, and the effect of the keeping time on the static recrystallization fraction based on a hot deformation test on a Gleeble-1500 simulator. In addition, the size changing of γ grains during continuous hot deformation was simulated by applying the model.
Cellular Automaton Rule 184++C A Simple Model for the Complex Dynamics of Various Particles Flow
Awazu, A
1999-01-01
A cellular automaton named Rule 184++C is proposed as a meta-model to investigate the flow of various complex particles. In this model, unlike the granular pipe flow and the traffic flow, not only the free-jam phase transition but also the free-intermediate, the intermediate-jam, and the dilute-dense phase transitions appear. Moreover, the freezing phenomena appear if the system contains two types of different particles.
Korpusik, Adam
2017-02-01
We present a nonstandard finite difference scheme for a basic model of cellular immune response to viral infection. The main advantage of this approach is that it preserves the essential qualitative features of the original continuous model (non-negativity and boundedness of the solution, equilibria and their stability conditions), while being easy to implement. All of the qualitative features are preserved independently of the chosen step-size. Numerical simulations of our approach and comparison with other conventional simulation methods are presented.
Dunes morphologies and superimposed bedforms in a cellular automaton dune model
Zhang, D.; Narteau, C.; Rozier, O.; Claudin, P.
2009-04-01
We use a new 3D cellular automaton model for bedform dynamics in which individual physical processes such as erosion, deposition and transport are implemented by nearest neighbor interactions and a time-dependent stochastic process. Simultaneously, a lattice gas cellular automaton model is used to compute the flow and quantify the bed shear stress on the topography. Local erosion rates are taken proportional to the shear stress in such a way that there is a complete feedback mechanism between flow and bedform dynamics. In the numerical simulations of dune fields, we observe the formation and the evolution of barchan, transverse, longitudinal and star dunes. For all these types of dunes, we observe the emergence of superimposed bedforms when dunes are large enough. Then, we use the same model under different initial conditions, and we perform the linear stability analysis of a flat sand bed disturbed by a small sinusoidal perturbation. Comparing the most unstable wavelength in the model with the characteristic size of secondary bedforms in nature, we determine the length and time scales of our cellular automaton model. Thus, we establish a link between discrete and continuous approaches and open new perspectives for modeling and quantification of complex patterns in dune fields.
Energy Technology Data Exchange (ETDEWEB)
Schmidt, Brian; Ebrahim, Ali; Metz, Thomas O.; Adkins, Joshua N.; Palsson, Bernard O.; Hyduke, Daniel R.
2013-11-15
Motivation: Genome-scale metabolic models have been used extensively to investigate alterations in cellular metabolism. The accuracy of these models to represent cellular metabolism in specific conditions has been improved by constraining the model with omics data sources. However, few practical methods for integrating metabolomics data with other omics data sources into genome-scale models of metabolism have been reported. Results: GIMMME (Gene Inactivation Moderated by Metabolism, Metabolomics, and Expression) is an algorithm that enables the development of condition-specific models based on an objective function, transcriptomics, and intracellular metabolomics data. GIMMME establishes metabolite utilization requirements with metabolomics data, uses model-paired transcriptomics data to find experimentally supported solutions, and also provides calculations of the turnover (production / consumption) flux of metabolites. GIMMME was employed to investigate the effects of integrating additional omics datasets to create increasingly constrained solution spaces of Salmonella Typhimurium metabolism during growth in both rich and virulence media. This integration proved to be informative and resulted in a requirement of additional active reactions (12 in each case) or metabolites (26 or 29, respectively). The addition of constraints from transcriptomics also impacted the allowed solution space, and the cellular metabolites with turnover fluxes that were necessarily altered by the change in conditions increased from 118 to 271 of 1397. Availability: GIMMME has been implemented in Python and requires a COBRApy 0.2.x. The algorithm and sample data described here are freely available at: http://opencobra.sourceforge.net/
Directory of Open Access Journals (Sweden)
Luciano Farage
2002-03-01
Full Text Available Relatamos caso de tratamento cirúrgico com instrumentação anterior em espondilite tuberculosa (mal de Pott, em mulher de 71 anos, que se encontrava em tratamento para tuberculose na forma pulmonar e evoluiu com dor lombar, dificuldade progressiva para deambular, cifose e disfunção vesical. A ressonância magnética revelou lesão nos corpos vertebrais de T12 e L1 com abcesso paravertebral. A paciente foi tratada cirurgicamente por acesso tóraco-abdominal lateral. Os corpos vertebrais foram ressecados, foi instalado uma gaiola vertical (mesh cage e a coluna foi estabilizada com placa lateral (Z plate e parafusos fixados em T11 e L2. Essa técnica permite boa artrodese dos corpos vertebrais remanescentes e boa estabilidade da coluna, sem comprometer a eficácia dos tuberculostáticos. A paciente foi avaliada um ano após a operação e não apresentava déficit motor, dor residual e a cifose foi desfeita.We report a case of a surgical treatment with anterior instrumentation in tuberculous spondylitis (Pott's disease, in a 71 years old woman, that was in treatment for pulmonary tuberculosis, with lumbar pain, progressive disability to walk, kyphotic deformit and vesical dysfunction. Magnetic resonance image presents a lesion in the bodies of T12 and L1, with paravertebral abscess. The patient was treated surgically by transthoracic-abdominal approach. The vertebral bodies were cut off and the spine were instrumented anteriorly with a mesh cage and a Z plate. This procedure permits a good arthrodesis and a immediately stabilization of the spine, without any complication of the infection. The patient was seen a year after the surgery and is free of infection, without motor deficit, pain or reminiscent kyphosis.
Modeling of time-dose-LET effects in the cellular response to radiation
Energy Technology Data Exchange (ETDEWEB)
Herr, Lisa Antje
2015-07-20
This work is dedicated to the elucidation of time-dose- and if applicable linear energy transfer (LET) effects in the cellular response to ion or photon radiation. In particular, the common concept of the Local Effect Model (LEM) and the Giant Loop Binary Lesion (GLOBLE) model, which explains cell survival probabilities on the hand of clustering of double-strand breaks (DSB) in micrometer-sized sub-structural units of the DNA, was investigated with regard to temporal aspects. In previous studies with the LEM and GLOBLE model, it has been demonstrated that the definition of two lesion classes, characterized by single or multiple DSB in a DNA giant loop, with two repair fidelities is adequate to comprehensively describe the dose dependence of the cellular response to instantaneous photon irradiation or ion irradiation with varying LET. Furthermore, with the GLOBLE model for photon radiation, it has been shown that the assignment of two repair time scales to the two lesion classes allows to adequately reproduce time-dose effects after photon irradiation with an arbitrary constant dose-rate. In this work, the results of four projects that strengthen the mechanistic consistency and the practical applicability of the LEM and GLOBLE model will be presented. First, it was found that the GLOBLE model is applicable to describe time-dose effects in the cellular response to two split photon doses and in the occurrence of deterministic radiation effects. Second, in a comparison of ten models for the temporal course of DSB rejoining, it was revealed that a bi-exponential approach, as suggested by the LEM and GLOBLE model, finds a relatively large support by 61 experimental data sets. Third, in a comparison of four kinetic photon cell survival models that was based on fits to 13 dose-rate experiments, it was shown that the GLOBLE model performs well with respect to e.g. accuracy, parsimony, reliability and other factors that characterize a good approach. Last but not least, the
Theoretical model for cellular shapes driven by protrusive and adhesive forces.
Directory of Open Access Journals (Sweden)
Doron Kabaso
2011-05-01
Full Text Available The forces that arise from the actin cytoskeleton play a crucial role in determining the cell shape. These include protrusive forces due to actin polymerization and adhesion to the external matrix. We present here a theoretical model for the cellular shapes resulting from the feedback between the membrane shape and the forces acting on the membrane, mediated by curvature-sensitive membrane complexes of a convex shape. In previous theoretical studies we have investigated the regimes of linear instability where spontaneous formation of cellular protrusions is initiated. Here we calculate the evolution of a two dimensional cell contour beyond the linear regime and determine the final steady-state shapes arising within the model. We find that shapes driven by adhesion or by actin polymerization (lamellipodia have very different morphologies, as observed in cells. Furthermore, we find that as the strength of the protrusive forces diminish, the system approaches a stabilization of a periodic pattern of protrusions. This result can provide an explanation for a number of puzzling experimental observations regarding cellular shape dependence on the properties of the extra-cellular matrix.
Li, Qi-Lang; Wong, S. C.; Min, Jie; Tian, Shuo; Wang, Bing-Hong
2016-08-01
This study examines the cellular automata traffic flow model, which considers the heterogeneity of vehicle acceleration and the delay probability of vehicles. Computer simulations are used to identify three typical phases in the model: free-flow, synchronized flow, and wide moving traffic jam. In the synchronized flow region of the fundamental diagram, the low and high velocity vehicles compete with each other and play an important role in the evolution of the system. The analysis shows that there are two types of bistable phases. However, in the original Nagel and Schreckenberg cellular automata traffic model, there are only two kinds of traffic conditions, namely, free-flow and traffic jams. The synchronized flow phase and bistable phase have not been found.
A Cellular Automaton Model for Tumor Dormancy: Emergence of a Proliferative Switch
Chen, Duyu; Torquato, Salvatore
2014-01-01
Malignant cancers that lead to fatal outcomes for patients may remain dormant for very long periods of time. Although individual mechanisms such as cellular dormancy, angiogenic dormancy and immunosurveillance have been proposed, a comprehensive understanding of cancer dormancy and the "switch" from a dormant to a proliferative state still needs to be strengthened from both a basic and clinical point of view. Computational modeling enables one to explore a variety of scenarios for possible but realistic microscopic dormancy mechanisms and their predicted outcomes. The aim of this paper is to devise such a predictive computational model of dormancy with an emergent "switch" behavior. Specifically, we generalize a previous cellular automaton (CA) model for proliferative growth of solid tumor that now incorporates a variety of cell-level tumor-host interactions and different mechanisms for tumor dormancy, for example the effects of the immune system. Our new CA rules induce a natural "competition" between the tu...
An Extended Cellular Automaton Model for Train Traffic Flow on the Dedicated Passenger Lines
Directory of Open Access Journals (Sweden)
Wenbo Zhao
2014-01-01
Full Text Available As one of the key components for the railway transportation system, the Train Operation Diagram can be greatly influenced by many extrinsic and intrinsic factors. Therefore, the railway train flow has shown the strong nonlinear characteristics, which makes it quite difficult to take further relative studies. Fortunately, the cellular automaton model has its own advantages in solving nonlinear problems and traffic flow simulation. Considering the mixed features of multispeed running trains on the passenger dedicated lines, this paper presents a new train model under the moving block system with different types of trains running with the cellular automaton idea. By analyzing such key factors as the maintenance skylight, the proportion of the multispeed running trains, and the distance between adjacent stations and departure intervals, the corresponding running rules for the cellular automaton model are reestablished herewith. By means of this CA model, the program of train running system is designed to analyze the potential impact on railway carrying capacity by various factors; the model can also be implemented to simulate the actual train running process and to draw the train operation diagram by computers. Basically the theory can be applied to organize the train operation on the dedicated passenger lines.
A generalized cellular automata approach to modeling first order enzyme kinetics
Indian Academy of Sciences (India)
Abhishek Dutta; Saurajyoti Kar; Advait Apte; Ingmar Nopens; Denis Constales
2015-04-01
Biochemical processes occur through intermediate steps which are associated with the formation of reaction complexes. These enzyme-catalyzed biochemical reactions are inhibited in a number of ways such as inhibitors competing for the binding site directly, inhibitors deforming the allosteric site or inhibitors changing the structure of active substrate. Using an in silico approach, the concentration of various reaction agents can be monitored at every single time step, which are otherwise difficult to analyze experimentally. Cell-based models with discrete state variables, such as Cellular Automata (CA) provide an understanding of the organizational principles of interacting cellular systems to link the individual cell (microscopic) dynamics wit a particular collective (macroscopic) phenomenon. In this study, a CA model representing a first order enzyme kinetics with inhibitor activity is formulated. The framework of enzyme reaction rules described in this study is probabilistic. An extended von Neumann neighborhood with periodic boundary condition is implemented on a two-dimensional (2D) lattice framework. The effect of lattice-size variation is studied followed by a sensitivity analysis of the model output to the probabilistic parameters which represent various kinetic reaction constants in the enzyme kinetic model. This provides a deeper insight into the sensitivity of the CA model to these parameters. It is observed that cellular automata can capture the essential features of a discrete real system, consisting of space, time and state, structured with simple local rules without making complex implementations but resulting in complex but explainable patterns.
Tratamiento quirúrgico de la enfermedad de Pott por vía anterior
2013-01-01
OBJETIVO: Evaluar la corrección de la deformidad cifótica, estabilidad y fusión que otorga la utilización de implantes de titanio (Synex - Ventrofix de Synthes) en la tuberculosis espinal. MÉTODOS: Entre enero de 2010 y agosto de 2012 ocho pacientes con diagnóstico de enfermedad del Pott se sometieron a intervención quirúrgica por vía anterior, con seguimiento de 18 meses. El procedimiento consistió en desbridamiento amplio del cuerpo afectado seguido de instrumentación con implantes de titan...
Pott's puffy tumor: a rare complication of acute otitis media in child: a case report.
Urík, Milan; Machač, Josef; Šlapák, Ivo; Hošnová, Dagmar
2015-09-01
To describe a rare case of Potts' puffy tumor (PPT) in the zygomatic area, which developed as a complication of acute otitis media in a 6-year-old child. To date, only one case of PPT has been described in the literature as a complication of latent mastoiditis in an adult, and one case of PPT as a complication of acute mastoiditis in a 10-year-old child. Urgent surgical intervention, including evacuation of the purulent lesion, removal of inflamed soft tissue and osteolysis of the involved bone, and antromastoidectomy, intravenous treatment with broad-spectrum antibiotics, including G+, G-, anaerobes and fungi, and local therapy.
A mathematical model to study the dynamics of epithelial cellular networks.
Abate, Alessandro; Vincent, Stéphane; Dobbe, Roel; Silletti, Alberto; Master, Neal; Axelrod, Jeffrey D; Tomlin, Claire J
2012-01-01
Epithelia are sheets of connected cells that are essential across the animal kingdom. Experimental observations suggest that the dynamical behavior of many single-layered epithelial tissues has strong analogies with that of specific mechanical systems, namely large networks consisting of point masses connected through spring-damper elements and undergoing the influence of active and dissipating forces. Based on this analogy, this work develops a modeling framework to enable the study of the mechanical properties and of the dynamic behavior of large epithelial cellular networks. The model is built first by creating a network topology that is extracted from the actual cellular geometry as obtained from experiments, then by associating a mechanical structure and dynamics to the network via spring-damper elements. This scalable approach enables running simulations of large network dynamics: the derived modeling framework in particular is predisposed to be tailored to study general dynamics (for example, morphogenesis) of various classes of single-layered epithelial cellular networks. In this contribution, we test the model on a case study of the dorsal epithelium of the Drosophila melanogaster embryo during early dorsal closure (and, less conspicuously, germband retraction).
Directory of Open Access Journals (Sweden)
Konstantinos B. Baltzis
2008-10-01
Full Text Available A common assumption in cellular communications is the circular-cell approximation. In this paper, an alternative analysis based on the hexagonal shape of the cells is presented. A geometrical-based stochastic model is proposed to describe the angle of arrival of the interfering signals in the reverse link of a cellular system. Explicit closed form expressions are derived, and simulations performed exhibit the characteristics and validate the accuracy of the proposed model. Applications in the capacity estimation of WCDMA cellular networks are presented. Dependence of system capacity of the sectorization of the cells and the base station antenna radiation pattern is explored. Comparisons with data in literature validate the accuracy of the proposed model. The degree of error of the hexagonal and the circular-cell approaches has been investigated indicating the validity of the proposed model. Results have also shown that, in many cases, the two approaches give similar results when the radius of the circle equals to the hexagon inradius. A brief discussion on how the proposed technique may be applied to broadband access networks is finally made.
Directory of Open Access Journals (Sweden)
Baltzis KonstantinosB
2008-01-01
Full Text Available Abstract 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.
Realistic multi-cellular dosimetry for 177Lu-labelled antibodies: model and application
Marcatili, S.; Pichard, A.; Courteau, A.; Ladjohounlou, R.; Navarro-Teulon, I.; Repetto-Llamazares, A.; Heyerdahl, H.; Dahle, J.; Pouget, J. P.; Bardiès, M.
2016-10-01
Current preclinical dosimetric models often fail to take account of the complex nature of absorbed dose distribution typical of in vitro clonogenic experiments in targeted radionuclide therapy. For this reason, clonogenic survival is often expressed as a function of added activity rather than the absorbed dose delivered to cells/cell nuclei. We designed a multi-cellular dosimetry model that takes into account the realistic distributions of cells in the Petri dish, for the establishment of survival curves as a function of the absorbed dose. General-purpose software tools were used for the generation of realistic, randomised 3D cell culture geometries based on experimentally determined parameters (cell size, cell density, cluster density, average cluster size, cell cumulated activity). A mixture of Monte Carlo and analytical approaches was implemented in order to achieve as accurate as possible results while reducing calculation time. The model was here applied to clonogenic survival experiments carried out to compare the efficacy of Betalutin®, a novel 177Lu-labelled antibody radionuclide conjugate for the treatment of non-Hodgkin lymphoma, to that of 177Lu-labelled CD20-specific (rituximab) and non-specific antibodies (Erbitux) on lymphocyte B cells. The 3D cellular model developed allowed a better understanding of the radiative and non-radiative processes associated with cellular death. Our approach is generic and can also be applied to other radiopharmaceuticals and cell distributions.
From Cells to Islands: An unified Model of Cellular Parallel Genetic Algorithms
Simoncini, David; Verel, Sébastien; Clergue, Manuel
2008-01-01
This paper presents the Anisotropic selection scheme for cellular Genetic Algorithms (cGA). This new scheme allows to enhance diversity and to control the selective pressure which are two important issues in Genetic Algorithms, especially when trying to solve difficult optimization problems. Varying the anisotropic degree of selection allows swapping from a cellular to an island model of parallel genetic algorithm. Measures of performances and diversity have been performed on one well-known problem: the Quadratic Assignment Problem which is known to be difficult to optimize. Experiences show that, tuning the anisotropic degree, we can find the accurate trade-off between cGA and island models to optimize performances of parallel evolutionary algorithms. This trade-off can be interpreted as the suitable degree of migration among subpopulations in a parallel Genetic Algorithm.
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.
Oh, Eung Seok; Heo, Chaejeong; Kim, Ji Seon; Suh, Minah; Lee, Young Hee; Kim, Jong-Min
2014-05-01
Parkinson's disease (PD) is characterized by progressive dopaminergic cell loss in the substantia nigra (SN) and elevated iron levels demonstrated by autopsy. Direct visualization of iron with live imaging techniques has not yet been successful. The aim of this study is to visualize and quantify the distribution of cellular iron using an intrinsic iron hyperspectral fluorescence signal. The 1-methyl-4-phenylpyridinium (MPP+)-induced cellular model of PD was established in SHSY5Y cells exposed to iron with ferric ammonium citrate (FAC, 100 μM). The hyperspectral fluorescence signal of iron was examined using a high-resolution dark-field optical microscope system with signal absorption for the visible/near infrared spectral range. The 6-h group showed heavy cellular iron deposition compared with the 1-h group. The cellular iron was dispersed in a small particulate form, whereas the extracellular iron was aggregated. In addition, iron particles were found to be concentrated on the cell membrane/edge of shrunken cells. The iron accumulation readily occurred in MPP+-induced cells, which is consistent with previous studies demonstrating elevated iron levels in the SN. This direct iron imaging could be applied to analyze the physiological role of iron, and its application might be expanded to various neurological disorders involving metals, such as copper, manganese, or zinc.
Institute of Scientific and Technical Information of China (English)
HE; Chunyang; SHI; Peijun; CHEN; Jin; Li; Xiaobing; PAN; Ya
2005-01-01
Modeling land use scenario changes and its potential impacts on the structure and function of the ecosystem in the typical regions are helpful to understanding the interactive mechanism between land use system and ecological system. A Land Use Scenario Dynamics (LUSD) model by the integration of System Dynamics (SD) model and Cellular Automata (CA) model is developed with land use scenario changes in northern China in the next 20 years simulated in this paper. The basic idea of LUSD model is to simulate the land use scenario demands by using SD model at first, then allocate the land use scenario patterns at the local scale with the considerations of land use suitability, inheritance ability and neighborhood effect by using CA model to satisfy the balance between land use scenario demands and supply. The application of LUSD model in northern China suggests that the model has the ability to reflect the complex behavior of land use system at different scales to some extent and is a useful tool for assessing the potential impacts of land use system on ecological system. In addition, the simulated results also indicate that obvious land use changes will take place in the farming-pastoral zone of northern China in the next 20 years with cultivated land and urban land being the most active land use types.
Modeling and Experimental Study of Soft Error Propagation Based on Cellular Automaton
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...
A Real-Space Cellular Automaton Laboratory for the modeling of complex dunefields
Rozier, Olivier; Narteau, Clement
2013-04-01
Using applications in the physics of sand dunes, we explore the capabilities of a Real Space Cellular Automaton Laboratory (ReSCAL), a generator of 3D stochastic cellular automaton stochastic cellular automaton models with continuous time. The objective of this software is to develop interdisciplinary research collaboration to investigate the dynamics of complex systems. In the vast majority of numerical models, any point in space is entirely characterized by a local set of physical variables (e. g. temperature, pressure, velocity) that are recalculated over time according to some predetermined set of fundamental laws. However, there is not always a satisfactory theoretical framework from which we can try to quantify the overall dynamics of the system. For this reason, we prefer concentrate on features of organization and ReSCAL is entirely constructed from a finite number of discrete states that represent the different phases of matter involved in the system under consideration. Then, an elementary cell is a real-space representation of the physical environment. Pairs of nearest neighbor cells are called doublets and each individual physical process is associated with a set of doublet transitions and a characteristic transition rate. Using a modular approach, we show how it is possible to model and combine a wide range of physical, chemical and/or anthropological processes. As an example, we discuss different dune morphologies with respect to rotating wind conditions.
Ozcan, H. Kurtulus; Bilgili, Erdem; Sahin, Ulku; Ucan, O. Nuri; Bayat, Cuma
2007-09-01
Tropospheric ozone concentrations, which are an important air pollutant, are modeled by the use of an artificial intelligence structure. Data obtained from air pollution measurement stations in the city of Istanbul are utilized in constituting the model. A supervised algorithm for the evaluation of ozone concentration using a genetically trained multi-level cellular neural network (ML-CNN) is introduced, developed, and applied to real data. A genetic algorithm is used in the optimization of CNN templates. The model results and the actual measurement results are compared and statistically evaluated. It is observed that seasonal changes in ozone concentrations are reflected effectively by the concentrations estimated by the multilevel-CNN model structure, with a correlation value of 0.57 ascertained between actual and model results. It is shown that the multilevel-CNN modeling technique is as satisfactory as other modeling techniques in associating the data in a complex medium in air pollution applications.
Institute of Scientific and Technical Information of China (English)
H. Kurtulus OZCAN; Erdem BILGILI; Ulku SAHIN; O. Nuri UCAN; Cuma BAYAT
2007-01-01
Tropospheric ozone concentrations, which are an important air pollutant, are modeled by the use of an artificial intelligence structure. Data obtained from air pollution measurement stations in the city of Istanbul are utilized in constituting the model. A supervised algorithm for the evaluation of ozone concentration using a genetically trained multi-level cellular neural network (ML-CNN) is introduced, developed, and applied to real data. A genetic algorithm is used in the optimization of CNN templates. The model results and the actual measurement results are compared and statistically evaluated. It is observed that seasonal changes in ozone concentrations are reflected effectively by the concentrations estimated by the multilevel-CNN model structure, with a correlation value of 0.57 ascertained between actual and model results. It is shown that the multilevel-CNN modeling technique is as satisfactory as other modeling techniques in associating the data in a complex medium in air pollution applications.
Silver Nanoparticle-Mediated Cellular Responses in Various Cell Lines: An in Vitro Model
Directory of Open Access Journals (Sweden)
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
Silver Nanoparticle-Mediated Cellular Responses in Various Cell Lines: An in Vitro Model
Zhang, Xi-Feng; Shen, Wei; Gurunathan, Sangiliyandi
2016-01-01
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 future perspectives
Chronobiology at the cellular and molecular levels: models and mechanisms for circadian timekeeping.
Edmunds, L N
1983-12-01
This review considers cellular chronobiology and examines, at least in a superficial way, several classes of models and mechanisms that have been proposed for circadian rhythmicity and some of the experimental approaches that have appeared to be most productive. After a brief discussion of temporal organization and the metabolic, epigenetic, and circadian time domains, the general properties of circadian rhythms are enumerated. A survey of independent oscillations in isolated organs, tissues, and cells is followed by a review of selected circadian rhythms in eukaryotic microorganisms, with particular emphasis placed on the rhythm of cell division in the algal flagellate Euglena as a model system illustrating temporal differentiation. In the ensuing section, experimental approaches to circadian clock mechanisms are considered. The dissection of the clock by the use of chemical inhibitors is illustrated for the rhythm of bioluminescence in the marine dinoflagellate Gonyaulax and for the rhythm of photosynthetic capacity in the unicellular green alga Acetabularia. Alternatively, genetic analysis of circadian oscillators is considered in the green alga Chlamydomonas and in the bread mold Neurospora, both of which have yielded clock mutants and mutants having biochemical lesions that exhibit altered clock properties. On the basis of the evidence generated by these experimental approaches, several classes of biochemical and molecular models for circadian clocks have been proposed. These include strictly molecular models, feedback loop (network) models, transcriptional (tape-reading) models, and membrane models; some of their key elements and predictions are discussed. Finally, a number of general unsolved problems at the cellular level are briefly mentioned: cell cycle interfaces, the evolution of circadian rhythmicity, the possibility of multiple cellular oscillators, chronopharmacology and chronotherapy, and cell-cycle clocks in development and aging.
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.
An improved multi-value cellular automata model for heterogeneous bicycle traffic flow
Energy Technology Data Exchange (ETDEWEB)
Jin, Sheng [College of Civil Engineering and Architecture, Zhejiang University, Hangzhou, 310058 China (China); Qu, Xiaobo [Griffith School of Engineering, Griffith University, Gold Coast, 4222 Australia (Australia); Xu, Cheng [Department of Transportation Management Engineering, Zhejiang Police College, Hangzhou, 310053 China (China); College of Transportation, Jilin University, Changchun, 130022 China (China); Ma, Dongfang, E-mail: mdf2004@zju.edu.cn [Ocean College, Zhejiang University, Hangzhou, 310058 China (China); Wang, Dianhai [College of Civil Engineering and Architecture, Zhejiang University, Hangzhou, 310058 China (China)
2015-10-16
This letter develops an improved multi-value cellular automata model for heterogeneous bicycle traffic flow taking the higher maximum speed of electric bicycles into consideration. The update rules of both regular and electric bicycles are improved, with maximum speeds of two and three cells per second respectively. Numerical simulation results for deterministic and stochastic cases are obtained. The fundamental diagrams and multiple states effects under different model parameters are analyzed and discussed. Field observations were made to calibrate the slowdown probabilities. The results imply that the improved extended Burgers cellular automata (IEBCA) model is more consistent with the field observations than previous models and greatly enhances the realism of the bicycle traffic model. - Highlights: • We proposed an improved multi-value CA model with higher maximum speed. • Update rules are introduced for heterogeneous bicycle traffic with maximum speed 2 and 3 cells/s. • Simulation results of the proposed model are consistent with field bicycle data. • Slowdown probabilities of both regular and electric bicycles are calibrated.
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.
Guided Inquiry and Consensus-Building Used to Construct Cellular Models
Directory of Open Access Journals (Sweden)
Joel I. Cohen
2015-02-01
Full Text Available Using models helps students learn from a “whole systems” perspective when studying the cell. This paper describes a model that employs guided inquiry and requires consensus building among students for its completion. The model is interactive, meaning that it expands upon a static model which, once completed, cannot be altered and additionally relates various levels of biological organization (molecular, organelle, and cellular to define cell and organelle function and interaction. Learning goals are assessed using data summed from final grades and from images of the student’s final cell model (plant, bacteria, and yeast taken from diverse seventh grade classes. Instructional figures showing consensus-building pathways and seating arrangements are discussed. Results suggest that the model leads to a high rate of participation, facilitates guided inquiry, and fosters group and individual exploration by challenging student understanding of the living cell.
Drosophila as a genetic and cellular model for studies on axonal growth
Directory of Open Access Journals (Sweden)
Whitington Paul
2007-05-01
Full Text Available Abstract One of the most fascinating processes during nervous system development is the establishment of stereotypic neuronal networks. An essential step in this process is the outgrowth and precise navigation (pathfinding of axons and dendrites towards their synaptic partner cells. This phenomenon was first described more than a century ago and, over the past decades, increasing insights have been gained into the cellular and molecular mechanisms regulating neuronal growth and navigation. Progress in this area has been greatly assisted by the use of simple and genetically tractable invertebrate model systems, such as the fruit fly Drosophila melanogaster. This review is dedicated to Drosophila as a genetic and cellular model to study axonal growth and demonstrates how it can and has been used for this research. We describe the various cellular systems of Drosophila used for such studies, insights into axonal growth cones and their cytoskeletal dynamics, and summarise identified molecular signalling pathways required for growth cone navigation, with particular focus on pathfinding decisions in the ventral nerve cord of Drosophila embryos. These Drosophila-specific aspects are viewed in the general context of our current knowledge about neuronal growth.
Mechanistic Modelling of DNA Repair and Cellular Survival Following Radiation-Induced DNA Damage
McMahon, Stephen J.; Schuemann, Jan; Paganetti, Harald; Prise, Kevin M.
2016-09-01
Characterising and predicting the effects of ionising radiation on cells remains challenging, with the lack of robust models of the underlying mechanism of radiation responses providing a significant limitation to the development of personalised radiotherapy. In this paper we present a mechanistic model of cellular response to radiation that incorporates the kinetics of different DNA repair processes, the spatial distribution of double strand breaks and the resulting probability and severity of misrepair. This model enables predictions to be made of a range of key biological endpoints (DNA repair kinetics, chromosome aberration and mutation formation, survival) across a range of cell types based on a set of 11 mechanistic fitting parameters that are common across all cells. Applying this model to cellular survival showed its capacity to stratify the radiosensitivity of cells based on aspects of their phenotype and experimental conditions such as cell cycle phase and plating delay (correlation between modelled and observed Mean Inactivation Doses R2 > 0.9). By explicitly incorporating underlying mechanistic factors, this model can integrate knowledge from a wide range of biological studies to provide robust predictions and may act as a foundation for future calculations of individualised radiosensitivity.
Reprint of Infinity computations in cellular automaton forest-fire model
Iudin, D. I.; Sergeyev, Ya. D.; Hayakawa, M.
2015-04-01
Recently a number of traditional models related to the percolation theory has been considered by means of a new computational methodology that does not use Cantor's ideas and describes infinite and infinitesimal numbers in accordance with the principle 'The whole is greater than the part' (Euclid's Common Notion 5). Here we apply the new arithmetic to a cellular automaton forest-fire model which is connected with the percolation methodology and in some sense combines the dynamic and the static percolation problems and under certain conditions exhibits critical fluctuations. It is well known that there exist two versions of the model: real forest-fire model where fire catches adjacent trees in the forest in the step by step manner and simplified version with instantaneous combustion. Using new approach we observe that in both situations we deal with the same model but with different time resolution. We show that depending on the "microscope" we use the same cellular automaton forest-fire model reveals either instantaneous forest combustion or step by step firing. By means of the new approach it was also observed that as far as we choose an infinitesimal tree growing rate and infinitesimal ratio between the ignition probability and the growth probability we determine the measure or extent of the system size infinity that provides the criticality of the system dynamics. Correspondent inequalities for grosspowers are derived.
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.
Modeling the dendritic evolution and micro-segregation of cast alloy with cellular automaton
Institute of Scientific and Technical Information of China (English)
Qiang Li; Dianzhong Li; Bainian Qian
2004-01-01
In order to precisely describe the dendritic morphology and micro-segregation during solidification process, a novel continuous model concerning the different physical properties in the solid phase, liquid phase and interface is developed. Coupling the heat and solute diffusion with the transition rules, the dendrite evolution is simulated by cellular automaton method. Then, the solidification microstructure evolution of a small ingot is simulated by using this method. The simulated results indicate that this model can simulate the dendrite growth, show the second dendrite arm and tertiary dendrite arm, and reveal the micro-segregation in the inter-dendritic zones. Furthermore, the columnar-to-equiaxed transition (CET) is predicted.
A Cellular Automaton Model for Heterogeneous and Incosistent Driver Behavior in Urban Traffic
Institute of Scientific and Technical Information of China (English)
LIUMing-Zhe; ZHAO Shi-Bo; WANG Rui-Li
2012-01-01
In this paper a cellular automaton model is proposed to describe driver behavior at a single-lane urban roundabout. Driver behavior has been considered as heterogeneous and inconsistent. Most traffic papers in the literature just discussed heterogeneous driver behavior, to our best knowledge. Two truncated Caussian distributions are used to model heterogeneous and inconsistent driver behavior, respectively. The physical meanings of two truncated distributions are indicated. This method may help enhance a better understanding of driver behavior at roundabout traffic, and even possibly provide references for roundabout design and management.
On a cellular automaton with time delay for modelling cancer tumors
Energy Technology Data Exchange (ETDEWEB)
Iarosz, K C; Martins, C C; Batista, A M [Departamento de Matematica e EstatIstica, Universidade Estadual de Ponta Grossa, 84030-900, Ponta Grossa, PR (Brazil); Viana, R L; Lopes, S R [Departamento de Fisica, Universidade Federal do Parana, 81531-990, Curitiba, PR (Brazil); Caldas, I L [Instituto de Fisica, Universidade de Sao Paulo, Caixa Postal 66316, 05315-970, Sao Paulo, SP (Brazil); Penna, T J P, E-mail: antoniomarcosbatista@gmail.com [Instituto de Fisica, Universidade Federal Fluminense, 24210-340, Niteroi, RJ (Brazil)
2011-03-01
In this work we considered cellular automaton model with time delay. Time delay included in this model reflects the delay between the time in which the site is affected and the time in which its variable is updated. We analyzed the effect of the rules on the dynamics through the cluster counting. According to this cluster counting, the dynamics behavior is investigated. We verified periodic oscillations same as delay differential equation. We also studied the relation between the time delay in the cell cycle and the time to start the metastasis, using suitable numerical diagnostics.
Modeling Mixed Bicycle Traffic Flow: A Comparative Study on the Cellular Automata Approach
Directory of Open Access Journals (Sweden)
Dan Zhou
2015-01-01
Full Text Available Simulation, as a powerful tool for evaluating transportation systems, has been widely used in transportation planning, management, and operations. Most of the simulation models are focused on motorized vehicles, and the modeling of nonmotorized vehicles is ignored. The cellular automata (CA model is a very important simulation approach and is widely used for motorized vehicle traffic. The Nagel-Schreckenberg (NS CA model and the multivalue CA (M-CA model are two categories of CA model that have been used in previous studies on bicycle traffic flow. This paper improves on these two CA models and also compares their characteristics. It introduces a two-lane NS CA model and M-CA model for both regular bicycles (RBs and electric bicycles (EBs. In the research for this paper, many cases, featuring different values for the slowing down probability, lane-changing probability, and proportion of EBs, were simulated, while the fundamental diagrams and capacities of the proposed models were analyzed and compared between the two models. Field data were collected for the evaluation of the two models. The results show that the M-CA model exhibits more stable performance than the two-lane NS model and provides results that are closer to real bicycle traffic.
DEFF Research Database (Denmark)
Osmanagic, Azra; Emamifar, Amir; Christian Bang, Jacob;
2016-01-01
BACKGROUND Pott's disease (PD) or spinal tuberculosis is a rare condition which accounts for less than 1% of total tuberculosis (TB) cases. The incidence of PD has recently increased in Europe and the United States, mainly due to immigration; however, it is still a rare diagnosis in Scandinavian...
2D cellular automaton model for the evolution of active region coronal plasmas
Fuentes, Marcelo López
2016-01-01
We study a 2D cellular automaton (CA) model for the evolution of coronal loop plasmas. The model is based on the idea that coronal loops are made of elementary magnetic strands that are tangled and stressed by the displacement of their footpoints by photospheric motions. The magnetic stress accumulated between neighbor strands is released in sudden reconnection events or nanoflares that heat the plasma. We combine the CA model with the Enthalpy Based Thermal Evolution of Loops (EBTEL) model to compute the response of the plasma to the heating events. Using the known response of the XRT telescope on board Hinode we also obtain synthetic data. The model obeys easy to understand scaling laws relating the output (nanoflare energy, temperature, density, intensity) to the input parameters (field strength, strand length, critical misalignment angle). The nanoflares have a power-law distribution with a universal slope of -2.5, independent of the input parameters. The repetition frequency of nanoflares, expressed in t...
A traffic flow cellular automaton model to considering drivers' learning and forgetting behaviour
Institute of Scientific and Technical Information of China (English)
Ding Jian-Xun; Huang Hai-Jun; Tian Qiong
2011-01-01
It is known that the commonly used NaSch cellular automaton (CA) model and its modifications can help explain the internal causes of the macro phenomena of traffic flow. However, the randomization probability of vehicle velocity used in these models is assumed to be an exogenous constant or a conditional constant, which cannot reflect the learning and forgetting behaviour of drivers with historical experiences. This paper further modifies the NaSch model by enabling the randomization probability to be adjusted on the bases of drivers' memory. The Markov properties of this modified model are discussed. Analytical and simulation results show that the traffic fundamental diagrams can be indeed improved when considering drivers' intelligent behaviour. Some new features of traffic are revealed by differently combining the model parameters representing learning and forgetting behaviour.
Band, Leah R; Fozard, John A; Godin, Christophe; Jensen, Oliver E; Pridmore, Tony; Bennett, Malcolm J; King, John R
2012-10-01
Over recent decades, we have gained detailed knowledge of many processes involved in root growth and development. However, with this knowledge come increasing complexity and an increasing need for mechanistic modeling to understand how those individual processes interact. One major challenge is in relating genotypes to phenotypes, requiring us to move beyond the network and cellular scales, to use multiscale modeling to predict emergent dynamics at the tissue and organ levels. In this review, we highlight recent developments in multiscale modeling, illustrating how these are generating new mechanistic insights into the regulation of root growth and development. We consider how these models are motivating new biological data analysis and explore directions for future research. This modeling progress will be crucial as we move from a qualitative to an increasingly quantitative understanding of root biology, generating predictive tools that accelerate the development of improved crop varieties.
Cellular Automata Modelling of Photo-Induced Oxidation Processes in Molecularly Doped Polymers
Directory of Open Access Journals (Sweden)
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.
Comparative Analysis of Empirical Path Loss Model for Cellular Transmission in Rivers State
Directory of Open Access Journals (Sweden)
B.O.H Akinwole, Biebuma J.J
2013-08-01
Full Text Available This paper presents a comparative analysis of three empirical path loss models with measured data for urban, suburban, and rural areas in Rivers State. The three models investigated were COST 231 Hata, SUI,ECC-33models. A downlink data was collected at operating frequency of 2100MHz using drive test procedure consisting of test mobile phones to determine the received signal power (RSCP at specified receiver distanceson a Globacom Node Bs located in some locations in the State. This test was carried out for investigating the effectiveness of the commonly used existing models for Cellular transmission. The results analysed were based on Mean Square Error (MSE and Standard Deviation (SD and were simulated on MATLAB (7.5.0. The results show that COST 231 Hata model gives better predictions and therefore recommended for path loss predictions in River State.
Numerical study on photoresist etching processes based on a cellular automata model
Institute of Scientific and Technical Information of China (English)
2007-01-01
For the three-dimensional (3-D) numerical study of photoresist etching processes, the 2-D dynamic cellular automata (CA) model has been successfully extended to a 3-D dynamic CA model. Only the boundary cells will be processed in the 3-D dy-namic CA model and the structure of “if-else” description in the simulation pro-gram is avoided to speed up the simulation. The 3-D dynamic CA model has found to be stable, fast and accurate for the numerical study of photoresist etching processes. The exposure simulation, post-exposure bake (PEB) simulation and etching simulation are integrated together to further investigate the performances of the CA model. Simulation results have been compared with the available ex-perimental results and the simulations show good agreement with the available experiments.
Numerical study on photoresist etching processes based on a cellular automata model
Institute of Scientific and Technical Information of China (English)
ZHOU ZaiFa; HUANG QingAn; LI WeiHua; LU Wei
2007-01-01
For the three-dimensional (3-D) numerical study of photoresist etching processes, the 2-D dynamic cellular automata (CA) model has been successfully extended to a 3-D dynamic CA model. Only the boundary cells will be processed in the 3-D dynamic CA model and the structure of "if-else" description in the simulation program is avoided to speed up the simulation. The 3-D dynamic CA model has found to be stable, fast and accurate for the numerical study of photoresist etching processes. The exposure simulation, post-exposure bake (PEB) simulation and etching simulation are integrated together to further investigate the performances of the CA model. Simulation results have been compared with the available experimental results and the simulations show good agreement with the available experiments.
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).
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.
Idealists in the Ruhr region; Idealisten im Pott
Energy Technology Data Exchange (ETDEWEB)
Meyer, J.P.
2001-07-01
In spite of a reimbursement of 99 DPf/kWh, installation of private PV systems still requires idealism. A model project was initiated by the local authorities of the town of Schwerte near Dortmund: It all started in 1991 with the carbon dioxide emissions reduction concept of the town of Schwerte. Private builder-owners were to be informed on alternative energy sources. In 1993, regular meetings were introduced with the aim of informing the public (including the use of tools like the web) and of getting as many PV systems as possible going on Schwerte roofs. [German] Trotz der 99 Pf/kWh braucht die Installation von privaten PV-Anlagen immer noch viel Engagement. Ein vorbildliches Projekt ist auf Initiative der Stadt Schwerte bei Dortmund entstanden und lebt heute dank der unermuedlichen Arbeit einzelner PV-Begeisterter weiter: der Schwerter Solarstammtisch. Begonnen hat es 1991 mit dem CO{sub 2}-Minderungskonzept der Stadt Schwerte. Private Bauherren sollten auf den Einsatz alternativer Energien hingewiesen werden. Aus dieser Idee entwickelte sich 1993 ein regelmaessiges Treffen mit dem Ziel 'die Menschen zu informieren (auch ueber das Internet) und moeglichst viele Anlagen auf Schwerter Daecher zu bekommen'. (orig.)
Synchronized Flow in a Cellular Automaton Model with Time Headway Dependent Randomization
Institute of Scientific and Technical Information of China (English)
CHEN Tao; JIA Bin; LI Xin-Gang; JIANG Rui; GAO Zi-You
2008-01-01
@@ We propose another possible mechanism of synchronized flow, I.e. That a time headway dependent randomization can exhibit synchronized flow. Based on this assumption, we present a new cellular automaton (CA) model for traffic flow, in which randomization effect is enhanced with the decrease of time headway. We study fundamental diagram and spatial-temporal diagrams of the model and perform microscopic analysis of time series data, which shows the model could reproduce synchronized flow as expected. It is also shown that a spontaneous transition from synchronized flow to jam could be observed by incorporating slow-to-start effect into the model. We expect that our work could contribute to the understanding of the real origin of synchronized flow.
Empirical results for pedestrian dynamics and their implications for cellular automata models
Schadschneider, Andreas
2010-01-01
A large number of models for pedestrian dynamics have been developed over the years. However, so far not much attention has been paid to their quantitative validation. Usually the focus is on the reproduction of empirically observed collective phenomena, as lane formation in counterflow. This can give an indication for the realism of the model, but practical applications, e.g. in safety analysis, require quantitative predictions. We discuss the current experimental situation, especially for the fundamental diagram which is the most important quantity needed for calibration. In addition we consider the implications for the modelling based on cellular automata. As specific example the floor field model is introduced. Apart from the properties of its fundamental diagram we discuss the implications of an egress experiment for the relevance of conflicts and friction effects.
Cellular automaton modeling of ductile iron microstructure in the thin wall
Directory of Open Access Journals (Sweden)
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.
A self-modifying cellular automaton model of historical urbanization in the San Francisco Bay area
Clarke, K.C.; Hoppen, S.; Gaydos, L.
1997-01-01
In this paper we describe a cellular automaton (CA) simulation model developed to predict urban growth as part of a project for estimating the regional and broader impact of urbanization on the San Francisco Bay area's climate. The rules of the model are more complex than those of a typical CA and involve the use of multiple data sources, including topography, road networks, and existing settlement distributions, and their modification over time. In addition, the control parameters of the model are allowed to self-modify: that is, the CA adapts itself to the circumstances it generates, in particular, during periods of rapid growth or stagnation. In addition, the model was written to allow the accumulation of probabilistic estimates based on Monte Carlo methods. Calibration of the model has been accomplished by the use of historical maps to compare model predictions of urbanization, based solely upon the distribution in year 1900, with observed data for years 1940, 1954, 1962, 1974, and 1990. The complexity of this model has made calibration a particularly demanding step. Lessons learned about the methods, measures, and strategies developed to calibrate the model may be of use in other environmental modeling contexts. With the calibration complete, the model is being used to generate a set of future scenarios for the San Francisco Bay area along with their probabilities based on the Monte Carlo version of the model. Animated dynamic mapping of the simulations will be used to allow visualization of the impact of future urban growth.
In situ sensing and modeling of molecular events at the cellular level
Yang, Ruiguo
We developed the Atomic Force Microscopy (AFM) based nanorobot in combination with other nanomechanical sensors for the investigation of cell signaling pathways. The AFM nanorobotics hinge on the superior spatial resolution of AFM in imaging and extends it into the measurement of biological processes and manipulation of biological matters. A multiple input single output control system was designed and implemented to solve the issues of nanomanipulation of biological materials, feedback, response frequency and nonlinearity. The AFM nanorobotic system therefore provide the human-directed position, velocity and force control with high frequency feedback, and more importantly it can feed the operator with the real-time imaging of manipulation result from the fast-imaging based local scanning. The use of the system has taken the study of cellular process at the molecular scale into a new level. The cellular response to the physiological conditions can be significantly manifested in cellular mechanics. Dynamic mechanical property has been regarded as biomarkers, sometimes even regulators of the signaling and physiological processes, thus the name mechanobiology. We sought to characterize the relationship between the structural dynamics and the molecular dynamics and the role of them in the regulation of cell behavior. We used the AFM nanorobotics to investigate the mechanical properties in real-time of cells that are stimulated by different chemical species. These reagents could result in similar ion channel responses but distinctive mechanical behaviors. We applied these measurement results to establish a model that describes the cellular stimulation and the mechanical property change, a "two-hit" model that comprises the loss of cell adhesion and the initiation of cell apoptosis. The first hit was verified by functional experiments: depletion of Calcium and nanosurgery to disrupt the cellular adhesion. The second hit was tested by a labeling of apoptotic markers that
Enayatifar, Rasul; Sadaei, Hossein Javedani; Abdullah, Abdul Hanan; Lee, Malrey; Isnin, Ismail Fauzi
2015-08-01
Currently, there are many studies have conducted on developing security of the digital image in order to protect such data while they are sending on the internet. This work aims to propose a new approach based on a hybrid model of the Tinkerbell chaotic map, deoxyribonucleic acid (DNA) and cellular automata (CA). DNA rules, DNA sequence XOR operator and CA rules are used simultaneously to encrypt the plain-image pixels. To determine rule number in DNA sequence and also CA, a 2-dimension Tinkerbell chaotic map is employed. Experimental results and computer simulations, both confirm that the proposed scheme not only demonstrates outstanding encryption, but also resists various typical attacks.
Modeling Mixed Traffic Flow at Crosswalks in Micro-Simulations Using Cellular Automata
Institute of Scientific and Technical Information of China (English)
DUAN Houli; ZHANG Yi
2007-01-01
The cellular automata (CA) micro-simulation model was used to describe the behavior of the mixed traffic flows at crosswalks where the pedestrians compete with the vehicles to cross the roadway. The focus of this paper is the behavior of pedestrians and the influence of pedestrians' behavior on the vehicle flow, pedestrian flows, and the vehicle waiting time. The proportion of pedestrians who do not obey traffic laws, the group effect, and expected waiting time of pedestrians, regarded as the most important pedestrian characteristics, are taken into consideration in the analysis. Simulation results show the ability of the microsimulation to capture the most important features of mixed traffic flow.
Heijman, Jordi; Erfanian Abdoust, Pegah; Voigt, Niels; Nattel, Stanley; Dobrev, Dobromir
2016-02-01
The complexity of the heart makes an intuitive understanding of the relative contribution of ion channels, transporters and signalling pathways to cardiac electrophysiology challenging. Computational modelling of cardiac cellular electrophysiology has proven useful to integrate experimental findings, extrapolate results obtained in expression systems or animal models to other systems, test quantitatively ideas based on experimental data and provide novel hypotheses that are experimentally testable. While the bulk of computational modelling has traditionally been directed towards ventricular bioelectricity, increasing recognition of the clinical importance of atrial arrhythmias, particularly atrial fibrillation, has led to widespread efforts to apply computational approaches to understanding atrial electrical function. The increasing availability of detailed, atrial-specific experimental data has stimulated the development of novel computational models of atrial-cellular electrophysiology and Ca(2+) handling. To date, more than 300 studies have employed mathematical simulations to enhance our understanding of atrial electrophysiology, arrhythmogenesis and therapeutic responses. Future modelling studies are likely to move beyond current whole-cell models by incorporating new data on subcellular architecture, macromolecular protein complexes, and localized ion-channel regulation by signalling pathways. At the same time, more integrative multicellular models that take into account regional electrophysiological and Ca(2+) handling properties, mechano-electrical feedback and/or autonomic regulation will be needed to investigate the mechanisms governing atrial arrhythmias. A combined experimental and computational approach is expected to provide the more comprehensive understanding of atrial arrhythmogenesis that is required to develop improved diagnostic and therapeutic options. Here, we review this rapidly expanding area, with a particular focus on Ca(2+) handling, and
Doutres, Olivier; Atalla, Noureddine; Osman, Haisam
2015-06-01
Porous materials are widely used for improving sound absorption and sound transmission loss of vibrating structures. However, their efficiency is limited to medium and high frequencies of sound. A solution for improving their low frequency behavior while keeping an acceptable thickness is to embed resonant structures such as Helmholtz resonators (HRs). This work investigates the absorption and transmission acoustic performances of a cellular porous material with a two-dimensional periodic arrangement of HR inclusions. A low frequency model of a resonant periodic unit cell based on the parallel transfer matrix method is presented. The model is validated by comparison with impedance tube measurements and simulations based on both the finite element method and a homogenization based model. At the HR resonance frequency (i) the transmission loss is greatly improved and (ii) the sound absorption of the foam can be either decreased or improved depending on the HR tuning frequency and on the thickness and properties of the host foam. Finally, the diffuse field sound absorption and diffuse field sound transmission loss performance of a 2.6 m(2) resonant cellular material are measured. It is shown that the improvements observed at the Helmholtz resonant frequency on a single cell are confirmed at a larger scale.
An implementation of cellular automaton model for single-line train working diagram
Institute of Scientific and Technical Information of China (English)
Hua Wei; Liu Jun
2006-01-01
According to the railway transportation system's characteristics,a new cellular automaton model for the singleline railway system is presented in this paper.Based on this model,several simulations were done to imitate the train operation under three working diagrams.From a different angle the results show how the organization of train operation impacts on the railway carrying capacity.By using the non-parallel train working diagram the influence of fast-train on slow-train is found to be the strongest.Many slow-trains have to wait in-between neighbouring stations to let the fast-train(s) pass through first.So the slow-train will advance like a wave propagating from the departure station to the arrival station.This also resembles the situation of a highway jammed traffic flow.Furthermore,the nonuniformity of travel times between the sections also greatly limits the railway carrying capacity.After converting the nonuniform sections into the sections with uniform travel times while the total travel time is kept unchanged,all three carrying capacities are improved greatly as shown by simulation.It also shows that the cellular automaton model is an effective and feasible way to investigate the railway transDortation system.
Transition between immune and disease states in a cellular automaton model of clonal immune response
Bezzi, M; Ruffo, S; Seiden, P E; Bezzi, Michele; Celada, Franco; Ruffo, Stefano; Seiden, Philip E.
1997-01-01
In this paper we extend the Celada-Seiden (CS) model of the humoral immune response to include infectious virus and cytotoxic T lymphocytes (cellular response). The response of the system to virus involves a competition between the ability of the virus to kill the host cells and the host's ability to eliminate the virus. We find two basins of attraction in the dynamics of this system, one is identified with disease and the other with the immune state. There is also an oscillating state that exists on the border of these two stable states. Fluctuations in the population of virus or antibody can end the oscillation and drive the system into one of the stable states. The introduction of mechanisms of cross-regulation between the two responses can bias the system towards one of them. We also study a mean field model, based on coupled maps, to investigate virus-like infections. This simple model reproduces the attractors for average populations observed in the cellular automaton. All the dynamical behavior connect...
Institute of Scientific and Technical Information of China (English)
2012-01-01
A cellular automaton （CA）-finite element （FE） model and a phase field （PF）-FE model were used to simulate equiaxed dendritic growth during the solidification of hexagonal metals. In the CA-FE model, the conservation equations of mass and energy were solved in order to calculate the temperature field, solute concentration, and the dendritic growth morphology. CA-FE simulation results showed reasonable agreement with the previously reported experimental data on secondary dendrite arm spacing （SDAS） vs cooling rate. In the PF model, a PF variable was used to distinguish solid and liquid phases similar to the conventional PF models for solidification of pure materials. Another PF variable was considered to determine the evolution of solute concentration. Validation of both models was performed by comparing the simulation results with the analytical model developed by Lipton-Glicksman-Kurz （LGK）, showing quantitatively good agreement in the tip growth velocity at a given melt undercooling. Application to magnesium alloy AZ91 （approximated with the binary Mg-8.9 wt% AI） illustrates the difficulty of modeling dendrite growth in hexagonal systems using CA-FE regarding mesh-induced anisotropy and a better performance of PF-FE in modeling multiple arbitrarily-oriented dendrites growth.
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.
A Two-Lane Cellular Automata Model with Influence of Next-Nearest Neighbor Vehicle
Institute of Scientific and Technical Information of China (English)
无
2006-01-01
In this paper, we propose a new two-lane cellular automata model in which the influence of the next-nearest neighbor vehicle is considered. The attributes of the traffic system composed of fast-lane and slow-lane are investigated by the new traffic model. The simulation results show that the proposed two-lane traffic model can reproduce some traffic phenomena observed in real traffic, and that maximum flux and critical density are close to the field measurements.Moreover, the initial density distribution of the fast-lane and slow-lane has much influence on the traffic flow states.With the ratio between the densities of slow lane and fast lane increasing the lane changing frequency increases, but maximum flux decreases. Finally, the influence of the sensitivity coefficients is discussed.
A three-dimensional cellular automaton model for simulation of dendritic growth of magnesium alloy
Institute of Scientific and Technical Information of China (English)
Mengwu WU; Shoumei XIONG
2012-01-01
A numerical model based on the cellular automaton method for the three-dimensional simulation of dendritic growth of magnesium alloy was developed.The growth kinetics was calculated from the complete solution of the transport equations.By constructing a three-dimensional anisotropy model with the cubic CA cells,simulation of dendritic growth of magnesium alloy with six-fold symmetry in the basal plane was achieved.The model was applied to simulate the equiaxed dendritic growth and columnar dendritic growth under directional solidification,and its capability was addressed by comparing the simulated results to experimental results and those in the previously published works.Meanwhile,the three-dimensional simulated results were also compared with that of in two dimensions,offering a deep insight into the microstructure formation of magnesium alloy during solidification.
Steady state speed distribution analysis for a combined cellular automaton traffic model
Institute of Scientific and Technical Information of China (English)
Wang Jun-Feng; Chen Gui-Sheng; Liu Jin
2008-01-01
Cellular Automaton (CA) baaed traffic flow models have been extensively studied due to their effectiveness and simplicity in recent years. This paper develops a discrete time Markov chain (DTMC) analytical framework for a Nagel-Schreckenberg and Fukui-Ishibashi combined CA model (W2H traffic flow model) from microscopic point of view to capture the macroscopic steady state speed distributions. The inter-vehicle spacing Markov chain and the steady state speed Markov chain are proved to be irreducible and ergodie. The theoretical speed probability distributions depending on the traffic density and stochastic delay probability are in good accordance with numerical simulations. The derived fundamental diagram of the average speed from theoretical speed distributions is equivalent to the results in the previous work.
An Integrated Framework to Model Cellular Phenotype as a Component of Biochemical Networks
Directory of Open Access Journals (Sweden)
Michael Gormley
2011-01-01
Full Text Available Identification of regulatory molecules in signaling pathways is critical for understanding cellular behavior. Given the complexity of the transcriptional gene network, the relationship between molecular expression and phenotype is difficult to determine using reductionist experimental methods. Computational models provide the means to characterize regulatory mechanisms and predict phenotype in the context of gene networks. Integrating gene expression data with phenotypic data in transcriptional network models enables systematic identification of critical molecules in a biological network. We developed an approach based on fuzzy logic to model cell budding in Saccharomyces cerevisiae using time series expression microarray data of the cell cycle. Cell budding is a phenotype of viable cells undergoing division. Predicted interactions between gene expression and phenotype reflected known biological relationships. Dynamic simulation analysis reproduced the behavior of the yeast cell cycle and accurately identified genes and interactions which are essential for cell viability.
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.
Dynamical critical behavior in a cellular model of superconducting vortex avalanches
Vadakkan, Tegy John
Bak, Tang, and Wiesenfeld showed that certain driven dissipative systems with many degrees of freedom organize into a critical state characterized by avalanche dynamics and power law distribution of avalanche sizes and durations. They called this phenomenon self-organized criticality and sandpile became the prototype of such dynamical systems. Universality in these systems is not yet well established. Forty years ago, de Gennes noted that the Bean state in a type-II superconductor is similar to a sandpile. Motivated by strong experimental evidences, Bassler and Paczuski (BP) proposed a 2D sandpile model to study self-organization in the dynamics of vortices in superconductors. In this dissertation, the effect of anisotropy in the vortex-vortex interaction, stochasticity in the vortex toppling rule, and the configuration of the pinning centers on the scaling properties of the avalanches in the BP model is studied. Also, universality in the cellular model of vortex dynamics is investigated.
Sezgin, Erdinc; Levental, Ilya; Grzybek, Michal; Schwarzmann, Günter; Mueller, Veronika; Honigmann, Alf; Belov, Vladimir N; Eggeling, Christian; Coskun, Unal; Simons, Kai; Schwille, Petra
2012-07-01
Several simplified membrane models featuring coexisting liquid disordered (Ld) and ordered (Lo) lipid phases have been developed to mimic the heterogeneous organization of cellular membranes, and thus, aid our understanding of the nature and functional role of ordered lipid-protein nanodomains, termed "rafts". In spite of their greatly reduced complexity, quantitative characterization of local lipid environments using model membranes is not trivial, and the parallels that can be drawn to cellular membranes are not always evident. Similarly, various fluorescently labeled lipid analogs have been used to study membrane organization and function in vitro, although the biological activity of these probes in relation to their native counterparts often remains uncharacterized. This is particularly true for raft-preferring lipids ("raft lipids", e.g. sphingolipids and sterols), whose domain preference is a strict function of their molecular architecture, and is thus susceptible to disruption by fluorescence labeling. Here, we analyze the phase partitioning of a multitude of fluorescent raft lipid analogs in synthetic Giant Unilamellar Vesicles (GUVs) and cell-derived Giant Plasma Membrane Vesicles (GPMVs). We observe complex partitioning behavior dependent on label size, polarity, charge and position, lipid headgroup, and membrane composition. Several of the raft lipid analogs partitioned into the ordered phase in GPMVs, in contrast to fully synthetic GUVs, in which most raft lipid analogs mis-partitioned to the disordered phase. This behavior correlates with the greatly enhanced order difference between coexisting phases in the synthetic system. In addition, not only partitioning, but also ligand binding of the lipids is perturbed upon labeling: while cholera toxin B binds unlabeled GM1 in the Lo phase, it binds fluorescently labeled GMI exclusively in the Ld phase. Fluorescence correlation spectroscopy (FCS) by stimulated emission depletion (STED) nanoscopy on intact
Mathematical modeling of ultrasound in tissue engineering: From bioreactors to the cellular scale
Louw, Tobias M.
Tissue engineering seeks to provide a means to treat injuries that are beyond the body's natural ability to repair without the issues associated with allografts. Autologous cells are cultured in a bioreactor which controls the cellular environment (including mechanical stimulation) for optimal tissue growth. We investigate ultrasound as an effective means of mechanical stimulation by predicting the ultrasonic field in a bioreactor, as well as ultrasonic bioeffects at the cellular level. The Transfer Matrix Angular Spectrum Approach was found to be the most accurate and computationally efficient bioreactor model. Three critical factors influence experimental results: (1) the diameter of the tissue engineering scaffold greatly affects the ultrasonic field; (2) the position of the ultrasonic transducer and liquid level in the tissue culture well determines the maximum pressure amplitude in the bioreactor, but the pressure can be controlled by measuring the transducer input electrical impedance and manipulating the applied voltage; and (3) the position of pressure nodes are influenced by ultrasonic frequency and liquid level; this will affect the response of cells to applied ultrasound. On the cellular level, it was shown that chondrocytes respond to ultrasound with frequency dependence. A predicted resonance frequency near 5MHz matched experimental results showing maximum expression of load inducible genes at 5MHz. Mechanical stresses are concentrated near the nucleus at resonance, alluding to the possibility that the nucleus may directly sense ultrasonic stimulation. We postulate that ultrasound influences the transport of p-ERK to the nucleus or causes minor chromatin reorganization, leading to the observed frequency dependent gene expression. We linked in vitro ultrasonic stimulation to in vivo mechanical stimulation generated by natural movement. The chondrocyte's response to impact is under-damped, and the cell oscillates with a frequency close to the model
A hybrid cellular automaton model of solid tumor growth and bioreductive drug transport.
Kazmi, Nabila; Hossain, M A; Phillips, Roger M
2012-01-01
Bioreductive drugs are a class of hypoxia selective drugs that are designed to eradicate the hypoxic fraction of solid tumors. Their activity depends upon a number of biological and pharmacological factors and we used a mathematical modeling approach to explore the dynamics of tumor growth, infusion, and penetration of the bioreductive drug Tirapazamine (TPZ). An in-silico model is implemented to calculate the tumor mass considering oxygen and glucose as key microenvironmental parameters. The next stage of the model integrated extra cellular matrix (ECM), cell-cell adhesion, and cell movement parameters as growth constraints. The tumor microenvironments strongly influenced tumor morphology and growth rates. Once the growth model was established, a hybrid model was developed to study drug dynamics inside the hypoxic regions of tumors. The model used 10, 50 and 100 \\mu {\\rm M} as TPZ initial concentrations and determined TPZ pharmacokinetic (PK) (transport) and pharmacodynamics (cytotoxicity) properties inside hypoxic regions of solid tumor. The model results showed that diminished drug transport is a reason for TPZ failure and recommend the optimization of the drug transport properties in the emerging TPZ generations. The modeling approach used in this study is novel and can be a step to explore the behavioral dynamics of TPZ.
Akbari, Mostafa; Asadi, Parviz; Besharati Givi, MohammadKazem; Zolghadr, Parisa
2016-03-01
To predict the grain size and microstructure evolution during friction stir welding (FSW) of AZ91 magnesium alloy, a finite element model (FEM) is developed based on the combination of a cellular automaton model and the Kocks - Mecking and Laasraoui-Jonas models. First, according to the flow stress curves and using the Kocks - Mecking model, the hardening and recovery parameters and the strain rate sensitivity were calculated. Next, an FEM model was established in Deform-3D software to simulate the FSW of AZ91 magnesium alloy. The results of the FEM model are used in microstructure evolution models to predict the grain size and microstructure of the weld zone. There is a good agreement between the simulated and experimental microstructures, and the proposed model can simulate the dynamic recrystallization (DRX) process during FSW of AZ91 alloy. Moreover, microstructural properties of different points in the SZ as well as the effect of the w/v parameter on the grain size and microstructure are considered.
Energy Technology Data Exchange (ETDEWEB)
Zhao, Yuchao; Conolly, Rory B; Andersen, Melvin E.
2006-11-21
This report describes the development of a computational systems biology approach to evaluate the hypotheses of molecular and cellular mechanisms of adaptive response to low dose ionizing radiation. Our concept is that computational models of signaling pathways can be developed and linked to biologically based dose response models to evaluate the underlying molecular mechanisms which lead to adaptive response. For development of quantitatively accurate, predictive models, it will be necessary to describe tissues consisting of multiple cell types where the different types each contribute in their own way to the overall function of the tissue. Such a model will probably need to incorporate not only cell type-specific data but also spatial information on the architecture of the tissue and on intercellular signaling. The scope of the current model was more limited. Data obtained in a number of different biological systems were synthesized to describe a chimeric, “average” population cell. Biochemical signaling pathways involved in sensing of DNA damage and in the activation of cell cycle checkpoint controls and the apoptotic path were also included. As with any computational modeling effort, it was necessary to develop these simplified initial descriptions (models) that can be iteratively refined. This preliminary model is a starting point which, with time, can evolve to a level of refinement where large amounts of detailed biological information are synthesized and a capability for robust predictions of dose- and time-response behaviors is obtained.
A Vector-based Cellular Automata Model for Simulating Urban Land Use Change
Institute of Scientific and Technical Information of China (English)
LU Yi; CAO Min; ZHANG Lei
2015-01-01
Cellular Automata (CA) is widely used for the simulation of land use changes.This study applied a vector-based CA model to simulate land use change in order to minimize or eliminate the scale sensitivity in traditional raster-based CA model.The cells of vector-based CA model are presented according to the shapes and attributes of geographic entities,and the transition rules of vector-based CA model are improved by taking spatial variables of the study area into consideration.The vector-based CA model is applied to simulate land use changes in downtown of Qidong City,Jiangsu Province,China and its validation is confirmed by the methods of visual assessment and spatial accuracy.The simulation result of vector-based CA model reveals that nearly 75％ of newly increased urban cells are located in the northwest and southwest parts of the study area from 2002 to 2007,which is in consistent with real land use map.In addition,the simulation results of the vector-based and raster-based CA models are compared to real land use data and their spatial accuracies are found to be 84.0％ and 81.9％,respectively.In conclusion,results from this study indicate that the vector-based CA model is a practical and applicable method for the simulation of urbanization processes.
Directory of Open Access Journals (Sweden)
Imène Achour
2016-08-01
Full Text Available Parkinson’s disease (PD is a progressive neurodegenerative disorder, primarily affecting dopaminergic neurons in the substantia nigra. There is currently no cure for PD and present medications aim to alleviate clinical symptoms, thus prevention remains the ideal strategy to reduce the prevalence of this disease. The goal of this study was to investigate whether oleuropein (OLE, the major phenolic compound in olive derivatives, may prevent neuronal degeneration in a cellular dopaminergic model of PD, differentiated PC12 cells exposed to the potent parkinsonian toxin 6-hydroxydopamine (6-OHDA. We also investigated OLE’s ability to mitigate mitochondrial oxidative stress and modulate the autophagic flux. Our results obtained by measuring cytotoxicity and apoptotic events demonstrate that OLE significantly decreases neuronal death. OLE could also reduce mitochondrial production of reactive oxygen species resulting from blocking superoxide dismutase activity. Moreover, quantification of autophagic and acidic vesicles in the cytoplasm alongside expression of specific autophagic markers uncovered a regulatory role for OLE against autophagic flux impairment induced by bafilomycin A1. Altogether, our results define OLE as a neuroprotective, anti-oxidative and autophagy-regulating molecule, in a neuronal dopaminergic cellular model.
Achour, Imène; Arel-Dubeau, Anne-Marie; Renaud, Justine; Legrand, Manon; Attard, Everaldo; Germain, Marc; Martinoli, Maria-Grazia
2016-01-01
Parkinson’s disease (PD) is a progressive neurodegenerative disorder, primarily affecting dopaminergic neurons in the substantia nigra. There is currently no cure for PD and present medications aim to alleviate clinical symptoms, thus prevention remains the ideal strategy to reduce the prevalence of this disease. The goal of this study was to investigate whether oleuropein (OLE), the major phenolic compound in olive derivatives, may prevent neuronal degeneration in a cellular dopaminergic model of PD, differentiated PC12 cells exposed to the potent parkinsonian toxin 6-hydroxydopamine (6-OHDA). We also investigated OLE’s ability to mitigate mitochondrial oxidative stress and modulate the autophagic flux. Our results obtained by measuring cytotoxicity and apoptotic events demonstrate that OLE significantly decreases neuronal death. OLE could also reduce mitochondrial production of reactive oxygen species resulting from blocking superoxide dismutase activity. Moreover, quantification of autophagic and acidic vesicles in the cytoplasm alongside expression of specific autophagic markers uncovered a regulatory role for OLE against autophagic flux impairment induced by bafilomycin A1. Altogether, our results define OLE as a neuroprotective, anti-oxidative and autophagy-regulating molecule, in a neuronal dopaminergic cellular model. PMID:27517912
Energy Technology Data Exchange (ETDEWEB)
Tian, Jun-fang, E-mail: tianhustbjtu@hotmail.com [MOE Key Laboratory for Urban Transportation Complex Systems Theory and Technology, Beijing Jiaotong University, Beijing 100044 (China); Yuan, Zhen-zhou; Jia, Bin; Fan, Hong-qiang; Wang, Tao [MOE Key Laboratory for Urban Transportation Complex Systems Theory and Technology, Beijing Jiaotong University, Beijing 100044 (China)
2012-09-10
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.
Cellular model studies of brain-mediated phototherapy on Alzheimer's disease
Zhu, Ling; Liu, Timon Cheng-Yi; Hu, Bina; Li, Xiao-Yun; Wang, Yong-Qing
2008-12-01
Alzheimer's disease (AD) is now the most common neurodegenerative disease. Despite approval of several drugs for AD, the disease continues to rob millions of their memories and their lives. We have studied the cellular models of brain-mediated phototherapy on AD, and the studies will be reviewed in this paper. Genetic studies have shown that dysfunction of amyloid β-protein (Aβ) or tau is sufficient to cause AD. Aβ or Aβ induced redox stress induced neuron apoptosis might be as a cellular model of AD. We found red light at 640+/-15 nm from light emitting diode array (RLED640) might inhibit Aβ 25-35 induced PC12 cell apoptosis, which is mediated by cyclic adenosine monophosphate, and it might inhibit hydrogen peroxide (H2O2) induced differentiated PC12 cell (dPC12) apoptosis, which is mediated by tyrosine hydroxylase. There is rhythm dysfunction in AD. We found low intensity 810 nm laser irradiation might rehabilitate TNF-alpha induced inhibition of clock gen expression of NIH 3T3 fibroblasts. Our studies provide a foundation for photobiomodulation on brain to rehabilitate AD.
Computation of steady-state probability distributions in stochastic models of cellular networks.
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Mark Hallen
2011-10-01
Full Text Available Cellular processes are "noisy". In each cell, concentrations of molecules are subject to random fluctuations due to the small numbers of these molecules and to environmental perturbations. While noise varies with time, it is often measured at steady state, for example by flow cytometry. When interrogating aspects of a cellular network by such steady-state measurements of network components, a key need is to develop efficient methods to simulate and compute these distributions. We describe innovations in stochastic modeling coupled with approaches to this computational challenge: first, an approach to modeling intrinsic noise via solution of the chemical master equation, and second, a convolution technique to account for contributions of extrinsic noise. We show how these techniques can be combined in a streamlined procedure for evaluation of different sources of variability in a biochemical network. Evaluation and illustrations are given in analysis of two well-characterized synthetic gene circuits, as well as a signaling network underlying the mammalian cell cycle entry.
A cellular automaton model adapted to sandboxes to simulate the transport of solutes
Lora, Boris; Donado, Leonardo; Castro, Eduardo; Bayuelo, Alfredo
2016-04-01
The increasingly use of groundwater sources for human consumption and the growth of the levels of these hydric sources contamination make imperative to reach a deeper understanding how the contaminants are transported by the water, in particular through a heterogeneous porous medium. Accordingly, the present research aims to design a model, which simulates the transport of solutes through a heterogeneous porous medium, using cellular automata. Cellular automata (CA) are a class of spatially (pixels) and temporally discrete mathematical systems characterized by local interaction (neighborhoods). The pixel size and the CA neighborhood were determined in order to reproduce accurately the solute behavior (Ilachinski, 2001). For the design and corresponding validation of the CA model were developed different conservative tracer tests using a sandbox packed heterogeneously with a coarse sand (size # 20 grain diameter 0,85 to 0,6 mm) and clay. We use Uranine and a saline solution with NaCl as a tracer which were measured taking snapshots each 20 seconds. A calibration curve (pixel intensity Vs Concentration) was used to obtain concentration maps. The sandbox was constructed of acrylic (caliber 0,8 cms) with 70 x 45 x 4 cms of dimensions. The "sandbox" had a grid of 35 transversal holes with a diameter of 4 mm each and an uniform separation from one to another of 10 cms. To validate the CA-model it was used a metric consisting in rating the number of correctly predicted pixels over the total per image throughout the entire test run. The CA-model shows that calibrations of pixels and neighborhoods allow reaching results over the 60 % of correctly predictions usually. This makes possible to think that the application of the CA- model could be useful in further researches regarding the transport of contaminants in hydrogeology.
Directory of Open Access Journals (Sweden)
Megan Olsen
Full Text Available Computational models in the field of cancer research have focused primarily on estimates of biological events based on laboratory generated data. We introduce a novel in-silico technology that takes us to the next level of prediction models and facilitates innovative solutions through the mathematical system. The model's building blocks are cells defined phenotypically as normal or tumor, with biological processes translated into equations describing the life protocols of the cells in a quantitative and stochastic manner. The essentials of communication in a society composed of normal and tumor cells are explored to reveal "protocols" for selective tumor eradication. Results consistently identify "citizenship properties" among cells that are essential for the induction of healing processes in a healthy system invaded by cancer. These properties act via inter-cellular communication protocols that can be optimized to induce tumor eradication along with system recovery. Within the computational systems, the protocols universally succeed in removing a wide variety of tumors defined by proliferation rates, initial volumes, and apoptosis resistant phenotypes; they show high adaptability for biological details and allow incorporation of population heterogeneity. These protocols work as long as at least 32% of cells obey extra-cellular commands and at least 28% of cancer cells report their deaths. This low percentage implies that the protocols are resilient to the suboptimal situations often seen in biological systems. We conclude that our in-silico model is a powerful tool to investigate, to propose, and to exercise logical anti-cancer solutions. Functional results should be confirmed in a biological system and molecular findings should be loaded into the computational model for the next level of directed experiments.
Directory of Open Access Journals (Sweden)
Meiyappan Lakshmanan
2016-11-01
Full Text Available Crop productivity is severely limited by various biotic and abiotic stresses. Thus, it is highly needed to understand the underlying mechanisms of environmental stress response and tolerance in plants, which could be addressed by systems biology approach. To this end, high-throughput omics profiling and in silico modeling can be considered to explore the environmental effects on phenotypic states and metabolic behaviors of rice crops at the systems level. Especially, the advent of constraint-based metabolic reconstruction and analysis paves a way to characterize the plant cellular physiology under various stresses by combining the mathematical network models with multi-omics data. Rice metabolic networks have been reconstructed since 2013 and currently 6 such networks are available, where 5 are at genome-scale. Since their publication, these models have been utilized to systematically elucidate the rice abiotic stress responses and identify agronomic traits for crop improvement. In this review, we summarize the current status of the existing rice metabolic networks and models with their applications. Furthermore, we also highlight future directions of rice modeling studies, particularly stressing how these models can be used to contextualize the affluent multi-omics data that are readily available in the public domain. Overall, we envisage a number of studies in the future, exploiting the available metabolic models to enhance the yield and quality of rice and other food crops.
Knowledge-guided fuzzy logic modeling to infer cellular signaling networks from proteomic data
Liu, Hui; Zhang, Fan; Mishra, Shital Kumar; Zhou, Shuigeng; Zheng, Jie
2016-10-01
Modeling of signaling pathways is crucial for understanding and predicting cellular responses to drug treatments. However, canonical signaling pathways curated from literature are seldom context-specific and thus can hardly predict cell type-specific response to external perturbations; purely data-driven methods also have drawbacks such as limited biological interpretability. Therefore, hybrid methods that can integrate prior knowledge and real data for network inference are highly desirable. In this paper, we propose a knowledge-guided fuzzy logic network model to infer signaling pathways by exploiting both prior knowledge and time-series data. In particular, the dynamic time warping algorithm is employed to measure the goodness of fit between experimental and predicted data, so that our method can model temporally-ordered experimental observations. We evaluated the proposed method on a synthetic dataset and two real phosphoproteomic datasets. The experimental results demonstrate that our model can uncover drug-induced alterations in signaling pathways in cancer cells. Compared with existing hybrid models, our method can model feedback loops so that the dynamical mechanisms of signaling networks can be uncovered from time-series data. By calibrating generic models of signaling pathways against real data, our method supports precise predictions of context-specific anticancer drug effects, which is an important step towards precision medicine.
Knowledge-guided fuzzy logic modeling to infer cellular signaling networks from proteomic data
Liu, Hui; Zhang, Fan; Mishra, Shital Kumar; Zhou, Shuigeng; Zheng, Jie
2016-01-01
Modeling of signaling pathways is crucial for understanding and predicting cellular responses to drug treatments. However, canonical signaling pathways curated from literature are seldom context-specific and thus can hardly predict cell type-specific response to external perturbations; purely data-driven methods also have drawbacks such as limited biological interpretability. Therefore, hybrid methods that can integrate prior knowledge and real data for network inference are highly desirable. In this paper, we propose a knowledge-guided fuzzy logic network model to infer signaling pathways by exploiting both prior knowledge and time-series data. In particular, the dynamic time warping algorithm is employed to measure the goodness of fit between experimental and predicted data, so that our method can model temporally-ordered experimental observations. We evaluated the proposed method on a synthetic dataset and two real phosphoproteomic datasets. The experimental results demonstrate that our model can uncover drug-induced alterations in signaling pathways in cancer cells. Compared with existing hybrid models, our method can model feedback loops so that the dynamical mechanisms of signaling networks can be uncovered from time-series data. By calibrating generic models of signaling pathways against real data, our method supports precise predictions of context-specific anticancer drug effects, which is an important step towards precision medicine. PMID:27774993
2017-01-01
Mathematical models of cardiac electrical excitation are increasingly complex, with multiscale models seeking to represent and bridge physiological behaviours across temporal and spatial scales. The increasing complexity of these models makes it computationally expensive to both evaluate long term (more than 60 s) behaviour and determine sensitivity of model outputs to inputs. This is particularly relevant in models of atrial fibrillation (AF), where individual episodes last from seconds to days, and interepisode waiting times can be minutes to months. Potential mechanisms of transition between sinus rhythm and AF have been identified but are not well understood, and it is difficult to simulate AF for long periods of time using state-of-the-art models. In this study, we implemented a Moe-type cellular automaton on a novel, topologically equivalent surface geometry of the left atrium. We used the model to simulate stochastic initiation and spontaneous termination of AF, arising from bursts of spontaneous activation near pulmonary veins. The simplified representation of atrial electrical activity reduced computational cost, and so permitted us to investigate AF mechanisms in a probabilistic setting. We computed large numbers (approx. 105) of sample paths of the model, to infer stochastic initiation and termination rates of AF episodes using different model parameters. By generating statistical distributions of model outputs, we demonstrated how to propagate uncertainties of inputs within our microscopic level model up to a macroscopic level. Lastly, we investigated spontaneous termination in the model and found a complex dependence on its past AF trajectory, the mechanism of which merits future investigation. PMID:28356539
Micro-macroscopic coupling in the cellular automaton model of solidification
Directory of Open Access Journals (Sweden)
Vinicius Bertolazzi Biscuola
2010-12-01
Full Text Available A cellular automaton (CA model to predict the formation of grain macrostructure during solidification has been implemented and the coupling between the microscopic and the macroscopic submodels has been investigated. The microscopic submodel simulates the nucleation and growth of grains, whereas the macroscopic solves the heat conduction equation. The directional solidification of an Al-7 wt. (% Si alloy was simulated, enabling the calculation of the temperature and solid fraction profiles. The calculated temperature was used to obtain the solid fraction profile by an application of Scheil equation. This solid fraction disagrees with that calculated in the micro-macro coupling of the model, although this coupling is completely based on Scheil equation. Careful examination of the discrepancies shows that it is a result of the undercoolings for nucleation and growth of grains and also of the interpolations of enthalpy change and temperature from the finite volume mesh to the CA cell mesh.
Cellular automaton model of precipitation/dissolution coupled with solute transport
Karapiperis, T
1995-01-01
ABSTRACT Precipitation/dissolution reactions coupled with solute transport are modelled as a cellular automaton in which solute molecules perform a random walk on a regular lattice and react according to a local probabilistic rule. Stationary solid particles dissolve with a certain probability and, provided solid is already present or the solution is saturated, solute particles have a probability to precipitate. In our simulation of the dissolution of a solid block inside uniformly flowing water we obtain solid precipitation downstream from the original solid edge, in contrast to the standard reaction-transport equations. The observed effect is the result of fluctuations in solute density and diminishes when we average over a larger ensemble. The additional precipitation of solid is accompanied by a substantial reduction in the relatively small solute concentration. The model is appropriate for the study of the rôle of intrinsic fluctuations in the presence of reaction thresholds and can be employed to inves...
An improved cellular automaton model considering the effect of traffic lights and driving behaviour
Institute of Scientific and Technical Information of China (English)
He Hong-Di; Lu Wei-Zhen; Dong Li-Yun
2011-01-01
This paper proposes an improved cellular automaton model to describe the urban traffic flow with the consideration of traffic light and driving behaviour effects. Based on the model, the characteristics of the urban traffic flow on a singlelane road are investigated under three different control strategies, i.e., the synchronized, the green wave and the random strategies. The fundamental diagrams and time-space patterns of the traffic flows are provided for these strategies respectively. It finds that the dynamical transition to the congested flow appears when the vehicle density is higher than a critical level. The saturated flow is less dependent on the cycle time and the strategies of the traffic light control,while the critical vehicle density varies with the cycle time and the strategies. Simulated results indicate that the green wave strategy is proven to be the most effective one among the above three control strategies.
Modeling and Simulation for Urban Rail Traffic Problem Based on Cellular Automata
Institute of Scientific and Technical Information of China (English)
许琰; 曹成铉; 李明华; 罗金龙
2012-01-01
Based on the Nagel-Schreckenberg model, we propose a new cellular automata model to simulate the urban rail traffic flow under moving block system and present a new minimum instantaneous distance formula under pure moving block. We also analyze the characteristics of the urban rail traffic flow under the influence of train density, station dwell times, the length of train, and the train velocity. Train delays can be decreased effectively through flexible departure intervals according to the preceding train type before its departure. The results demonstrate that a suitable adjustment of the current train velocity based on the following train velocity can greatly shorten the minimum departure intervals and then increase the capacity of rail transit.
An improved cellular automaton model considering the effect of traffic lights and driving behaviour
He, Hong-Di; Lu, Wei-Zhen; Dong, Li-Yun
2011-04-01
This paper proposes an improved cellular automaton model to describe the urban traffic flow with the consideration of traffic light and driving behaviour effects. Based on the model, the characteristics of the urban traffic flow on a single-lane road are investigated under three different control strategies, i.e., the synchronized, the green wave and the random strategies. The fundamental diagrams and time-space patterns of the traffic flows are provided for these strategies respectively. It finds that the dynamical transition to the congested flow appears when the vehicle density is higher than a critical level. The saturated flow is less dependent on the cycle time and the strategies of the traffic light control, while the critical vehicle density varies with the cycle time and the strategies. Simulated results indicate that the green wave strategy is proven to be the most effective one among the above three control strategies.
Genome editing of human pluripotent stem cells to generate human cellular disease models
Directory of Open Access Journals (Sweden)
Kiran Musunuru
2013-07-01
Full Text Available Disease modeling with human pluripotent stem cells has come into the public spotlight with the awarding of the Nobel Prize in Physiology or Medicine for 2012 to Drs John Gurdon and Shinya Yamanaka for the discovery that mature cells can be reprogrammed to become pluripotent. This discovery has opened the door for the generation of pluripotent stem cells from individuals with disease and the differentiation of these cells into somatic cell types for the study of disease pathophysiology. The emergence of genome-editing technology over the past few years has made it feasible to generate and investigate human cellular disease models with even greater speed and efficiency. Here, recent technological advances in genome editing, and its utility in human biology and disease studies, are reviewed.
Genome editing of human pluripotent stem cells to generate human cellular disease models.
Musunuru, Kiran
2013-07-01
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.
Cellular Automaton Models of Highway Traffic Flow Considering Lane-Control and Speed-Control
Institute of Scientific and Technical Information of China (English)
钱勇生; 李文俊; 曾俊伟; 王敏; 杜加伟; 广晓平
2011-01-01
As two kinds of management modes of highway tramc control, lane-control, and speed-control produce different effect under different conditions. In this paper, traffic flow cellular automaton models for four-lane highway system with two opposing directions under the above two modes are established considering car and truck mixed running. Through computer numerical simulating, the fundamental diagrams with different parameters are obtained, and after the analysis of density-flux diagrams, the variation discipline of flux with traffic density under different control models is gained. The results indicate that, compared with lane-control, utilization ratio of road can be further improved with speed-control when the truck number increases. The research result is of great significance for reasonable providing theoretical guidance for highway traffic control.
An Urban Cellular Automata Model for Simulating Dynamic States on a Local Scale
Directory of Open Access Journals (Sweden)
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
A refined cellular automaton model to rectify impractical vehicular movement behavior
Lan, Lawrence W.; Chiou, Yu-Chiun; Lin, Zih-Shin; Hsu, Chih-Cheng
2009-09-01
When implementing cellular automata (CA) into a traffic simulation, one common defect yet to be rectified is the abrupt deceleration when vehicles encounter stationary obstacles or traffic jams. To be more in line with real world vehicular movement, this paper proposes a piecewise-linear movement to replace the conventional particle-hopping movement adopted in most previous CA models. Upon this adjustment and coupled with refined cell system, a new CA model is developed using the rationale of Forbes’ et al. car-following concept. The proposed CA model is validated on a two-lane freeway mainline context. It shows that this model can fix the unrealistic deceleration behaviors, and thus can reflect genuine driver behavior in the real world. The model is also capable of revealing Kerner’s three-phase traffic patterns and phase transitions among them. Furthermore, the proposed CA model is applied to simulate a highway work zone wherein traffic efficiency (maximum flow rates) and safety (speed deviations) impacted by various control schemes are tested.
A Multitarget Land Use Change Simulation Model Based on Cellular Automata and Its Application
Directory of Open Access Journals (Sweden)
Jun Yang
2014-01-01
Full Text Available Based on the analysis of the existing land use change simulation model, combined with macroland use change driving factors and microlocal land use competition, and through the application of Python language integrated technical approaches such as CA, GIS, AHP, and Markov, a multitarget land use change simulation model based on cellular automata(CA is established. This model was applied to conduct scenario simulation of land use/cover change of the Jinzhou New District, based on 1:10000 map scale land use, planning, topography, statistics, and other data collected in the year of 1988, 2003, and 2012. The simulation results indicate the following: (1 this model can simulate the mutual transformation of multiple land use types in a relatively satisfactory way; it takes land use system as a whole and simultaneously takes the land use demand in the macrolevel and the land use suitability in the local scale into account; and (2 the simulation accuracy of the model reaches 72%, presenting higher creditability. The model is capable of providing auxiliary decision-making support for coastal regions with the analysis of the land use change driving mechanism, prediction of land use change tendencies, and establishment of land resource sustainable utilization policies.
CellLab-CTS 2015: continuous-time stochastic cellular automaton modeling using Landlab
Tucker, Gregory E.; Hobley, Daniel E. J.; Hutton, Eric; Gasparini, Nicole M.; Istanbulluoglu, Erkan; Adams, Jordan M.; Siddartha Nudurupati, Sai
2016-02-01
CellLab-CTS 2015 is a Python-language software library for creating two-dimensional, continuous-time stochastic (CTS) cellular automaton models. The model domain consists of a set of grid nodes, with each node assigned an integer state code that represents its condition or composition. Adjacent pairs of nodes may undergo transitions to different states, according to a user-defined average transition rate. A model is created by writing a Python code that defines the possible states, the transitions, and the rates of those transitions. The code instantiates, initializes, and runs one of four object classes that represent different types of CTS models. CellLab-CTS provides the option of using either square or hexagonal grid cells. The software provides the ability to treat particular grid-node states as moving particles, and to track their position over time. Grid nodes may also be assigned user-defined properties, which the user can update after each transition through the use of a callback function. As a component of the Landlab modeling framework, CellLab-CTS models take advantage of a suite of Landlab's tools and capabilities, such as support for standardized input and output.
Modeling and Analysis of K-Tier Downlink Heterogeneous Cellular Networks
Dhillon, Harpreet S; Baccelli, Francois; Andrews, Jeffrey G
2011-01-01
Cellular networks are in a major transition from a carefully planned set of large tower-mounted base-stations (BSs) to an irregular deployment of heterogeneous infrastructure elements that often additionally includes micro, pico, and femtocells, as well as distributed antennas. In this paper, we develop a tractable, flexible, and accurate model for a downlink heterogeneous cellular network (HCN) consisting of K tiers of randomly located BSs, where each tier may differ in terms of average transmit power, supported data rate and BS density. Assuming a mobile user connects to the strongest candidate BS, the resulting Signal-to-Interference-plus-Noise-Ratio (SINR) is greater than 1 when in coverage, Rayleigh fading, we derive an expression for the probability of coverage (equivalently outage) over the entire network under both open and closed access, which assumes a strikingly simple closed-form in the high SINR regime and is accurate down to -4 dB even under weaker assumptions. For external validation, we compar...
Directory of Open Access Journals (Sweden)
Marko eUutela
2014-05-01
Full Text Available Fluoxetine is used as a therapeutic agent for autism spectrum disorder (ASD, including Fragile X syndrome (FXS. The treatment often associates with disruptive behaviors such as agitation and disinhibited behaviors in FXS. To identify mechanisms that increase the risk to poor treatment outcome, we investigated the behavioral and cellular effects of fluoxetine on adult Fmr1 knockout (KO mice, a mouse model for FXS. We found that fluoxetine reduced anxiety-like behavior of both wild type and Fmr1 KO mice seen as shortened latency to enter the center area in the open field test. In Fmr1 KO mice, fluoxetine normalized locomotor hyperactivity but abnormally increased exploratory activity. Reduced Brain-derived neurotrophic factor (BDNF and increased TrkB receptor expression levels in the hippocampus of Fmr1 KO mice associated with inappropriate coping responses under stressful condition and abolished antidepressant activity of fluoxetine. Fluoxetine response in the cell proliferation was also missing in the hippocampus of Fmr1 KO mice when compared with wild type controls. The postnatal expression of serotonin transporter was reduced in the thalamic nuclei of Fmr1 KO mice during the time of transient innervation of somatosensory neurons suggesting that developmental changes of serotonin transporter (SERT expression were involved in the differential cellular and behavioral responses to fluoxetine in wild type and Fmr1 mice. The results indicate that changes of BDNF/TrkB signaling contribute to differential behavioral responses to fluoxetine among individuals with ASD.
Xu, Xiaoming; Du, Ziqiang; Zhang, Hong
2016-10-01
Land use and land cover change (LULCC) is a widely researched topic in related studies. A number of models have been established to simulate LULCC patterns. However, the integration of the system dynamic (SD) and the cellular automata (CA) model have been rarely employed in LULCC simulations, although it allows for combining the advantages of each approach and therefore improving the simulation accuracy. In this study, we integrated an SD model and a CA model to predict LULCC under three future development scenarios in Northern Shanxi province of China, a typical agro-pastoral transitional zone. The results indicated that our integrated approach represented the impacts of natural and socioeconomic factors on LULCC well, and could accurately simulate the magnitude and spatial pattern of LULCC. The modeling scenarios illustrated that different development pathways would lead to various LULCC patterns. This study demonstrated the advantages of the integration approach for simulating LULCC and suggests that LULCC is affected to a large degree by natural and socioeconomic factors.
A cellular automata-based model of Earth's magnetosphere in relation with Dst index
Banerjee, Adrija; Bej, Amaresh; Chatterjee, T. N.
2015-05-01
The disturbance storm time (Dst) index, a measure of the strength of a geomagnetic storm, is difficult to predict by some conventional methods due to its abstract structural complexity and stochastic nature though a timely geomagnetic storm warning could save society from huge economic losses and hours of related hazards. Self-organized criticality and the concept of many-body interactive nonlinear system can be considered an explanation for the fundamental mechanism of the nonstationary geomagnetic disturbances controlled by the perturbed interplanetary conditions. The present paper approaches this natural phenomena by a sandpile-like cellular automata-based model of magnetosphere, taking the real-time solar wind and both the direction and magnitude of the BZ component of the real-time interplanetary magnetic field as the system-controlling input parameters. Moreover, three new parameters had been introduced in the model which modify the functional relationships between the variables and regulate the dynamical behavior of the model to closely approximate the actual geomagnetic fluctuations. The statistical similarities between the dynamics of the model and that of the actual Dst index series during the entire 22nd solar cycle signifies the acceptability of the model.
A Modified Cellular Automaton Method for the Modeling of the Dendritic Morphology of Binary Alloys
Institute of Scientific and Technical Information of China (English)
LIU Ying; XU Qingyan; LIU Baicheng
2006-01-01
A cellular automaton (CA)-based model for the precise two-dimensional simulation of the dendritic morphology of cast aluminum alloys was developed. Compared with previous CA models, the new model considers the solidification process in more detail, solving the solute and heat conservation equations in the modeling domain, including calculation of the solid fraction, the tip velocity, and the solute diffusion process, all of which have significant influence on the dendrite evolution. The rotating grids technique was used in the simulation to avoid anisotropy introduced by the square grid. Dendritic grain profiles for different crystallographic orientations show the existence of a great number of regular and parallel secondary and tertiary arms. The simulation results for the secondary arm spacing and grain size were compared with experimental data and with results reported in the literature. A good agreement was found between the simulated results and the experimental data. It can be concluded that the model can be used to predict the dendritic microstructure of aluminum alloy in a quantitative manner.
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.
ONE-DIMENSIONAL CELLULAR AUTOMATON MODEL OF TRAFFIC FLOW BASED ON CAR-FOLLOWING IDEA
Institute of Scientific and Technical Information of China (English)
董力耘; 薛郁; 戴世强
2002-01-01
An improved one-dimensional CA (Cellular Automaton) traffic model was proposed to describe the highway traffic under the periodic boundary conditions. This model was based on the idea of the car-following model, which claims that the motion of a vehicle at one time step depends on both its headway and the synchronous motion of the front vehicle,thus including indirectly the influence of its sub-neighboring vehicle. In addition, the socalled safety distance was introduced to consider the deceleration behavior of vehicles and the stochastic factor was taken into account by introducing the deceleration probability.Meanwhile, the conditional deceleration in the model gives a better description of the phenomena observed on highways. It is found that there exists the metastability and hysteresis effect of traffic flow in the neighborhood of critical density under different initial conditions.Since this model gives a reasonable depiction of the motion of a single vehicle, it is easy to be extended to the case of traffic flow under the control of traffic lights in cities.
A MULTISCALE, CELL-BASED FRAMEWORK FOR MODELING CANCER DEVELOPMENT
Energy Technology Data Exchange (ETDEWEB)
JIANG, YI [Los Alamos National Laboratory
2007-01-16
Cancer remains to be one of the leading causes of death due to diseases. We use a systems approach that combines mathematical modeling, numerical simulation, in vivo and in vitro experiments, to develop a predictive model that medical researchers can use to study and treat cancerous tumors. The multiscale, cell-based model includes intracellular regulations, cellular level dynamics and intercellular interactions, and extracellular level chemical dynamics. The intracellular level protein regulations and signaling pathways are described by Boolean networks. The cellular level growth and division dynamics, cellular adhesion and interaction with the extracellular matrix is described by a lattice Monte Carlo model (the Cellular Potts Model). The extracellular dynamics of the signaling molecules and metabolites are described by a system of reaction-diffusion equations. All three levels of the model are integrated through a hybrid parallel scheme into a high-performance simulation tool. The simulation results reproduce experimental data in both avasular tumors and tumor angiogenesis. By combining the model with experimental data to construct biologically accurate simulations of tumors and their vascular systems, this model will enable medical researchers to gain a deeper understanding of the cellular and molecular interactions associated with cancer progression and treatment.
Weinmann, Andreas; Storath, Martin
2015-04-08
Signals with discontinuities appear in many problems in the applied sciences ranging from mechanics, electrical engineering to biology and medicine. The concrete data acquired are typically discrete, indirect and noisy measurements of some quantities describing the signal under consideration. The task is to restore the signal and, in particular, the discontinuities. In this respect, classical methods perform rather poor, whereas non-convex non-smooth variational methods seem to be the correct choice. Examples are methods based on Mumford-Shah and piecewise constant Mumford-Shah functionals and discretized versions which are known as Blake-Zisserman and Potts functionals. Owing to their non-convexity, minimization of such functionals is challenging. In this paper, we propose a new iterative minimization strategy for Blake-Zisserman as well as Potts functionals and a related jump-sparsity problem dealing with indirect, noisy measurements. We provide a convergence analysis and underpin our findings with numerical experiments.
Jiao, Yang
2011-01-01
Understanding tumor invasion and metastasis is of crucial importance for both fundamental cancer research and clinical practice. In vitro experiments have established that the invasive growth of malignant tumors is characterized by the dendritic invasive branches composed of chains of tumor cells emanating from the primary tumor mass. The preponderance of previous tumor simulations focused on non-invasive (or proliferative) growth. The formation of the invasive cell chains and their interactions with the primary tumor mass and host microenvironment are not well understood. Here, we present a novel cellular automaton (CA) model that enables one to efficiently simulate invasive tumor growth in a heterogeneous host microenvironment. By taking into account a variety of microscopic-scale tumor-host interactions, including the short-range mechanical interactions between tumor cells and tumor stroma, degradation of extracellular matrix by the invasive cells and oxygen/nutrient gradient driven cell motions, our CA mo...
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.
Oehlke, J; Birth, P; Klauschenz, E; Wiesner, B; Beyermann, M; Oksche, A; Bienert, M
2002-08-01
The uptake by mammalian cells of phosphorothioate oligonucleotides was compared with that of their respective complexes or conjugates with cationic, cell-penetrating model peptides of varying helix-forming propensity and amphipathicity. An HPLC-based protocol for the synthesis and purification of disulfide bridged conjugates in the 10-100 nmol range was developed. Confocal laser scanning microscopy (CLSM) in combination with gel-capillary electrophoresis and laser induced fluorescence detection (GCE-LIF) revealed cytoplasmic and nuclear accumulationin all cases. The uptake differences between naked oligonucleotides and their respective peptide complexes or conjugates were generally confined to one order of magnitude. No significant influence of the structural properties of the peptide components upon cellular uptake was found. Our results question the common belief that the increased biological activity of oligonucleotides after derivatization with membrane permeable peptides may be primarily due to improved membrane translocation.
Fatigue design of a cellular phone folder using regression model-based multi-objective optimization
Kim, Young Gyun; Lee, Jongsoo
2016-08-01
In a folding cellular phone, the folding device is repeatedly opened and closed by the user, which eventually results in fatigue damage, particularly to the front of the folder. Hence, it is important to improve the safety and endurance of the folder while also reducing its weight. This article presents an optimal design for the folder front that maximizes its fatigue endurance while minimizing its thickness. Design data for analysis and optimization were obtained experimentally using a test jig. Multi-objective optimization was carried out using a nonlinear regression model. Three regression methods were employed: back-propagation neural networks, logistic regression and support vector machines. The AdaBoost ensemble technique was also used to improve the approximation. Two-objective Pareto-optimal solutions were identified using the non-dominated sorting genetic algorithm (NSGA-II). Finally, a numerically optimized solution was validated against experimental product data, in terms of both fatigue endurance and thickness index.
Phase transition in the economically modeled growth of a cellular nervous system
Nicosia, Vincenzo; Schafer, William R; Latora, Vito; Bullmore, Edward T; 10.1073/pnas.1300753110
2013-01-01
Spatially-embedded complex networks, such as nervous systems, the Internet and transportation networks, generally have non-trivial topological patterns of connections combined with nearly minimal wiring costs. However the growth rules shaping these economical trade-offs between cost and topology are not well understood. Here we study the cellular nervous system of the nematode worm C. elegans, together with information on the birth times of neurons and on their spatial locations. We find that the growth of this network undergoes a transition from an accelerated to a constant increase in the number of links (synaptic connections) as a function of the number of nodes (neurons). The time of this phase transition coincides closely with the observed moment of hatching, when development switches metamorphically from oval to larval stages. We use graph analysis and generative modelling to show that the transition between different growth regimes, as well as its coincidence with the moment of hatching, can be explain...
Stability Analysis of a Hybrid Cellular Automaton Model of Cell Colony Growth
Gerlee, P
2007-01-01
Cell colonies of bacteria, tumour cells and fungi, under nutrient limited growth conditions, exhibit complex branched growth patterns. In order to investigate this phenomenon we present a simple hybrid cellular automaton model of cell colony growth. In the model the growth of the colony is limited by a nutrient that is consumed by the cells and which inhibits cell division if it falls below a certain threshold. Using this model we have investigated how the nutrient consumption rate of the cells affects the growth dynamics of the colony. We found that for low consumption rates the colony takes on a Eden-like morphology, while for higher consumption rates the morphology of the colony is branched with a fractal geometry. These findings are in agreement with previous results, but the simplicity of the model presented here allows for a linear stability analysis of the system. By observing that the local growth of the colony is proportional to the flux of the nutrient we derive an approximate dispersion relation fo...
González-Díaz, Humberto; Uriarte, Eugenio
2005-04-05
Stochastic moments may be applied as molecular descriptors in quantitative structure-activity relationship (QSAR) studies for small molecules (H. González-Dìaz et al., Journal of Molecular Modeling, 2002, Vol. 8, pp. 237-245; 2003, Vol. 9, pp. 395-407). However, applications in the field of biopolymers are less known. Recently, the MARCH-INSIDE approach has been generalized to encode structural features of proteins and other biopolymers (H. González-Dáaz et al., Bioinformatics, 2003, Vol. 19, pp. 2079-2087; Bioorganic & Medicinal Chemistry Letters, 2004, Vol. 14, pp. 4691-4695; Polymers, 2004, Vol. 45, pp. 3845-3853; Bioorganic & Medicinal Chemistry, 2005, Vol. 13, pp. 323-331). The present article attempts to extend this research by introducing for the first time stochastic moments for a surface road map of viral proteins. These moments are afterward used to seek a model that predicts the cellular receptor for human rhinoviruses. The model correctly classified 100% of 10 viruses binding to low-density lipoprotein receptor (LDLR) and 88.9% of 9 viruses binding to the intracellular adhesion molecule (ICAM) receptors in training. The same results have been obtained in four cross-validation experiments using a resubstitution technique. The present model favorably compares, in terms of complexity, with other previously reported based on entropy considerations, and offers a quantitative basis for the visual rule previously reported by Vlasak et al.
Cellular replication limits in the Luria-Delbrück mutation model
Rodriguez-Brenes, Ignacio A.; Wodarz, Dominik; Komarova, Natalia L.
2016-08-01
Originally developed to elucidate the mechanisms of natural selection in bacteria, the Luria-Delbrück model assumed that cells are intrinsically capable of dividing an unlimited number of times. This assumption however, is not true for human somatic cells which undergo replicative senescence. Replicative senescence is thought to act as a mechanism to protect against cancer and the escape from it is a rate-limiting step in cancer progression. Here we introduce a Luria-Delbrück model that explicitly takes into account cellular replication limits in the wild type cell population and models the emergence of mutants that escape replicative senescence. We present results on the mean, variance, distribution, and asymptotic behavior of the mutant population in terms of three classical formulations of the problem. More broadly the paper introduces the concept of incorporating replicative limits as part of the Luria-Delbrück mutational framework. Guidelines to extend the theory to include other types of mutations and possible applications to the modeling of telomere crisis and fluctuation analysis are also discussed.
Scarella, Gilles; Clatz, Olivier; Lanteri, Stéphane; Beaume, Grégory; Oudot, Steve; Pons, Jean-Philippe; Piperno, Sergo; Joly, Patrick; Wiart, Joe
2006-06-01
The ever-rising diffusion of cellular phones has brought about an increased concern for the possible consequences of electromagnetic radiation on human health. Possible thermal effects have been investigated, via experimentation or simulation, by several research projects in the last decade. Concerning numerical modeling, the power absorption in a user's head is generally computed using discretized models built from clinical MRI data. The vast majority of such numerical studies have been conducted using Finite Differences Time Domain methods, although strong limitations of their accuracy are due to heterogeneity, poor definition of the detailed structures of head tissues (staircasing effects), etc. In order to propose numerical modeling using Finite Element or Discontinuous Galerkin Time Domain methods, reliable automated tools for the unstructured discretization of human heads are also needed. Results presented in this article aim at filling the gap between human head MRI images and the accurate numerical modeling of wave propagation in biological tissues and its thermal effects. To cite this article: G. Scarella et al., C. R. Physique 7 (2006).
Development of in vitro models for cellular and molecular studies in toxicology and chemoprevention
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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.)
Evaluation of biological activities of highly diluted nucleotide sequences by using cellular models
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Pierre Dorfman
2012-09-01
Full Text Available Background: highly diluted specific nucleic acids (SNAÃ‚Â®, designed to modulate viral and cytokine genes expression, are currently used in Micro-Immunotherapy to treat viral infections and immune disorders. Although some preliminary studies have showed clinical benefit of these homeopathic preparations [1], no experimental data are available to explain their mechanism of action. Aims: to investigate the in vitro effect of two sets of highly diluted (HD SNA targeting i latent/lytic Epstein-Barr virus (SNA EBV and ii TNF-ÃŽÂ± and its receptor p55 involved in rheumatoid arthritis (SNA RA on cellular models. Methodology: serial homeopathic dilutions of SNA EBV and SNA RA (15cH-18cH were tested on a EBV-positive B-lymphoblastoid (B95-8 and on a LPS-stimulated macrophage (THP1 cell lines respectively, in comparison with agitated/diluted water and scramble DNA sequences prepared in the same conditions (negative controls. For B95-8 proliferative model, high mobility group box 1 protein (HMGB1 was used as reference. Analyzed biological parameters on B95-8 were i cell proliferation measured after 24 and 48h of incubation with HD SNA and ii expression of the EBV ZEBRA protein in response to TGF-ÃŽÂ² by Western-blotting (T+24h. For THP1 model, TNF-ÃŽÂ± synthesis and release were determined by RT-qPCR and ELISA (protein, after stimulation by LPS (1Ã‚Âµg/ml and HD SNA co-administration. Results: we demonstrated that HD SNA RA significantly down-regulated TNF-ÃŽÂ± synthesis and release. This biological activity was showed to be specific (no effect of HD scramble SNA and related to the level of dilution (maximal effect with higher dilutions. Unexpectedly, a biological effect of agitated/diluted water was also detected in both cellular models. For B95-8 model, this effect resulted in a significant decrease of B95-8 proliferation (comparable to the HMGB1 reference and an inhibition of ZEBRA expression. Similarly, a reproducible
A mathematical model of cortical bone remodeling at cellular level under mechanical stimulus
Institute of Scientific and Technical Information of China (English)
Qing-Hua Qin; Ya-Nan Wang
2012-01-01
A bone cell population dynamics model for cortical bone remodeling under mechanical stimulus is developed in this paper.The external experiments extracted from the literature which have not been used in the creation of the model are used to test the validity of the model.Not only can the model compare reasonably well with these experimental results such as the increase percentage of final values of bone mineral content (BMC) and bone fracture energy (BFE) among different loading schemes (which proves the validity of the model),but also predict the realtime development pattern of BMC and BFE,as well as the dynamics of osteoblasts (OBA),osteoclasts (OCA),nitric oxide (NO) and prostaglandin E2 (PGE2) for each loading scheme,which can hardly be monitored through experiment.In conclusion,the model is the first of its kind that is able to provide an insight into the quantitative mechanism of bone remodeling at cellular level by which bone cells are activated by mechanical stimulus in order to start resorption/formation of bone mass.More importantly,this model has laid a solid foundation based on which future work such as systemic control theory analysis of bone remodeling under mechanical stimulus can be investigated.The to-be identified control mechanism will help to develop effective drugs and combined nonpharmacological therapies to combat bone loss pathologies.Also this deeper understanding of how mechanical forces quantitatively interact with skeletal tissue is essential for the generation of bone tissue for tissue replacement purposes in tissue engineering.
Cellular automaton modelling of lightning-induced and man made forest fires
Krenn, R.; Hergarten, S.
2009-10-01
The impact of forest fires on nature and civilisation is conflicting: on one hand, they play an irreplaceable role in the natural regeneration process, but on the other hand, they come within the major natural hazards in many regions. Their frequency-area distributions show power-law behaviour with scaling exponents α in a quite narrow range, relating wildfire research to the theoretical framework of self-organised criticality. Examples of self-organised critical behaviour can be found in computer simulations of simple cellular automaton models. The established self-organised critical Drossel-Schwabl forest fire model is one of the most widespread models in this context. Despite its qualitative agreement with event-size statistics from nature, its applicability is still questioned. Apart from general concerns that the Drossel-Schwabl model apparently oversimplifies the complex nature of forest dynamics, it significantly overestimates the frequency of large fires. We present a modification of the model rules that distinguishes between lightning-induced and man made forest fires and enables a systematic increase of the scaling exponent α by approximately 1/3. In addition, combined simulations using both the original and the modified model rules predict a dependence of the overall event-size distribution on the ratio of lightning induced and man made fires as well as a splitting of their partial distributions. Lightning is identified as the dominant mechanism in the regime of the largest fires. The results are confirmed by the analysis of the Canadian Large Fire Database and suggest that lightning-induced and man made forest fires cannot be treated separately in wildfire modelling, hazard assessment and forest management.
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
A refined and dynamic cellular automaton model for pedestrian-vehicle mixed traffic flow
Liu, Mianfang; Xiong, Shengwu
2016-12-01
Mixed traffic flow sharing the “same lane” and having no discipline on road is a common phenomenon in the developing countries. For example, motorized vehicles (m-vehicles) and nonmotorized vehicles (nm-vehicles) may share the m-vehicle lane or nm-vehicle lane and pedestrians may share the nm-vehicle lane. Simulating pedestrian-vehicle mixed traffic flow consisting of three kinds of traffic objects: m-vehicles, nm-vehicles and pedestrians, can be a challenge because there are some erratic drivers or pedestrians who fail to follow the lane disciplines. In the paper, we investigate various moving and interactive behavior associated with mixed traffic flow, such as lateral drift including illegal lane-changing and transverse crossing different lanes, overtaking and forward movement, and propose some new moving and interactive rules for pedestrian-vehicle mixed traffic flow based on a refined and dynamic cellular automaton (CA) model. Simulation results indicate that the proposed model can be used to investigate the traffic flow characteristic in a mixed traffic flow system and corresponding complicated traffic problems, such as, the moving characteristics of different traffic objects, interaction phenomenon between different traffic objects, traffic jam, traffic conflict, etc., which are consistent with the actual mixed traffic system. Therefore, the proposed model provides a solid foundation for the management, planning and evacuation of the mixed traffic flow.
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Liqiang Ji
2013-01-01
Full Text Available In public places, the high pedestrian density is one of the direct causes leading to crowding and trample disaster, so it is very necessary to investigate the collective and evacuation characteristics for pedestrian movement. In the occupants’ evacuation process, the people-people interaction and the people-environment interaction are sufficiently considered in this paper, which have been divided into the exit attraction, the repulsion force between people, the friction between people, the repulsion force between human and barrier, and the attraction of surrounding people. Through analyzing the existing models, a new occupant evacuation cellular automata (CA model based on the social force model is presented, which overcomes the shortage of the high density crowd simulation and combines the advantages that CA has sample rules and faster calculating speed. The simulating result shows a great applicability for evacuation under the high density crowd condition, and the segregation phenomena have also been found in the bidirectional pedestrian flow. Besides these, setting isolated belt near the exit or entrance of underpass not only remarkably decreases the density and the risk of tramper disaster but also increases the evacuation efficiency, so it provides a new idea for infrastructure design about the exits and entrances.
Jamshidi, Saeid; Boozarjomehry, Ramin Bozorgmehry; Pishvaie, Mahmoud Reza
2009-10-01
In pore network modeling, the void space of a rock sample is represented at the microscopic scale by a network of pores connected by throats. Construction of a reasonable representation of the geometry and topology of the pore space will lead to a reliable prediction of the properties of porous media. Recently, the theory of multi-cellular growth (or L-systems) has been used as a flexible tool for generation of pore network models which do not require any special information such as 2D SEM or 3D pore space images. In general, the networks generated by this method are irregular pore network models which are inherently closer to the complicated nature of the porous media rather than regular lattice networks. In this approach, the construction process is controlled only by the production rules that govern the development process of the network. In this study, genetic algorithm has been used to obtain the optimum values of the uncertain parameters of these production rules to build an appropriate irregular lattice network capable of the prediction of both static and hydraulic information of the target porous medium.
Channel modeling for fifth generation cellular networks and wireless sensor networks
Torabi, Amir
In view of exponential growth in data traffic demand, the wireless communications industry has aimed to increase the capacity of existing networks by 1000 times over the next 20 years. A combination of extreme cell densification, more bandwidth, and higher spectral efficiency is needed to support the data traffic requirements for fifth generation (5G) cellular communications. In this research, the potential improvements achieved by using three major 5G enabling technologies (i.e., small cells, millimeter-wave spectrum, and massive MIMO) in rural and urban environments are investigated. This work develops SPM and KA-based ray models to investigate the impact of geometrical parameters on terrain-based multiuser MIMO channel characteristic. Moreover, a new directional 3D channel model is developed for urban millimeter-wave (mmW) small cells. Path-loss, spatial correlation, coverage distance, and coherence length are studied in urban areas. Exploiting physical optics (PO) and geometric optics (GO) solutions, closed form expressions are derived for spatial correlation. Achievable spatial diversity is evaluated using horizontal and vertical linear arrays as well as planar 2D arrays. In another study, a versatile near-ground field prediction model is proposed to facilitate accurate wireless sensor network (WSN) simulations. Monte Carlo simulations are used to investigate the effects of antenna height, frequency of operation, polarization, and terrain dielectric and roughness properties on WSNs performance.
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.
Quasi-classical modeling of molecular quantum-dot cellular automata multidriver gates
Rahimi, Ehsan; Nejad, Shahram Mohammad
2012-05-01
Molecular quantum-dot cellular automata (mQCA) has received considerable attention in nanoscience. Unlike the current-based molecular switches, where the digital data is represented by the on/off states of the switches, in mQCA devices, binary information is encoded in charge configuration within molecular redox centers. The mQCA paradigm allows high device density and ultra-low power consumption. Digital mQCA gates are the building blocks of circuits in this paradigm. Design and analysis of these gates require quantum chemical calculations, which are demanding in computer time and memory. Therefore, developing simple models to probe mQCA gates is of paramount importance. We derive a semi-classical model to study the steady-state output polarization of mQCA multidriver gates, directly from the two-state approximation in electron transfer theory. The accuracy and validity of this model are analyzed using full quantum chemistry calculations. A complete set of logic gates, including inverters and minority voters, are implemented to provide an appropriate test bench in the two-dot mQCA regime. We also briefly discuss how the QCADesigner tool could find its application in simulation of mQCA devices.
Effect of Driver Scope Awareness in the Lane Changing Maneuvers Using Cellular Automaton Model
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Kohei Arai
2013-07-01
Full Text Available This paper investigated the effect of drivers’ visibility and their perception (e.g., to estimate the speed and arrival time of another vehicle on the lane changing maneuver. The term of scope awareness was used to describe the visibility required by the driver to make a perception about road condition and the speed of vehicle that exist in that road. A computer simulation model was conducted to show this driver awareness behavior. This studying attempt to precisely catching the lane changing behavior and illustrate the scope awareness parameter that reflects driver behavior. This paper proposes a simple cellular automata model for studying driver visibility effects of lane changing maneuver and driver perception of estimated speed. Different values of scope awareness were examined to capture its effect on the traffic flow. Simulation results show the ability of this model to capture the important features of lane changing maneuver and revealed the appearance of the short-thin solid line jam and the wide solid line jam in the traffic flow as the consequences of lane changing maneuver.
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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.
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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.
Briffa, Michelle; Ghio, Stephanie; Neuner, Johanna; Gauci, Alison J; Cacciottolo, Rebecca; Marchal, Christelle; Caruana, Mario; Cullin, Christophe; Vassallo, Neville; Cauchi, Ruben J
2017-01-18
A signature feature of age-related neurodegenerative proteinopathies is the misfolding and aggregation of proteins, typically amyloid-β (Aβ) in Alzheimer's disease (AD) and α-synuclein (α-syn) in Parkinson's disease (PD), into soluble oligomeric structures that are highly neurotoxic. Cellular and animal models that faithfully replicate the hallmark features of these disorders are being increasing exploited to identify disease-modifying compounds. Natural compounds have been identified as a useful source of bioactive molecules with promising neuroprotective capabilities. In the present report, we investigated whether extracts derived from two ubiquitous Mediterranean plants namely, the prickly pear Opuntia ficus-indica (EOFI) and the brown alga Padina pavonica (EPP) alleviate neurodegenerative phenotypes in yeast (Saccharomyces cerevisiae) and fly (Drosophila melanogaster) models of AD and PD. Pre-treatment with EPP or EOFI in the culture medium significantly improved the viability of yeast expressing the Arctic Aβ42 (E22G) mutant. Supplementing food with EOFI or EPP dramatically ameliorated lifespan and behavioural signs of flies with brain-specific expression of wild-type Aβ42 (model of late-onset AD) or the Arctic Aβ42 variant (model of early-onset AD). Additionally, we show that either extract prolonged the survival of a PD fly model based on transgenic expression of the human α-syn A53T mutant. Taken together, our findings suggest that the plant-derived extracts interfere with shared mechanisms of neurodegeneration in AD and PD. This notion is strengthened by evidence demonstrating that EOFI and to a greater extent EPP, while strongly inhibiting the fibrillogenesis of both Aβ42 and α-syn, accumulate remodelled oligomeric aggregates that are less effective at disrupting lipid membrane integrity. Our work therefore opens new avenues for developing therapeutic applications of these natural plant extracts in the treatment of amyloidogenic
Chen, Qingcai; Shi, Jianghong; Liu, Xiaowei; Wu, Wei; Liu, Bo; Zhang, Hui
2013-03-01
A cellular automata model (CA model) was used to simulate the soil column leaching process of estrogens during the processes of migration and transformation. The results of the simulated leaching experiment showed that the first-order degradation rates of 17α-ethynylestradiol (EE2), 17β-estradiol (E2) and estrone (E1) were 0.131 h- 1 for E2, 0.099 h- 1 for E1 and 0.064 h- 1 for EE2 in the EE2 and E2 leaching process, and the first-order sorption rates were 5.94 h- 1 for E2, 5.63 h- 1 for EE2, 3.125 h- 1 for E1. Their sorption rates were positively correlated with the n-octanol/water partition coefficients. When the diffusion rate was low, its impact on the simulation results was insignificant. The increase in sorption and degradation rates caused the decrease in the total estrogens that leached. In addition, increasing the sorption rate could delay the emerging time of the maximum concentration of estrogen that leached, whereas increasing the degradation rate could shorten the emerging time of the maximum concentration of estrogen that leached. The comparison made between the experimental data and the simulation results of the CA model and the HYDRUS-1D software showed that the establishment of one-component and multi-component CA models could simulate EE2 and E2 soil column leaching processes, and the CA models achieve an intuitive, dynamic, and visual simulation.
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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.
Adiponectin fine-tuning of liver regeneration dynamics revealed through cellular network modeling.
Correnti, Jason M; Cook, Daniel; Aksamitiene, Edita; Swarup, Aditi; Ogunnaike, Babatunde; Vadigepalli, Rajanikanth; Hoek, Jan B
2014-11-10
Following partial hepatectomy, the liver initiates a regenerative program involving hepatocyte priming and replication driven by coordinated cytokine and growth factor actions. We investigated the mechanisms underlying Adiponectin's (Adn) regulation of liver regeneration through modulation of these mediators. Adn-/- mice showed delayed onset of hepatocyte replication, but accelerated cell cycle progression relative to wild-type mice, suggesting Adn has multiple effects fine-tuning the kinetics of liver regeneration. We developed a computational model describing the molecular and physiological kinetics of liver regeneration in Adn-/- mice. We employed this computational model to evaluate the underlying regulatory mechanisms. Our analysis predicted that Adn is required for an efficient early cytokine response to partial hepatectomy, but is inhibitory to later growth factor actions. Consistent with this prediction, Adn knockout reduced hepatocyte responses to IL-6 during the priming phase, but enhanced growth factor levels through peak hepatocyte replication. By contrast, supraphysiological concentrations of Adn resulting from rosiglitazone treatment suppressed regeneration by reducing growth factor levels during S phase, consistent with computational predictions. Together, these results revealed that Adn fine-tunes the progression of liver regeneration through dynamically modulating molecular mediator networks and cellular interactions within the liver. This article is protected by copyright. All rights reserved.
Adiponectin fine-tuning of liver regeneration dynamics revealed through cellular network modelling.
Correnti, Jason M; Cook, Daniel; Aksamitiene, Edita; Swarup, Aditi; Ogunnaike, Babatunde; Vadigepalli, Rajanikanth; Hoek, Jan B
2015-01-15
Following partial hepatectomy, the liver initiates a regenerative programme involving hepatocyte priming and replication driven by the coordinated actions of cytokine and growth factors. We investigated the mechanisms underlying adiponectin's (Adn) regulation of liver regeneration through modulation of these mediators. Adn(-/-) mice showed delayed onset of hepatocyte replication, but accelerated cell cycle progression relative to wild-type mice, suggesting Adn has multiple effects fine-tuning the kinetics of liver regeneration. We developed a computational model describing the molecular and physiological kinetics of liver regeneration in Adn(-/-) mice. We employed this computational model to evaluate the underlying regulatory mechanisms. Our analysis predicted that Adn is required for an efficient early cytokine response to partial hepatectomy, but is inhibitory to later growth factor actions. Consistent with this prediction, Adn knockout reduced hepatocyte responses to interleukin-6 during the priming phase, but enhanced growth factor levels through peak hepatocyte replication. By contrast, supraphysiological concentrations of Adn resulting from rosiglitazone treatment suppressed regeneration by reducing growth factor levels during S phase, consistent with computational predictions. Together, these results revealed that Adn fine-tunes the progression of liver regeneration through dynamically modulating molecular mediator networks and cellular interactions within the liver.
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.
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.
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Burbelko A. A.
2007-01-01
Full Text Available Modelling of solidification process by the method of cellular automaton (CA requires determination of geometrical characteristics of the interface, i.e. of its direction and curvature. In previous studies the authors proposed a method to reduce the well-known effect of an artificial symmetry of the simulation results caused by the anisotropy of the CA computation grid (e.g. a preferred growth of the main dendrite arms along the grid lines or at an angle of 45° in the case of grids with square cells. The aim was achieved by application of the developed methods of computation of the transformation rate and front direction. In this study the authors examined the problem of an accuracy of the computations of an interface curvature. The obtained results show us that the error of the curvature computation introduced by some well-known methods exceeds by 100% a nominal value of this parameter. A method to estimate the accuracy of the applied solution has been proposed. Practical application of the proposed tests enables selection of a best solution, including the authors' own solutions, thus considerably improving an accuracy of the solidification modelling by the method of CA.
Muscle memory and a new cellular model for muscle atrophy and hypertrophy.
Gundersen, Kristian
2016-01-01
Memory is a process in which information is encoded, stored, and retrieved. For vertebrates, the modern view has been that it occurs only in the brain. This review describes a cellular memory in skeletal muscle in which hypertrophy is 'remembered' such that a fibre that has previously been large, but subsequently lost its mass, can regain mass faster than naive fibres. A new cell biological model based on the literature, with the most reliable methods for identifying myonuclei, can explain this phenomenon. According to this model, previously untrained fibres recruit myonuclei from activated satellite cells before hypertrophic growth. Even if subsequently subjected to grave atrophy, the higher number of myonuclei is retained, and the myonuclei seem to be protected against the elevated apoptotic activity observed in atrophying muscle tissue. Fibres that have acquired a higher number of myonuclei grow faster when subjected to overload exercise, thus the nuclei represent a functionally important 'memory' of previous strength. This memory might be very long lasting in humans, as myonuclei are stable for at least 15 years and might even be permanent. However, myonuclei are harder to recruit in the elderly, and if the long-lasting muscle memory also exists in humans, one should consider early strength training as a public health advice. In addition, myonuclei are recruited during steroid use and encode a muscle memory, at least in rodents. Thus, extending the exclusion time for doping offenders should be considered.
Cellular resolution models for even skipped regulation in the entire Drosophila embryo
Ilsley, Garth R; Fisher, Jasmin; Apweiler, Rolf; DePace, Angela H; Luscombe, Nicholas M
2013-01-01
Transcriptional control ensures genes are expressed in the right amounts at the correct times and locations. Understanding quantitatively how regulatory systems convert input signals to appropriate outputs remains a challenge. For the first time, we successfully model even skipped (eve) stripes 2 and 3+7 across the entire fly embryo at cellular resolution. A straightforward statistical relationship explains how transcription factor (TF) concentrations define eve’s complex spatial expression, without the need for pairwise interactions or cross-regulatory dynamics. Simulating thousands of TF combinations, we recover known regulators and suggest new candidates. Finally, we accurately predict the intricate effects of perturbations including TF mutations and misexpression. Our approach imposes minimal assumptions about regulatory function; instead we infer underlying mechanisms from models that best fit the data, like the lack of TF-specific thresholds and the positional value of homotypic interactions. Our study provides a general and quantitative method for elucidating the regulation of diverse biological systems. DOI: http://dx.doi.org/10.7554/eLife.00522.001 PMID:23930223
Inferring cellular regulatory networks with Bayesian model averaging for linear regression (BMALR).
Huang, Xun; Zi, Zhike
2014-08-01
Bayesian network and linear regression methods have been widely applied to reconstruct cellular regulatory networks. In this work, we propose a Bayesian model averaging for linear regression (BMALR) method to infer molecular interactions in biological systems. This method uses a new closed form solution to compute the posterior probabilities of the edges from regulators to the target gene within a hybrid framework of Bayesian model averaging and linear regression methods. We have assessed the performance of BMALR by benchmarking on both in silico DREAM datasets and real experimental datasets. The results show that BMALR achieves both high prediction accuracy and high computational efficiency across different benchmarks. A pre-processing of the datasets with the log transformation can further improve the performance of BMALR, leading to a new top overall performance. In addition, BMALR can achieve robust high performance in community predictions when it is combined with other competing methods. The proposed method BMALR is competitive compared to the existing network inference methods. Therefore, BMALR will be useful to infer regulatory interactions in biological networks. A free open source software tool for the BMALR algorithm is available at https://sites.google.com/site/bmalr4netinfer/.
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ChengHe Guan
2016-12-01
Full Text Available The formation of ‘Urban Networks’ has become a wide-spread phenomenon around the world. In the study of metropolitan regions, there are competing or diverging views about management and control of environmental and land-use factors as well as about scales and arrangements of settlements. Especially in China, these matters alongside of regulatory aspects, infrastructure applications, and resource allocations, are important because of population concentrations and the overlapping of urban areas with other land resources. On the other hand, the increasing sophistication of models operating on iterative computational power and widely-available spatial information and analytical techniques make it possible to simulate and investigate the spatial distribution of urban territories at a regional scale. This research applies a scenario-based Cellular Automata model to a case study of the Changjiang Delta Region, which produces useful and predictive scenario-based projections within the region, using quantitative methods and baseline conditions that address issues of regional urban development. The contribution of the research includes the improvement of computer simulation of urban growth, the application of urban form and other indices to evaluate complex urban conditions, and a heightened understanding of the performance of an urban network in the Changjiang Delta Region composed of big, medium, and small-sized cities and towns.
A biofidelic 3D culture model to study the development of brain cellular systems
Ren, M.; Du, C.; Herrero Acero, E.; Tang-Schomer, M. D.; Özkucur, N.
2016-01-01
Little is known about how cells assemble as systems during corticogenesis to generate collective functions. We built a neurobiology platform that consists of fetal rat cerebral cortical cells grown within 3D silk scaffolds (SF). Ivermectin (Ivm), a glycine receptor (GLR) agonist, was used to modulate cell resting membrane potential (Vmem) according to methods described in a previous work that implicated Ivm in the arrangement and connectivity of cortical cell assemblies. The cells developed into distinct populations of neuroglial stem/progenitor cells, mature neurons or epithelial-mesenchymal cells. Importantly, the synchronized electrical activity in the newly developed cortical assemblies could be recorded as local field potential (LFP) measurements. This study therefore describes the first example of the development of a biologically relevant cortical plate assembly outside of the body. This model provides i) a preclinical basis for engineering cerebral cortex tissue autografts and ii) a biofidelic 3D culture model for investigating biologically relevant processes during the functional development of cerebral cortical cellular systems. PMID:27112667
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.
Simulating debris flows through a hexagonal cellular automata model: SCIDDICA S3–hex
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D. D’Ambrosio
2003-01-01
Full Text Available Cellular Automata (CA represent a formal frame for dynamical systems, which evolve on the base of local interactions. Some types of landslide, such as debris flows, match well this requirement. The latest hexagonal release (S3–hex of the deterministic model SCIDDICA, specifically developed for simulating debris flows, is described. For CA simulation purposes, landslides can be viewed as a dynamical system, subdivided into elementary parts, whose state evolves exclusively as a consequence of local interactions within a spatial and temporal discretum. Space is the world of the CA, here constituted by hexagonal cells. The attributes of each cell ("substates" describe physical characteristics. For computational reasons, the natural phenomenon is "decomposed" into a number of elementary processes, whose proper composition makes up the "transition function" of the CA. By simultaneously applying this function to all the cells, the evolution of the phenomenon can be simulated in terms of modifications of the substates. SCIDDICA S3–hex exhibits a great flexibility in modelling debris flows. With respect to the previous releases of the model, the mechanism of progressive erosion of the soil cover has been added to the transition function. Considered substates are: altitude; thickness and energy of landslide debris; depth of erodable soil cover; debris outflows. Considered elementary processes are: mobilisation triggering and effect (T1, debris outflows (I1, update of landslide debris thickness and energy (I2, and energy loss (T2. Simulations of real debris flows, occurred in Campania (Southern Italy in May 1998 (Sarno and December 1999 (San Martino V.C. and Cervinara, have been performed for model calibration purposes; some examples of analysis are briefly described. Possible applications of the method are: risk mapping, also based on a statistical approach; evaluating the effects of mitigation actions (e.g. stream deviations, topographic
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Alice Hettler
Full Text Available Although electrosurgical instruments are widely used in surgery to cut tissue layers or to achieve hemostasis by coagulation (electrocautery, only little information is available concerning the inflammatory or immune response towards the debris generated. Given the elevated local temperatures required for successful electrocautery, the remaining debris is likely to contain a plethora of compounds entirely novel to the intracorporal setting. A very common in vitro method to study cell migration after mechanical damage is the scratch assay, however, there is no established model for thermomechanical damage to characterise cellular reactions. In this study, we established a new in vitro model to investigate exposure to high temperature in a carefully controlled cell culture system. Heatable thermostat-controlled aluminium stamps were developed to induce local damage in primary human umbilical vein endothelial cells (HUVEC. The thermomechanical damage invoked is reproducibly locally confined, therefore allowing studies, under the same experimental conditions, of cells affected to various degrees as well as of unaffected cells. We show that the unaffected cells surrounding the thermomechanical damage zone are able to migrate into the damaged area, resulting in a complete closure of the 'wound' within 48 h. Initial studies have shown that there are significant morphological and biological differences in endothelial cells after thermomechanical damage compared to the mechanical damage inflicted by using the unheated stamp as a control. Accordingly, after thermomechanical damage, cell death as well as cell protection programs were activated. Mononuclear cells adhered in the area adjacent to thermomechanical damage, but not to the zone of mechanical damage. Therefore, our model can help to understand the differences in wound healing during the early phase of regeneration after thermomechanical vs. mechanical damage. Furthermore, this model lends itself
Evolving Transport Networks With Cellular Automata Models Inspired by Slime Mould.
Tsompanas, Michail-Antisthenis I; Sirakoulis, Georgios Ch; Adamatzky, Andrew I
2015-09-01
Man-made transport networks and their design are closely related to the shortest path problem and considered amongst the most debated problems of computational intelligence. Apart from using conventional or bio-inspired computer algorithms, many researchers tried to solve this kind of problem using biological computing substrates, gas-discharge solvers, prototypes of a mobile droplet, and hot ice computers. In this aspect, another example of biological computer is the plasmodium of acellular slime mould Physarum polycephalum (P. polycephalum), which is a large single cell visible by an unaided eye and has been proven as a reliable living substrate for implementing biological computing devices for computational geometry, graph-theoretical problems, and optimization and imitation of transport networks. Although P. polycephalum is easy to experiment with, computing devices built with the living slime mould are extremely slow; it takes slime mould days to execute a computation. Consequently, mapping key computing mechanisms of the slime mould onto silicon would allow us to produce efficient bio-inspired computing devices to tackle with hard to solve computational intelligence problems like the aforementioned. Toward this direction, a cellular automaton (CA)-based, Physarum-inspired, network designing model is proposed. This novel CA-based model is inspired by the propagating strategy, the formation of tubular networks, and the computing abilities of the plasmodium of P. polycephalum. The results delivered by the CA model demonstrate a good match with several previously published results of experimental laboratory studies on imitation of man-made transport networks with P. polycephalum. Consequently, the proposed CA model can be used as a virtual, easy-to-access, and biomimicking laboratory emulator that will economize large time periods needed for biological experiments while producing networks almost identical to the tubular networks of the real-slime mould.
fA cellular automaton model of crystalline cellulose hydrolysis by cellulases
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Little Bryce A
2011-10-01
Full Text Available Abstract Background Cellulose from plant biomass is an abundant, renewable material which could be a major feedstock for low emissions transport fuels such as cellulosic ethanol. Cellulase enzymes that break down cellulose into fermentable sugars are composed of different types - cellobiohydrolases I and II, endoglucanase and β-glucosidase - with separate functions. They form a complex interacting network between themselves, soluble hydrolysis product molecules, solution and solid phase substrates and inhibitors. There have been many models proposed for enzymatic saccharification however none have yet employed a cellular automaton approach, which allows important phenomena, such as enzyme crowding on the surface of solid substrates, denaturation and substrate inhibition, to be considered in the model. Results The Cellulase 4D model was developed de novo taking into account the size and composition of the substrate and surface-acting enzymes were ascribed behaviors based on their movements, catalytic activities and rates, affinity for, and potential for crowding of, the cellulose surface, substrates and inhibitors, and denaturation rates. A basic case modeled on literature-derived parameters obtained from Trichoderma reesei cellulases resulted in cellulose hydrolysis curves that closely matched curves obtained from published experimental data. Scenarios were tested in the model, which included variation of enzyme loadings, adsorption strengths of surface acting enzymes and reaction periods, and the effect on saccharide production over time was assessed. The model simulations indicated an optimal enzyme loading of between 0.5 and 2 of the base case concentrations where a balance was obtained between enzyme crowding on the cellulose crystal, and that the affinities of enzymes for the cellulose surface had a large effect on cellulose hydrolysis. In addition, improvements to the cellobiohydrolase I activity period substantially improved overall
Modeling of aluminum-silicon irregular eutectic growth by cellular automaton model
Institute of Scientific and Technical Information of China (English)
Rui Chen; Qing-yan Xu; Bai-cheng Liu
2016-01-01
Due to the extensive application of Al-Si aloys in the automotive and aerospace industries as structural components, an understanding of their microstructural formation, such as dendrite and (Al+Si) eutectic, is of great importance to control the desirable microstructure, so as to modify the performance of castings. Since previous major themes of microstructural simulation are dendrite and regular eutectic growth, few efforts have been paid to simulate the irregular eutectic growth. Therefore, a multiphase celular automaton (CA) model is developed and applied to simulate the time-dependent Al-Si irregular eutectic growth. Prior to model establishment, related experiments were carried out to investigate the inlfuence of cooling rate and Sr modiifcation on the growth of eutectic Si. This CA model incorporates several aspects, including growth algorithms and nucleation criterion, to achieve the competitive and cooperative growth mechanism for nonfaceted-faceted Al-Si irregular eutectic. The growth kinetics considers thermal undercooling, constitutional undercooling, and curvature undercooling, as wel as the anisotropic characteristic of eutectic Si growth. The capturing rule takes into account the effects of modiifcation on the silicon growth behaviors. The simulated results indicate that for unmodiifed aloy, the higher eutectic undercooling results in the higher eutectic growth velocity, and a more reifned eutectic microstructure as wel as narrower eutectic lamelar spacing. For modiifed aloy, the eutectic silicon tends to be obvious ifbrous morphology and the morphology of eutectic Si is determined by both chemical modiifer and cooling rate. The predicted microstructure of Al-7Si aloy under different solidiifcation conditions shows that this proposed model can successfuly reproduce both dendrite and eutectic microstructures.
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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.
Institute of Scientific and Technical Information of China (English)
Zheng Zhi-Zhen; Wang Ai-Ling
2009-01-01
Spatially explicit models have become widely used in today's mathematical ecology and epidemiology to study the persistence of populations. For simplicity, population dynamics is often analysed by using ordinary differential equations (ODEs) or partial differential equations (PDEs) in the one-dimensional (1D) space. An important question is to predict species extinction or persistence rate by mean of computer simulation based on the spatial model. Recently, it has been reported that stable turbulent and regular waves are persistent based on the spatial susceptible-infected-resistant-susceptible (SIRS) model by using the cellular automata (CA) method in the two-dimensional (2D) space [Proc. Natl. Acad. Sci. USA 101, 18246 (2004)]. In this paper, we address other important issues relevant to phase transitions of epidemic persistence. We are interested in assessing the significance of the risk of extinction in 1D space. Our results show that the 2D space can considerably increase the possibility of persistence of spread of epidemics when the degree distribution of the individuals is uniform, I.e. The pattern of 2D spatial persistence corresponding to extinction in a 1D system with the same parameters. The trade-offs of extinction and persistence between the infection period and infection rate are observed in the 1D case. Moreover, near the trade-off (phase transition) line, an independent estimation of the dynamic exponent can be performed, and it is in excellent agreement with the result obtained by using the conjectured relationship of directed percolation. We find that the introduction of a short-range diffusion and a long-range diffusion among the neighbourhoods can enhance the persistence and global disease spread in the space.
Gérard, Claude; Goldbeter, Albert
2012-05-01
The cell division cycle and the circadian clock represent two major cellular rhythms. These two periodic processes are coupled in multiple ways, given that several molecular components of the cell cycle network are controlled in a circadian manner. For example, in the network of cyclin-dependent kinases (Cdks) that governs progression along the successive phases of the cell cycle, the synthesis of the kinase Wee1, which inhibits the G2/M transition, is enhanced by the complex CLOCK-BMAL1 that plays a central role in the circadian clock network. Another component of the latter network, REV-ERBα, inhibits the synthesis of the Cdk inhibitor p21. Moreover, the synthesis of the oncogene c-Myc, which promotes G1 cyclin synthesis, is repressed by CLOCK-BMAL1. Using detailed computational models for the two networks we investigate the conditions in which the mammalian cell cycle can be entrained by the circadian clock. We show that the cell cycle can be brought to oscillate at a period of 24 h or 48 h when its autonomous period prior to coupling is in an appropriate range. The model indicates that the combination of multiple modes of coupling does not necessarily facilitate entrainment of the cell cycle by the circadian clock. Entrainment can also occur as a result of circadian variations in the level of a growth factor controlling entry into G1. Outside the range of entrainment, the coupling to the circadian clock may lead to disconnected oscillations in the cell cycle and the circadian system, or to complex oscillatory dynamics of the cell cycle in the form of endoreplication, complex periodic oscillations or chaos. The model predicts that the transition from entrainment to 24 h or 48 h might occur when the strength of coupling to the circadian clock or the level of growth factor decrease below critical values.
Askland, Kathleen
2006-08-01
Current epidemiologic and genetic evidence strongly supports the heritability of bipolar disease. Inconsistencies across linkage and association analyses have been primarily interpreted as suggesting polygenic, nonMendelian and variably-penetrant inheritance (i.e., in terms of interacting disease models). An equally-likely explanation for this genetic complexity is that trait, locus and allelic heterogeneities (i.e., a heterogeneous disease model) are primarily responsible for observed variability at the population level. The two models of genetic complexity are not mutually-exclusive, and are in fact likely to co-exist both in trait determination and disease expression. However, the current model proposes that, while both types of complex genetics are likely central to observable affective trait spectra, inheritance patterns, gross phenotypic categories and treatment-responsiveness in affective disease (as well as the widespread inconsistencies across such studies) may be primarily explained in terms of a heterogeneous disease model. Gene-gene, gene-protein and protein-protein interactions, then, are most likely to serve as trait determinants and 'phenotypic modifiers' rather than as primary pathogenic determinants. Moreover, while locus heterogeneity indicates the presence of multiple susceptibility genes at the population level, it does not necessitate polygenic inheritance at the individual or pedigree level. Rather, it is compatible with the possibility of mono- or bigenic determination of disease susceptibility within individuals/pedigrees. More specifically, the biaxial model proposes that integration of specific findings from genetic linkage and association studies, ion channels research as well as pharmacologic mechanism, phenotypic specificity and effectiveness studies suggests that each gene of potential etiologic significance in primary affective illness might be categorized into one of two classes, according to their primary role in neuronal
Directed Ligand Passage Over the Surface of Diffusion-Controlled Enzymes: A Cellular Automata Model
Ghaemi, M; Sarbolouki, M N; Ghaemi, Mehrdad; Rezaei-Ghaleh, Nasrollah; Sarbolouki, Mohammad-Nabi
2004-01-01
The rate-limiting step of some enzymatic reactions is a physical step, i.e. diffusion. The efficiency of such reactions can be improved through an increase in the arrival rate of the substrate molecules, e.g. by a directed passage of substrate (ligand) to active site after its random encounter with the enzyme surface. Herein, we introduce a cellular automata model simulating the ligand passage over the protein surface to its destined active site. The system is simulated using the lattice gas automata with probabilistic transition rules. Different distributions of amino acids over the protein surface are examined. For each distribution, the hydration pattern is achieved and the mean number of iteration steps needed for the ligand to arrive at the active site calculated. Comparison of results indicates that the rate at which ligand arrives at the active site is clearly affected by the distribution of amino acids outside the active side. Such a process can facilitate the ligand diffusion towards the active site ...
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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.
The Investigation of the Traffic Flow Behavior in Tollbooths Using Cellular Automaton Model
Jetto, K.; Ez-Zahraouy, H.; Benyoussef, A.
Tollbooths are used to collect tolls and to control traffic flow. However, the presence of these tollbooths will slow down traffic, especially in heavily traveled roads. As a consequence, drivers and goods will spend more time and fuel waiting in a long queue. Unfortunately, there are a few papers in the literature, which have been addressed the effect of tollbooths on the traffic flow; whereas in this paper is, the properties of traffic flow inside the tollbooths are investigated. The proposed cellular automaton traffic model, with open boundaries, is based on some changing lane rules, which are inspired on the situations inside the toll plaza. The vehicles enter the plaza with an injecting rate α, and they leave with an extracting rate β, which is inversely proportional to the time service Tw. The simulation results show the existence of three phases in the phase diagram (α, β), namely: the low density phase, the congested phase, and the jamming phase. Furthermore, it is found that the vehicles does not spend the same time Tm in the plaza, even if they have the same time service. This analysis states clearly that the existence of the congested phase and the fluctuation Tm are due to the non-zero values of the probability P of changing the lane. Such phenomena disappear when P = 0, i.e., the drivers move without changing their lane. In other words, the human behavior (spontaneous changing lanes) is responsible for the congestion observed in the tollbooth.
The Toxic Effects of Pathogenic Ataxin-3 Variants in a Yeast Cellular Model.
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Marcella Bonanomi
Full Text Available Ataxin-3 (AT3 is a deubiquitinating enzyme that triggers an inherited neurodegenerative disorder, spinocerebellar ataxia type 3, when its polyglutamine (polyQ stretch close to the C-terminus exceeds a critical length. AT3 variants carrying the expanded polyQ are prone to associate with each other into amyloid toxic aggregates, which are responsible for neuronal death with ensuing neurodegeneration. We employed Saccharomyces cerevisiae as a eukaryotic cellular model to better clarify the mechanism by which AT3 triggers the disease. We expressed three variants: one normal (Q26, one expanded (Q85 and one truncated for a region lying from the beginning of its polyQ stretch to the end of the protein (291Δ. We found that the expression of the expanded form caused reduction in viability, accumulation of reactive oxygen species, imbalance of the antioxidant defense system and loss in cell membrane integrity, leading to necrotic death. The truncated variant also exerted a qualitatively similar, albeit milder, effect on cell growth and cytotoxicity, which points to the involvement of also non-polyQ regions in cytotoxicity. Guanidine hydrochloride, a well-known inhibitor of the chaperone Hsp104, almost completely restored wild-type survival rate of both 291Δ- and Q85-expressing strains. This suggests that AT3 aggregation and toxicity is mediated by prion forms of yeast proteins, as this chaperone plays a key role in their propagation.
The Toxic Effects of Pathogenic Ataxin-3 Variants in a Yeast Cellular Model
Bonanomi, Marcella; Visentin, Cristina; Invernizzi, Gaetano; Tortora, Paolo; Regonesi, Maria Elena
2015-01-01
Ataxin-3 (AT3) is a deubiquitinating enzyme that triggers an inherited neurodegenerative disorder, spinocerebellar ataxia type 3, when its polyglutamine (polyQ) stretch close to the C-terminus exceeds a critical length. AT3 variants carrying the expanded polyQ are prone to associate with each other into amyloid toxic aggregates, which are responsible for neuronal death with ensuing neurodegeneration. We employed Saccharomyces cerevisiae as a eukaryotic cellular model to better clarify the mechanism by which AT3 triggers the disease. We expressed three variants: one normal (Q26), one expanded (Q85) and one truncated for a region lying from the beginning of its polyQ stretch to the end of the protein (291Δ). We found that the expression of the expanded form caused reduction in viability, accumulation of reactive oxygen species, imbalance of the antioxidant defense system and loss in cell membrane integrity, leading to necrotic death. The truncated variant also exerted a qualitatively similar, albeit milder, effect on cell growth and cytotoxicity, which points to the involvement of also non-polyQ regions in cytotoxicity. Guanidine hydrochloride, a well-known inhibitor of the chaperone Hsp104, almost completely restored wild-type survival rate of both 291Δ- and Q85-expressing strains. This suggests that AT3 aggregation and toxicity is mediated by prion forms of yeast proteins, as this chaperone plays a key role in their propagation. PMID:26052945
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Alejandro Martínez-Herrera
2015-09-01
Full Text Available Dystrophin Dp40 is the shortest protein encoded by the DMD (Duchenne muscular dystrophy gene. This protein is unique since it lacks the C-terminal end of dystrophins. In this data article, we describe the subcellular localization, nuclear export signals and the three-dimensional structure modeling of putative Dp40 proteins using bioinformatics tools. The Dp40 wild type protein was predicted as a cytoplasmic protein while the Dp40n4 was predicted to be nuclear. Changes L93P and L170P are involved in the nuclear localization of Dp40n4 protein. A close analysis of Dp40 protein scored that amino acids 93LEQEHNNLV101 and 168LLLHDSIQI176 could function as NES sequences and the scores are lost in Dp40n4. In addition, the changes L93/170P modify the tertiary structure of putative Dp40 mutants. The analysis showed that changes of residues 93 and 170 from leucine to proline allow the nuclear localization of Dp40 proteins. The data described here are related to the research article entitled “EF-hand domains are involved in the differential cellular distribution of dystrophin Dp40” (J. Aragón et al. Neurosci. Lett. 600 (2015 115–120 [1].
Modeling and Simulation of Polarization in Internet Group Opinions Based on Cellular Automata
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Yaofeng Zhang
2015-01-01
Full Text Available Hot events on Internet always attract many people who usually form one or several opinion camps through discussion. For the problem of polarization in Internet group opinions, we propose a new model based on Cellular Automata by considering neighbors, opinion leaders, and external influences. Simulation results show the following: (1 It is easy to form the polarization for both continuous opinions and discrete opinions when we only consider neighbors influence, and continuous opinions are more effective in speeding the polarization of group. (2 Coevolution mechanism takes more time to make the system stable, and the global coupling mechanism leads the system to consensus. (3 Opinion leaders play an important role in the development of consensus in Internet group opinions. However, both taking the opinion leaders as zealots and taking some randomly selected individuals as zealots are not conductive to the consensus. (4 Double opinion leaders with consistent opinions will accelerate the formation of group consensus, but the opposite opinions will lead to group polarization. (5 Only small external influences can change the evolutionary direction of Internet group opinions.
Institute of Scientific and Technical Information of China (English)
A.Yu. SMOLIN; E.V. SHILKO; S.V. ASTAFUROV; I.S. KONOVALENKO; S.P. BUYAKOVA; S.G. PSAKHIE
2015-01-01
Two classes of composite materials are considered: classical metaleceramic composites with reinforcing hard inclusions as well as hard ceramics matrix with soft gel inclusions. Movable cellular automaton method is used for modeling the mechanical behaviors of such different heterogeneous materials. The method is based on particle approach and may be considered as a kind of discrete element method. The main feature of the method is the use of many-body forces of inter-element interaction within the formalism of simply deformable element approximation. It was shown that the strength of reinforcing particles and the width of particle-binder interphase boundaries had determining influence on the service characteristics of metaleceramic composite. In particular, the increasing of strength of carbide inclusions may lead to significant increase in the strength and ultimate strain of composite material. On the example of porous zirconia ceramics it was shown that the change in the mechanical properties of pore surface leads to the corresponding change in effective elastic modulus and strength limit of the ceramic sample. The less is the pore size, the more is this effect. The increase in the elastic properties of pore surface of ceramics may reduce its fracture energy.
Path Loss, Shadow Fading, and Line-Of-Sight Probability Models for 5G Urban Macro-Cellular Scenarios
DEFF Research Database (Denmark)
Sun, Shu; Thomas, Timothy; Rappaport, Theodore S.
2015-01-01
This paper presents key parameters including the line-of-sight (LOS) probability, large-scale path loss, and shadow fading models for the design of future fifth generation (5G) wireless communication systems in urban macro-cellular (UMa) scenarios, using the data obtained from propagation measure...
Simulating Debris Flows Through A Hexagonal Cellular Automata Model: Sciddica (release S3a).
Iovine, G.; di Gregorio, S.; D'Ambrosio, D.; Lupiano, V.; Rongo, R.; Spataro, W.
Cellular Automata (CA) are a powerful tool for modelling natural and artificial sys- tems that can be described in terms of local interactions among their constituent parts. Some types of landslides, such as debris flows, match well this requirement. The general frame and the latest, hexagonal release (S3a) of the deterministic, CA-based model SCIDDICA - specifically developed for simulating debris flows - are described. For simulation purposes, landslides can be viewed as a dynamical system, subdivided into elementary parts, whose state evolves exclusively as a consequence of local in- teractions within a spatial and temporal discretum. Space is the world of the CA, constituted by hexagonal cells. The attributes of each cell (namely "substates") de- scribe their average, physical characteristics. For computational reasons, the natural phenomenon to be simulated is "decomposed" into a number of elementary processes (local interactions), whose proper composition makes up the "transition function" of the CA. By simultaneously applying this function to all the cells, the evolution of the phenomenon can be simulated in terms of modifications of the substates. SCIDDICA- S3a exhibited great flexibility in modelling debris flows. With respect to its previous releases, the mechanism of progressive erosion of the detrital cover has been added to the transition function. Considered substates are: altitude, landslide debris amount and energy, depth and type of detrital cover, water content of the debris, debris out- flows and inflows. Considered elementary processes are: outflows and inflows, energy variation, detrital cover mobilisation, water loss, debris solidification. Simulations of real debris flows, occurred in Campania (Southern Italy) on May 1998 (Sarno) and on December 1999 (San Martino V.C. and Cervinara), are presented. The validation of the model required the best assessment of values to be assigned to empirical param- eters. After that, the application of the
Recurrence time statistics of landslide events simulated by a cellular automaton model
Piegari, Ester; Di Maio, Rosa; Avella, Adolfo
2014-05-01
The recurrence time statistics of a cellular automaton modelling landslide events is analyzed by performing a numerical analysis in the parameter space and estimating Fano factor behaviors. The model is an extended version of the OFC model, which is a paradigm for SOC in non-conserved systems, but it works differently from the original OFC model as a finite value of the driving rate is applied. By driving the system to instability with different rates, the model exhibits a smooth transition from a correlated to an uncorrelated regime as the effect of a change in predominant mechanisms to propagate instability. If the rate at which instability is approached is small, chain processes dominate the landslide dynamics, and power laws govern probability distributions. However, the power-law regime typical of SOC-like systems is found in a range of return intervals that becomes shorter and shorter by increasing the values of the driving rates. Indeed, if the rates at which instability is approached are large, domino processes are no longer active in propagating instability, and large events simply occur because a large number of cells simultaneously reach instability. Such a gradual loss of the effectiveness of the chain propagation mechanism causes the system gradually enter to an uncorrelated regime where recurrence time distributions are characterized by Weibull behaviors. Simulation results are qualitatively compared with those from a recent analysis performed by Witt et al.(Earth Surf. Process. Landforms, 35, 1138, 2010) for the first complete databases of landslide occurrences over a period as large as fifty years. From the comparison with the extensive landslide data set, the numerical analysis suggests that statistics of such landslide data seem to be described by a crossover region between a correlated regime and an uncorrelated regime, where recurrence time distributions are characterized by power-law and Weibull behaviors for short and long return times
Hung, Shih-Han; Su, Chin-Hui; Tseng, How
2016-08-01
It is important to have a standardized tympanic membrane (TM) perforation platform to evaluate the various myringoplasty materials that have been studied and developed extensively during recent years. However, currently there are no cellular models specifically designed for this purpose, and animal models remain unsatisfactory. The purpose of this study is to propose an inexpensive, readily available, well-controlled, and easy-to-create cellular model as a substitute for use in the evaluation of TM repairing materials. A trans-well model was created using a cell culture insert with a round hole created at the center of the polycarbonate membrane. HaCaT cells were cultured on the fenestrated culture insert, and the desired myringoplasty graft was placed at the center of the window for one week and observed by fluorescent microscopy under vital staining. Under this cellular model, there was notable migration of HaCaT cells onto the positive control graft (rabbit fascia), while only a few cell clusters were observed on the negative control graft (paper). Model validation showed that the cell migration ratio for the PLLA + 1% hyaluronic acid (HA) graft is significantly higher than using myringoplasty paper, poly L-lactide (PLLA), or PLLA + 0.5% HA (p model might be a useful pre-evaluation platform for the evaluation of TM repairing materials. The model is inexpensive, readily available, easy to create, and standardized for use.
Model of Handover and Traffic Based on Cellular Geometry with Smart Antenna
Directory of Open Access Journals (Sweden)
Zufan Zhang
2014-01-01
Full Text Available Based on the application of smart antennas in cellular mobile communications, this paper introduces the impact of the width of the antenna beams playing on the dwell time probability density function in cellular geometry with smart antenna. The research results indicate that the smart cell structure can improve the dwell time of users within the cell and improve the traffic system performance.
N-acetyl-L-cysteine prevents stress-induced desmin aggregation in cellular models of desminopathy.
Directory of Open Access Journals (Sweden)
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
Crawling and Gliding: A Computational Model for Shape-Driven Cell Migration.
Niculescu, Ioana; Textor, Johannes; de Boer, Rob J
2015-10-01
Cell migration is a complex process involving many intracellular and extracellular factors, with different cell types adopting sometimes strikingly different morphologies. Modeling realistically behaving cells in tissues is computationally challenging because it implies dealing with multiple levels of complexity. We extend the Cellular Potts Model with an actin-inspired feedback mechanism that allows small stochastic cell rufflings to expand to cell protrusions. This simple phenomenological model produces realistically crawling and deforming amoeboid cells, and gliding half-moon shaped keratocyte-like cells. Both cell types can migrate randomly or follow directional cues. They can squeeze in between other cells in densely populated environments or migrate collectively. The model is computationally light, which allows the study of large, dense and heterogeneous tissues containing cells with realistic shapes and migratory properties.
Crawling and Gliding: A Computational Model for Shape-Driven Cell Migration.
Directory of Open Access Journals (Sweden)
Ioana Niculescu
2015-10-01
Full Text Available Cell migration is a complex process involving many intracellular and extracellular factors, with different cell types adopting sometimes strikingly different morphologies. Modeling realistically behaving cells in tissues is computationally challenging because it implies dealing with multiple levels of complexity. We extend the Cellular Potts Model with an actin-inspired feedback mechanism that allows small stochastic cell rufflings to expand to cell protrusions. This simple phenomenological model produces realistically crawling and deforming amoeboid cells, and gliding half-moon shaped keratocyte-like cells. Both cell types can migrate randomly or follow directional cues. They can squeeze in between other cells in densely populated environments or migrate collectively. The model is computationally light, which allows the study of large, dense and heterogeneous tissues containing cells with realistic shapes and migratory properties.
Institute of Scientific and Technical Information of China (English)
Syed ABBAS; Yonghui XIA
2013-01-01
In this paper we discuss the existence and global attractivity of k-almost automorphic sequence solution of a model of cellular neural networks.We consider the corresponding difference equation analogue of the model system using suitable discretization method and obtain certain conditions for the existence of solution.Almost automorphic function is a good generalization of almost periodic function.This is the first paper considering such solutions of the neural networks.
DEFF Research Database (Denmark)
Skiadas, Ioannis V.; Ahring, Birgitte Kiær
2002-01-01
characteristics and lead to different reactor behaviour. A dynamic mathematical model has been developed for the anaerobic digestion of a glucose based synthetic wastewater in UASB reactors. Cellular automata (CA) theory has been applied to simulate the granule development process. The model takes...... 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....
A conceptual mathematical model of the dynamic self-organisation of distinct cellular organelles.
Directory of Open Access Journals (Sweden)
Bernd Binder
Full Text Available Formation, degradation and renewal of cellular organelles is a dynamic process based on permanent budding, fusion and inter-organelle traffic of vesicles. These processes include many regulatory proteins such as SNAREs, Rabs and coats. Given this complex machinery, a controversially debated issue is the definition of a minimal set of generic mechanisms necessary to enable the self-organization of organelles differing in number, size and chemical composition. We present a conceptual mathematical model of dynamic organelle formation based on interacting vesicles which carry different types of fusogenic proteins (FP playing the role of characteristic marker proteins. Our simulations (ODEs show that a de novo formation of non-identical organelles, each accumulating a different type of FP, requires a certain degree of disproportionation of FPs during budding. More importantly however, the fusion kinetics must indispensably exhibit positive cooperativity among these FPs, particularly for the formation of larger organelles. We compared different types of cooperativity: sequential alignment of corresponding FPs on opposite vesicle/organelles during fusion and pre-formation of FP-aggregates (equivalent, e.g., to SNARE clusters prior to fusion described by Hill kinetics. This showed that the average organelle size in the system is much more sensitive to the disproportionation strength of FPs during budding if the vesicular transport system gets along with a fusion mechanism based on sequential alignments of FPs. Therefore, pre-formation of FP aggregates within the membranes prior to fusion introduce robustness with respect to organelle size. Our findings provide a plausible explanation for the evolution of a relatively large number of molecules to confer specificity on the fusion machinery compared to the relatively small number involved in the budding process. Moreover, we could speculate that a specific cooperativity which may be described by Hill
de Curtis, M; Radici, C; Forti, M
1999-01-01
The cellular mechanisms involved in the generation of spontaneous epileptiform potentials were investigated in the pirifom cortex of the in vitro isolated guinea-pig brain. A single, unilateral injection of bicuculline (150-200 nmol) in the anterior piriform cortex induced locally spontaneous interictal spikes that recurred with a period of 8.81+/-4.47 s and propagated caudally to the ipsi- and contralateral hemispheres. Simultaneous extra- and intracellular recordings from layer II and III principal cells showed that the spontaneous interictal spike correlates to a burst of action potentials followed by a large afterdepolarization. Intracellular application of the sodium conductance blocker, QX-314 (80 mM), abolished bursting activity and unmasked a high-threshold slow spike enhanced by the calcium chelator EGTA (50 mM). The slow spike was abolished by membrane hyperpolarization and by local perfusion with 2 mM cadmium. The depolarizing potential that followed the primary burst was reduced by arterial perfusion with the N-methyl-D-aspartate receptor antagonist, DL-2-amino-5-phosphonopentanoic acid (100-200 microM). The non-N-methyl-D-aspartate glutamate receptor antagonist, 6-cyano-7-nitroquinoxaline-2,3-dione (20 microM), completely and reversibly blocked the spontaneous spikes. The interictal spikes were terminated by a large afterpotential blocked either by intracellular QX-314 (80 mM) or by extracellular application of phaclofen and 2-hydroxysaclofen (10 and 4 mM, respectively). The present study demonstrates that, in an acute model of epileptogenesis, spontaneous interictal spikes are fostered by a primary burst of fast action potentials that ride on a regenerative high-threshold, possibly calcium-mediated spike, which activates a recurrent, glutamate-mediated potential responsible for the entrainment of adjacent and remote cortical regions. The bursting activity is controlled by a GABA(B) receptor-mediated inhibitory synaptic potential.
Effect of preoperative immunonutrition and other nutrition models on cellular immune parameters
Institute of Scientific and Technical Information of China (English)
Yusuf Gunerhan; Neset Koksal; Umit Yasar Sahin; Mehmet Ali Uzun; Emel Ek(s)ioglu-Demiralp
2009-01-01
AIM: To evaluate the effects of preoperative immunonutrition and other nutrition models on the cellular immunity parameters of patients with gastrointestinal tumors before surgical intervention. In addition, effects on postoperative complications were examined.METHODS: Patients with gastrointestinal tumors were randomized into 3 groups. The immunonutrition group received a combination of arginine, fatty acids and nucleotides. The second and third group received normal nutrition and standard enteral nutrition,respectively. Nutrition protocols were administered for 7 d prior to the operation. Nutritional parameters,in particular prealbumin levels and lymphocyte subpopulations (CD4+, CD8+, CD16+/56+, and CD69 cells) were evaluated before and after the nutrition protocols. Groups were compared in terms of postoperative complications and duration of hospital stay.RESULTS: Of the 42 patients who completed the study, 16 received immunonutrition, 13 received normal nutrition and 13 received standard enteral nutrition.prealbumin values were low in every group, but this parameter was improved after the nutritional protocol only in the immunonutrition group (13.64 ± 8.83vs 15.98 ± 8.66, P = 0.037). Groups were similar in terms of CD4+, CD16+/56, and CD69+ prior to the nutritional protocol; whereas CD8+ was higher in the standard nutrition group compared to the immunonutrition group. After nutritional protocols,none of the groups had an increase in their lymphocyte subpopulations. Also, groups did not differ in terms of postoperative complications and postoperative durations of hospital stay.CONCLUSION: Preoperative immunonutrition provided a significant increase in prealbumin levels,while it did not significantly alter T lymphocyte subpopulation counts, the rate of postoperative complications and the duration of hospital stay.
A computational model of cellular mechanisms of temporal coding in the medial geniculate body (MGB.
Directory of Open Access Journals (Sweden)
Cal F Rabang
Full Text Available Acoustic stimuli are often represented in the early auditory pathway as patterns of neural activity synchronized to time-varying features. This phase-locking predominates until the level of the medial geniculate body (MGB, where previous studies have identified two main, largely segregated response types: Stimulus-synchronized responses faithfully preserve the temporal coding from its afferent inputs, and Non-synchronized responses, which are not phase locked to the inputs, represent changes in temporal modulation by a rate code. The cellular mechanisms underlying this transformation from phase-locked to rate code are not well understood. We use a computational model of a MGB thalamocortical neuron to test the hypothesis that these response classes arise from inferior colliculus (IC excitatory afferents with divergent properties similar to those observed in brain slice studies. Large-conductance inputs exhibiting synaptic depression preserved input synchrony as short as 12.5 ms interclick intervals, while maintaining low firing rates and low-pass filtering responses. By contrast, small-conductance inputs with Mixed plasticity (depression of AMPA-receptor component and facilitation of NMDA-receptor component desynchronized afferent inputs, generated a click-rate dependent increase in firing rate, and high-pass filtered the inputs. Synaptic inputs with facilitation often permitted band-pass synchrony along with band-pass rate tuning. These responses could be tuned by changes in membrane potential, strength of the NMDA component, and characteristics of synaptic plasticity. These results demonstrate how the same synchronized input spike trains from the inferior colliculus can be transformed into different representations of temporal modulation by divergent synaptic properties.
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.
Cellular parameters for track structure modelling of radiation hazard in space
Hollmark, M.; Lind, B.; Gudowska, I.; Waligorski, M.
Based on irradiation with 45 MeV/u N and B ions and with Co-60 gamma rays, track structure cellular parameters have been fitted for V 79-379A Chinese hamster lung fibroblasts and for human melanoma cells (AA wtp53). These sets of parameters will be used to develop a calculation of radiation hazard in deep space, based on the system for evaluating, summing and reporting occupational exposures proposed in 1967 by subcommittee of the NCRP, but never issued as an NCRP report. The key concepts of this system were: i) expression of the risk from all radiation exposures relative to that from a whole-body exposure to Co-60 radiation; ii) relating the risk from any exposure to that of the standard (Co-60) radiation through an "effectiveness factor" (ef), a product of sub-factors representing radiation quality, body region irradiated, and depth of penetration of radiation; the product of absorbed dose by ef being termed the "exposure record unit" (eru); iii) development of ef values and a cumulative eru record for external and internal emitters. Application of this concept should provide a better description of the Gy -equivalent presently in use by NASA for evaluating risk in deep space than the equivalent dose, following ICRP-60 recommendations. Dose and charged particle fluence levels encountered in space, particularly after Solar Particle Events, require that deterministic rather than stochastic effects be considered. Also, synergistic effects due to simultaneous multiple charged particle transfers, may have to be considered. Thus, models applicable in radiotherapy, where the Gy -equivalent is also applied, in conjunction with transport calculations performed using, e.g. the ADAM and EVA phantoms, along the concepts of the 1967 NCRP system, may be more appropriate for evaluating the radiation hazard from external fields with a large flux and a major high-LET component.
DEFF Research Database (Denmark)
Qing, Hai; Mishnaevsky, Leon
2009-01-01
A 3D hierarchical computational model of deformation and stiffness of wood, which takes into account the structures of wood at several scale levels (cellularity, multilayered nature of cell walls, composite-like structures of the wall layers) is developed. At the mesoscale, the softwood cell...... is presented as a 3D hexagon-shape-tube with multilayered walls. The layers in the softwood cell are considered as considered as composite reinforced by microfibrils (celluloses). The elastic properties of the layers are determined with Halpin–Tsai equations, and introduced into mesoscale finite element...... 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...
Induced pluripotent stem cells as a cellular model for studying Down Syndrome
Brigida, Anna Lisa; Siniscalco, Dario
2016-01-01
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 the same
Jacquin, Hugo; Shakhnovich, Eugene; Cocco, Simona; Monasson, Rémi
2016-01-01
Inverse statistical approaches to determine protein structure and function from Multiple Sequence Alignments (MSA) are emerging as powerful tools in computational biology. However the underlying assumptions of the relationship between the inferred effective Potts Hamiltonian and real protein structure and energetics remain untested so far. Here we use lattice protein model (LP) to benchmark those inverse statistical approaches. We build MSA of highly stable sequences in target LP structures, and infer the effective pairwise Potts Hamiltonians from those MSA. We find that inferred Potts Hamiltonians reproduce many important aspects of 'true' LP structures and energetics. Careful analysis reveals that effective pairwise couplings in inferred Potts Hamiltonians depend not only on the energetics of the native structure but also on competing folds; in particular, the coupling values reflect both positive design (stabilization of native conformation) and negative design (destabilization of competing folds). In addi...
DEFF Research Database (Denmark)
Mahshid, Rasoul; Hansen, Hans Nørgaard; Loft Højbjerre, Klaus
2016-01-01
Additive manufacturing is rapidly developing and gaining popularity for direct metal fabrication systems like selective laser melting (SLM). The technology has shown significant improvement for high-quality fabrication of lightweight design-efficient structures such as conformal cooling channels...... in injection molding tools and lattice structures. This research examines the effect of cellular lattice structures on the strength of workpieces additively manufactured from ultra high-strength steel powder. Two commercial SLM machines are used to fabricate cellular samples based on four architectures— solid...
Alber, M; Glimm, T; Lushnikov, P M; Alber, Mark; Chen, Nan; Glimm, Tilmann; Lushnikov, Pavel M.
2006-01-01
The Cellular Potts Model (CPM) has been used for simulating various biological phenomena such as differential adhesion, fruiting body formation of the slime mold Dictyostelium discoideum, angiogenesis, cancer invasion, chondrogenesis in embryonic vertebrate limbs, and many others. In this paper, we derive continuous limit of discrete one dimensional CPM with the chemotactic interactions between cells in the form of a Fokker-Planck equation for the evolution of the cell probability density function. This equation is then reduced to the classical macroscopic Keller-Segel model. In particular, all coefficients of the Keller-Segel model are obtained from parameters of the CPM. Theoretical results are verified numerically by comparing Monte Carlo simulations for the CPM with numerics for the Keller-Segel model.
Slomka, Noa; Gefen, Amit
2010-06-18
This study introduces a new confocal microscopy-based three-dimensional cell-specific finite element (FE) modeling methodology for simulating cellular mechanics experiments involving large cell deformations. Three-dimensional FE models of undifferentiated skeletal muscle cells were developed by scanning C2C12 myoblasts using a confocal microscope, and then building FE model geometries from the z-stack images. Strain magnitudes and distributions in two cells were studied when the cells were subjected to compression and stretching, which are used in pressure ulcer and deep tissue injury research to induce large cell deformations. Localized plasma membrane and nuclear surface area (NSA) stretches were observed for both the cell compression and stretching simulation configurations. It was found that in order to induce large tensile strains (>5%) in the plasma membrane and NSA, one needs to apply more than approximately 15% of global cell deformation in cell compression tests, or more than approximately 3% of tensile strains in the elastic plate substrate in cell stretching experiments. Utilization of our modeling can substantially enrich experimental cellular mechanics studies in classic cell loading designs that typically involve large cell deformations, such as static and cyclic stretching, cell compression, micropipette aspiration, shear flow and hydrostatic pressure, by providing magnitudes and distributions of the localized cellular strains specific to each setup and cell type, which could then be associated with the applied stimuli.
Cheng, Y.; Kekenes-Huskey, P.; Hake, J. E.; Holst, M. J.; McCammon, J. A.; Michailova, A. P.
2012-01-01
This paper presents a brief review of multi-scale modeling at the molecular to cellular scale, with new results for heart muscle cells. A finite element-based simulation package (SMOL) was used to investigate the signaling transduction at molecular and sub-cellular scales (http://mccammon.ucsd.edu/smol/, http://FETK.org) by numerical solution of the time-dependent Smoluchowski equations and a reaction-diffusion system. At the molecular scale, SMOL has yielded experimentally validated estimates of the diffusion-limited association rates for the binding of acetylcholine to mouse acetylcholinesterase using crystallographic structural data. The predicted rate constants exhibit increasingly delayed steady-state times, with increasing ionic strength, and demonstrate the role of an enzyme's electrostatic potential in influencing ligand binding. At the sub-cellular scale, an extension of SMOL solves a nonlinear, reaction-diffusion system describing Ca2+ ligand buffering and diffusion in experimentally derived rodent ventricular myocyte geometries. Results reveal the important role of mobile and stationary Ca2+ buffers, including Ca2+ indicator dye. We found that alterations in Ca2+-binding and dissociation rates of troponin C (TnC) and total TnC concentration modulate sub-cellular Ca2+ signals. The model predicts that reduced off-rate in the whole troponin complex (TnC, TnI, TnT) versus reconstructed thin filaments (Tn, Tm, actin) alters cytosolic Ca2+ dynamics under control conditions or in disease-linked TnC mutations. The ultimate goal of these studies is to develop scalable methods and theories for the integration of molecular-scale information into simulations of cellular-scale systems.
Chen, Ting-Jung; Wu, Chia-Ching; Su, Fong-Chin
2012-12-01
The cytoskeleton, which is the major mechanical component of cells, supports the cell body and regulates the cellular motility to assist the cell in performing its biological functions. Several cytoskeletal network models have been proposed to investigate the mechanical properties of cells. This review paper summarizes these models with a focus on the prestressed cable network, the semi-flexible chain network, the open-cell foam, the tensegrity, and the granular models. The components, material parameters, types of connection joints, tension conditions, and the advantages and disadvantages of each model are evaluated from a structural and biological point of view. The underlying mechanisms that are associated with the morphological changes of spreading cells are expected to be simulated using a cytoskeletal model; however, it is still paid less attention most likely due to the lack of a suitable cytoskeletal model that can accurately model the spreading process. In this review article, the established cytoskeletal models are hoped to provide useful information for the development of future cytoskeletal models with different degrees of cell attachment for the study of the mechanical mechanisms underlying the cellular behaviors in response to external stimulations.
Honda, Hisao; Nagai, Tatsuzo
2015-03-01
Morphogenesis of multi-cellular organisms occurs through cell behaviours within a cell aggregate. Cell behaviours have been described using cell models involving equations of motion for cells. Cells in cell models construct shapes of the cell aggregate by themselves. Here, a history of cell models, the cell centre model and the vertex cell model, which we have constructed, are described. Furthermore, the application of these cell models is explained in detail. These cell models have been applied to transformation of cell aggregates to become spherical, formation of mammalian blastocysts and cell intercalation in elongating tissues. These are all elemental processes of morphogenesis and take place in succession during the whole developmental process. A chain of successive elemental processes leads to morphogenesis. Finally, we highlight that cell models are indispensable to understand the process whereby genes direct biological shapes.
Finite-size scaling relations for a four-dimensional Ising model on Creutz cellular automatons
Merdan, Z.; Güzelsoy, E.
2011-06-01
The four-dimensional Ising model is simulated on Creutz cellular automatons using finite lattices with linear dimensions 4 ≤ L ≤ 8. The temperature variations and finite-size scaling plots of the specific heat and the Binder parameter verify the theoretically predicted expression near the infinite lattice critical temperature for 7, 14, and 21 independent simulations. Approximate values for the critical temperature of the infinite lattice of Tc(∞) = 6.6965(35), 6.6961(30), 6.6960(12), 6.6800(3), 6.6801(2), 6.6802(1) and 6.6925(22) (without the logarithmic factor), 6.6921(22) (without the logarithmic factor), 6.6909(2) (without the logarithmic factor), 6.6822(13) (with the logarithmic factor), 6.6819(11) (with the logarithmic factor), and 6.6808(8) (with the logarithmic factor) are obtained from the intersection points of the specific heat curves, the Binder parameter curves, and straight line fits of specific heat maxima for 7, 14, and 21 independent simulations, respectively. As the number of independent simulations increases, the results, 6.6802(1) and 6.6808(8), are in very good agreement with the results of a series expansion of Tc(∞), 6.6817(15) and 6.6802(2), the dynamic Monte Carlo value Tc(∞) = 6.6803(1), the cluster Monte Carlo value Tc(∞) = 6.680(1), and the Monte Carlo value using the Metropolis-Wolff cluster algorithm Tc(∞) = 6.6802632 ± 5 . 10-5. The average values calculated for the critical exponent of the specific heat are α =- 0.0402(15), - 0.0393(12), - 0.0391(11) with 7, 14, and 21 independent simulations, respectively. As the number of independent simulations increases, the result, α =- 0.0391(11), agrees with the series expansions result, α =- 0.12 ± 0.03 and the Monte Carlo result using the Metropolis-Wolff cluster algorithm, α ≥ 0 ± 0.04. However, α =- 0.0391(11) is inconsistent with the renormalization group prediction of α = 0.
Alart, P.; Barboteu, M.; Gril, J.
2004-09-01
In this paper a numerical modelling of non linear problems involving large deformations and frictional contact conditions is proposed. The motivation of this work comes from the study of the cellular materials (such as wood or foams) undergoing strong deformations. We restrict our study to a regular cellular network of hexagonal cells with thin walls. Strong loadings can generate at first buckling phenomena, then self-contact in the cell. Renouncing homogenization procedures, not always pertinent in this case, we have developed direct simulations. After giving the mechanical and mathematical formulations of the problem, we present two advanced numerical tools to solve large non linear frictional multicontact problems. This numerical modelling is based on an arc-length continuation method which permits to snap through singular points due to buckling phenomena and on an optimal domain decomposition method adapted to frictional contact problems. Finally, mechanical investigations of the contactless buckling and the post-buckling provide some pertinent parameters controlling the deformation process.
Mente, Carsten; Prade, Ina; Brusch, Lutz; Breier, Georg; Deutsch, Andreas
2011-07-01
Lattice-gas cellular automata (LGCAs) can serve as stochastic mathematical models for collective behavior (e.g. pattern formation) emerging in populations of interacting cells. In this paper, a two-phase optimization algorithm for global parameter estimation in LGCA models is presented. In the first phase, local minima are identified through gradient-based optimization. Algorithmic differentiation is adopted to calculate the necessary gradient information. In the second phase, for global optimization of the parameter set, a multi-level single-linkage method is used. As an example, the parameter estimation algorithm is applied to a LGCA model for early in vitro angiogenic pattern formation.
Institute of Scientific and Technical Information of China (English)
MIN LeQuan; YU Na
2002-01-01
Some criteria for the local activity theory in two-port cellular neural network cells with three local state variables are applied to a coupled Lorenz-cell model. The numerical simulation exhibited that emergence may exist if the selected cell parameters are nearby or on the edge of chaos domain. The local activity theory has provided a new tool of studying the complexity of high dimensional coupled nonlinear physical systems.
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.
Energy Technology Data Exchange (ETDEWEB)
L.H. Toburen, Principal Investigator; J.L. Shinpaugh; M. Dingfelder; and G. Lapicki; Co-Investigators
2007-01-07
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
Activity-based Calculation Models for the Brazilian Air Force Cellular Unit of Intendancy
2013-03-01
readiness (Operations “Aghata” and “Cruzex”), humanitarian missions (support to combat dengue in the city of Rio de Janeiro ; support of the military...disinfection, sanitary and barber shop; u) water supply ; v) water treatment; x) providing electrical power. 1.8 Organization This research will be...recreation, and water and electricity supply . 2.1.1 Cellular Unit of Intendancy. The CUI provides the Air Force with the necessary mobility to
Tuberculose ostéoarticulaire (mal de Pott exclu): à propos de 120 cas à Abidjan
Gbané-Koné, Mariam; Koné, Samba; Ouali, Boubacar; Djaha, Kouassi Jean -Mermoz; Akoli, Ekoya Ondzala; Nseng, Ingrid Nseng; Eti, Edmond; Daboiko, Jean Claude; Touré, Stanislas André; Kouakou, N'zué Marcel
2015-01-01
Introduction La tuberculose ostéoarticulaire (TOA) représente 2 à 5% de l'ensemble des tuberculoses. Elle demeure d'actualité surtout dans les pays à forte endémicité tuberculeuse. L'objectif était de déterminer la prévalence, les aspects topographiques, radiologiques de la TOA en milieu hospitalier ivoirien. Méthodes Les auteurs rapportent une expérience de 11 ans, à travers une étude rétrospective de 120 dossiers de patients atteints de la tuberculose ostéoarticulaire (le mal de Pott est exclu de cette étude). N'ont pas été inclus dans l’étude les dossiers ne comportant pas d'imagerie. Résultats L'atteinte extra vertébrale représentait 09,2% de la tuberculose ostéoarticulaire. Il s'agissait de 54 hommes et 66 femmes, l’âge moyen était de 43,13 ans. On notait 123 cas d'ostéoarthrites, et 8 cas d'ostéites des os plats. L'atteinte des membres inférieurs prédominait dans 91,87% des cas. La hanche était la première localisation (45,04%), suivie du genou (25,19%). Les atteintes étaient multifocales dans 20% des cas. L'atteinte osseuse était associée à une tuberculose pulmonaire dans 05,83% des cas. Des localisations inhabituelles ont été rapportées: poignet (n = 2), branches ischiopubiennes (n = 4), atteinte sternoclaviculaire (n = 4), médiopieds (n = 2). Les lésions radiologiques étaient avancées (stades III et IV) dans 55,73% des cas. A la TDM, la prévalence des abcès était de 77%. Un geste chirurgical a été réalisé sur 16 articulations (2 épaules, 13 genoux, une cheville). Conclusion La TOA des membres est peu fréquente contrairement à l'atteinte vertébrale. La hanche est la principale localisation. Le retard au diagnostic explique l’étendue des lésions anatomoradiologiques. PMID:26587129
Tratamiento quirúrgico de la enfermedad de Pott por vía anterior
Directory of Open Access Journals (Sweden)
Elio Ramírez
2013-12-01
Full Text Available OBJETIVO: Evaluar la corrección de la deformidad cifótica, estabilidad y fusión que otorga la utilización de implantes de titanio (Synex - Ventrofix de Synthes en la tuberculosis espinal. MÉTODOS: Entre enero de 2010 y agosto de 2012 ocho pacientes con diagnóstico de enfermedad del Pott se sometieron a intervención quirúrgica por vía anterior, con seguimiento de 18 meses. El procedimiento consistió en desbridamiento amplio del cuerpo afectado seguido de instrumentación con implantes de titanio (Synex - Ventrofix de Synthes y autoinjerto de costilla. La indicación quirúrgica fue déficit neurológico y cifosis del segmento. Previamente recibieron tratamiento antifímico por tres semanas. Estudios de imagen como radiografía frente y perfil pre operatoria y post operatoria evaluaron la cifosis. La tomografía simple post operatoria evaluó la fusión. En el preoperatorio se realizó resonancia magnética. Además de las pruebas de imagen, se realizaron las siguientes pruebas: biometría hemática, velocidad de sedimentación globular (VSG, proteína C reactiva (PCR y las pruebas microbiológicas baciloscopia en orina y esputo, cultivo de expectoración o de orina. RESULTADOS: Ocho pacientes se operaron a través de abordaje anterior, siendo cinco hombres con edad promedio de 37,2 años y tres mujeres con edad promedio de 56,3 años. Todos los pacientes presentaron déficit neurológico. Seis con lesiones incompletas mejoraron algún grado neurológico. Dos parapléjicos no recuperaron la función neurológica. Cifosis preoperatoria promedio 14,38 grados y postoperatoria 6,8 grados. No hubo pérdida significativa de corrección ni recurrencia de la enfermedad. CONCLUSIÓN: El abordaje anterior más instrumentación es un método eficaz para tratar infección tuberculosa vertebral al mismo tiempo de evitar la progresión o corregir la cifosis.
Chaudhari, Pooja; Tian, Lipeng; Deshmukh, Abhijeet; Jang, Yoon-Young
2016-09-01
Due to the limitations of research using human embryos and the lack of a biological model of human liver development, the roles of the various markers associated with liver stem or progenitor cell potential in humans are largely speculative, and based on studies utilizing animal models and certain patient tissues. Human pluripotent stem cell-based in vitro multistage hepatic differentiation systems may serve as good surrogate models for mimicking normal human liver development, pathogenesis and injury/regeneration studies. Here, we describe the implications of various liver stem or progenitor cell markers and their bipotency (i.e. hepatocytic- and biliary-epithelial cell differentiation), based on the pluripotent stem cell-derived model of human liver development. Future studies using the human cellular model(s) of liver and biliary development will provide more human relevant biological and/or pathological roles of distinct markers expressed in heterogeneous liver stem/progenitor cell populations.
Vechernin, V V
2003-01-01
A simple cellular model for the description of the long-range multiplicity and $p_t$ correlations in high-energy nuclear collisions originating from the string fusion model is proposed. Three versions of the model: without fusion, with local and with global string fusion are formulated. A Gauss approximation which enables explicit analytical calculations of the correlation functions in some asymptotic cases in the framework of the model is developed. The assumptions of the model and the validity of a Gauss approximation are checked up in the simplest (no fusion) case when the explicit solution of the model can be found. The role of a size of cells is analysed. The modification of the results in the case of non-Poissonian distributions is also discussed.
Maerivoet, S; Immers, B; De Moor, B; Maerivoet, Sven; Logghe, Steven; Immers, Ben; Moor, Bart De
2005-01-01
In this paper, we describe a relation between a microscopic traffic cellular automaton (TCA) model (i.e., the stochastic TCA model of Nagel and Schreckenberg) and the macroscopic first-order hydrodynamic model of Lighthill, Whitham, and Richards (LWR). The innovative aspect of our approach, is that we explicitly derive the LWR's fundamental diagram directly from the STCA's rule set, by assuming a stationarity condition that converts the STCA's rules into a set of linear inequalities. In turn, these constraints define the shape of the fundamental diagram, which is then specified to the LWR model. Application of our methodology to a simulation case study, allows us to compare the tempo-spatial behavior of both models. Our results indicate that, in the presence of noise, the capacity flows in the derived fundamental diagram are overestimations of those of the STCA model. Directly specifying the STCA's capacity flows to the LWR fundamental diagram, effectively remedies most of the mismatches between both approach...
Gil, Lázaro; López, Carlos; Blanco, Aracelys; Lazo, Laura; Martín, Jorge; Valdés, Iris; Romero, Yaremis; Figueroa, Yassel; Guillén, Gerardo; Hermida, Lisset
2009-02-01
For several years, researchers have known that the generation of neutralizing antibodies is a prerequisite for attaining adequate protection against dengue virus. Nevertheless, the cellular immune response is the principal arm of the adaptive immune system against non-cytopathic viruses such as dengue, as once the virus enters into the cell it is necessary to destroy it to eliminate the virus. To define the role of the cellular immune response in the protection against dengue, we selected the mouse encephalitis model. Mice were immunized with a single dose of infective dengue 2 virus and different markers of both branches of the induced adaptive immunity were measured. Animals elicited a broad antibody response against the four dengue virus serotypes, but neutralizing activity was only detected against the homologous serotype. On the other hand, the splenocytes of the infected animals strongly proliferated after in vitro stimulation with the homologous virus, and specifically the CD8 T-cell subset was responsible for the secretion of the cytokine IFN-gamma. Finally, to define the role of T cells in in vivo protection, groups of animals were inoculated with the depleting monoclonal antibodies anti-CD4 or anti-CD8. Only depletion with anti-CD8 decreased to 50% the level of protection reached in the non-depleted mice. The present work constitutes the first report defining the role of the cellular immune response in protection against dengue virus in the mouse model.
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.
Directory of Open Access Journals (Sweden)
Mohit Kumar Jolly
Full Text Available Planar Cell Polarity (PCP is an evolutionarily conserved characteristic of animal tissues marked by coordinated polarization of cells or structures in the plane of a tissue. In insect wing epithelium, for instance, PCP is characterized by en masse orientation of hairs orthogonal to its apical-basal axis and pointing along the proximal-distal axis of the organ. Directional cue for PCP has been proposed to be generated by complex sets of interactions amongst three proteins - Fat (Ft, Dachsous (Ds and Four-jointed (Fj. Ft and Ds are two atypical cadherins, which are phosphorylated by Fj, a Golgi kinase. Ft and Ds from adjacent cells bind heterophilically via their tandem cadherin repeats, and their binding affinities are regulated by Fj. Further, in the wing epithelium, sub-cellular levels of Ft-Ds heterodimers are seen to be elevated at the distal edges of individual cells, prefiguring their PCP. Mechanisms generating this sub-cellular asymmetry of Ft-Ds heterodimer in proximal and distal edges of cells, however, have not been resolved yet. Using a mathematical modeling approach, here we provide a framework for generation of this sub-cellular asymmetry of Ft-Ds heterodimer. First, we explain how the known interactions within Ft-Ds-Fj system translate into sub-cellular asymmetry of Ft-Ds heterodimer. Second, we show that this asymmetric localization of Ft-Ds heterodimer is lost when tissue-level gradient of Fj is flattened, or when phosphorylation of Ft by Fj is abolished, but not when tissue-level gradient of Ds is flattened or when phosphorylation of Ds is abrogated. Finally, we show that distal enrichment of Ds also amplifies Ft-Ds asymmetry. These observations reveal that gradient of Fj expression, phosphorylation of Ft by Fj and sub-cellular distal accumulation of Ds are three critical elements required for generating sub-cellular asymmetry of Ft-Ds heterodimer. Our model integrates the known experimental data and presents testable predictions
Codd, E F
1968-01-01
Cellular Automata presents the fundamental principles of homogeneous cellular systems. This book discusses the possibility of biochemical computers with self-reproducing capability.Organized into eight chapters, this book begins with an overview of some theorems dealing with conditions under which universal computation and construction can be exhibited in cellular spaces. This text then presents a design for a machine embedded in a cellular space or a machine that can compute all computable functions and construct a replica of itself in any accessible and sufficiently large region of t
Cellular Approach to Long-Range $p_t$ and Multiplicity Correlations in the String Fusion Model
Vechernin, V V
2003-01-01
The long-range $p_t$ and multiplicity($n$) correlations in high-energy nuclear collisions are studied in the framework of a simple cellular analog of the string fusion model. Two cases with local and global string fusion is considered. The $p_t$--$n$ and $n$--$n$ correlation functions and correlation coefficients are calculated analytically in some asymptotic cases using suggested Gauss approximation. It's shown that at large string density the $p_t$--$n$ and $n$--$n$ correlation coefficients are connected and the scaling takes place. The behavior of the correlations at small string density is also studied. The asymptotic results are compared with results of the numerical calculations in the framework of proposed cellular approach.
Directory of Open Access Journals (Sweden)
Alpaugh Mary L
2009-12-01
Full Text Available Abstract Background The initial step of metastasis in carcinomas, often referred to as the epithelial-mesenchymal transition (EMT, occurs via the loss of adherens junctions (e.g. cadherins by the tumor embolus. This leads to a subsequent loss of cell polarity and cellular differentiation and organization, enabling cells of the embolus to become motile and invasive. However highly malignant inflammatory breast cancer (IBC over-expresses E-cadherin. The human xenograft model of IBC (MARY-X, like IBC, displays the signature phenotype of an exaggerated degree of lymphovascular invasion (LVI in situ by tumor emboli. An intact E-cadherin/α, β-catenin axis mediates the tight, compact clump of cells found both in vitro and in vivo as spheroids and tumor emboli, respectively. Methods Using electron microscopy and focused ion beam milling to acquire in situ sections, we performed ultrastructural analysis of both an IBC and non-IBC, E-cadherin positive cell line to determine if retention of this adhesion molecule contributed to cellular organization. Results Here we report through ultrastructural analysis that IBC exhibits a high degree of cellular organization with polar elements such as apical/lateral positioning of E-cadherin, apical surface microvilli, and tortuous lumen-like (canalis structures. In contrast, agarose-induced spheroids of MCF-7, a weakly invasive E-cadherin positive breast carcinoma cell line, do not exhibit ultrastructural polar features. Conclusions This study has determined that the highly metastatic IBC with an exaggerated malignant phenotype challenges conventional wisdom in that instead of displaying a loss of cellular organization, IBC acquires a highly structured architecture. These findings suggest that the metastatic efficiency might be linked to the formation and maintenance of these architectural features. The comparative architectural features of both the spheroid and embolus of MARY-X provide an in vitro model with
Aburas, Maher Milad; Ho, Yuek Ming; Ramli, Mohammad Firuz; Ash'aari, Zulfa Hanan
2016-10-01
In recent years, several types of simulation and prediction models have been used within a GIS environment to determine a realistic future for urban growth patterns. These models include quantitative and spatio-temporal techniques that are implemented to monitor urban growth. The results derived through these techniques are used to create future policies that take into account sustainable development and the demands of future generations. The aim of this paper is to provide a basis for a literature review of urban Cellular Automata (CA) models to find the most suitable approach for a realistic simulation of land use changes. The general characteristics of simulation models of urban growth and urban CA models are described, and the different techniques used in the design of these models are classified. The strengths and weaknesses of the various models are identified based on the analysis and discussion of the characteristics of these models. The results of the review confirm that the CA model is one of the strongest models for simulating urban growth patterns owing to its structure, simplicity, and possibility of evolution. Limitations of the CA model, namely weaknesses in the quantitative aspect, and the inability to include the driving forces of urban growth in the simulation process, may be minimized by integrating it with other quantitative models, such as via the Analytic Hierarchy Process (AHP), Markov Chain and frequency ratio models. Realistic simulation can be achieved when socioeconomic factors and spatial and temporal dimensions are integrated in the simulation process.
Cellular resolution models for even skipped regulation in the entire Drosophila embryo
Ilsley, Garth R; Fisher, Jasmin; Apweiler, Rolf; Angela H. DePace; Nicholas M Luscombe
2013-01-01
eLife digest The transcription of genes into messenger RNA (mRNA) molecules is one of the most important processes in biology, but our present understanding of this process is largely qualitative. Molecules such as transcription factors and regions of DNA other than the region that codes for the mRNA are known to interact with each other to influence the onset of transcription, and also the rate at which it occurs. However, given the cellular concentrations of transcription factors in a devel...
An analytical model for evaluating outage and handover probability of cellular wireless networks
Decreusefond, Laurent; Vu, Than-Tung
2010-01-01
We consider stochastic cellular networks where base stations locations form a homogenous Poisson point process and each mobile is attached to the base station that provides the best mean signal power. The mobile is in outage if the SINR falls below some threshold. The handover decision has to be made if the mobile is in outage for some time slots. The outage probability and the handover probability is evaluated in taking into account the effect of path loss, shadowing, Rayleigh fast fading, frequency factor reuse and conventional beamforming. The main assumption is that the Rayleigh fast fading changes each time slot while other network components remain static during the period of study.
Phase-Type Models of Channel-Holding Times in Cellular Communication Systems
DEFF Research Database (Denmark)
Christensen, Thomas Kaare; Nielsen, Bo Friis; Iversen, Villy Bæk
2004-01-01
In this paper, we derive the distribution of the channel-holding time when both cell-residence and call-holding times are phase-type distributed. Furthermore, the distribution of the number of handovers, the conditional channel-holding time distributions, and the channel-holding time when cell re...... residence times are correlated are derived. All distributions are of phase type, making them very general and flexible. The channel-holding times are of importance in performance evaluation and simulation of cellular mobile communication systems....
Condition monitoring of 3G cellular networks through competitive neural models.
Barreto, Guilherme A; Mota, João C M; Souza, Luis G M; Frota, Rewbenio A; Aguayo, Leonardo
2005-09-01
We develop an unsupervised approach to condition monitoring of cellular networks using competitive neural algorithms. Training is carried out with state vectors representing the normal functioning of a simulated CDMA2000 network. Once training is completed, global and local normality profiles (NPs) are built from the distribution of quantization errors of the training state vectors and their components, respectively. The global NP is used to evaluate the overall condition of the cellular system. If abnormal behavior is detected, local NPs are used in a component-wise fashion to find abnormal state variables. Anomaly detection tests are performed via percentile-based confidence intervals computed over the global and local NPs. We compared the performance of four competitive algorithms [winner-take-all (WTA), frequency-sensitive competitive learning (FSCL), self-organizing map (SOM), and neural-gas algorithm (NGA)] and the results suggest that the joint use of global and local NPs is more efficient and more robust than current single-threshold methods.
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.
Multiplex profiling of cellular invasion in 3D cell culture models.
Directory of Open Access Journals (Sweden)
Gerald Burgstaller
Full Text Available To-date, most invasion or migration assays use a modified Boyden chamber-like design to assess migration as single-cell or scratch assays on coated or uncoated planar plastic surfaces. Here, we describe a 96-well microplate-based, high-content, three-dimensional cell culture assay capable of assessing invasion dynamics and molecular signatures thereof. On applying our invasion assay, we were able to demonstrate significant effects on the invasion capacity of fibroblast cell lines, as well as primary lung fibroblasts. Administration of epidermal growth factor resulted in a substantial increase of cellular invasion, thus making this technique suitable for high-throughput pharmacological screening of novel compounds regulating invasive and migratory pathways of primary cells. Our assay also correlates cellular invasiveness to molecular events. Thus, we argue of having developed a powerful and versatile toolbox for an extensive profiling of invasive cells in a 96-well format. This will have a major impact on research in disease areas like fibrosis, metastatic cancers, or chronic inflammatory states.
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.
Hu, Dandan; Ronhovde, Peter; Bloch, Sharon; Achilefu, Samuel; Nussinov, Zohar
2012-01-01
We apply a multiresolution community detection algorithm to perform unsupervised segmentation of complex intracellular signals derived using fluorescent dyes. In our earlier work, when applying our method to benchmarks, our algorithm was shown to be one of the best and to be especially suited to the detection of camouflage images. In the current manuscript, we have explored this algorithm in a more complex scenario. The current image processing problem is framed as identifying clusters with respective average fluorescent lifetimes (FLTs) against a background or "solvent" in fluorescence lifetime imaging microscopy (FLIM) images derived using NIR fluorescent dyes. We have identified significant multiresolution structures using replica correlations in these images, where such correlations are manifested by information theoretic overlaps of the independent solutions ("replicas") attained using the proposed algorithm from different starting points. Our method is more efficient than a well-known image segmentation...
The two-dimensional 4-state Potts model in a magnetic field
Berche, Bertrand; Shchur, Lev
2013-01-01
We present a solution of the non-linear renormalization group equations leading to the dominant and subdominant singular behaviours of physical quantities (free energy density, correlation length, internal energy, specific heat, magnetization, susceptibility and magnetocaloric coefficient) at the critical temperature in a non- vanishing magnetic field. The solutions i) lead to exact cancellation of logarithmic corrections in universal amplitude ratios and ii) prove recently proposed relations among logarithmic exponents.
Energy Technology Data Exchange (ETDEWEB)
Meireles, Sincler P. de; Santos, Adriano M.; Grynberg, Suely Epsztein, E-mail: spm@cdtn.b, E-mail: amsantos@cdtn.b, E-mail: seg@cdtn.b [Centro de Desenvolvimento da Tecnologia Nuclear (CDTN/CNEN-MG), Belo Horizonte, MG (Brazil); Nunes, Maria Eugenia S., E-mail: mariaeugenia@iceb.ufop.b [Universidade Federal de Ouro Preto (UFOP), MG (Brazil)
2011-07-01
During recent years, there has been a shift from an approach focused entirely on DNA as the main target of ionizing radiation to a vision that considers complex signaling pathways in cells and among cells within tissues. Several newly recognized responses were classified as the so-called non-target responses in which the biological effects are not directly related to the amount of energy deposited in the DNA of cells that were traversed by radiation. In 1992 the bystander effect was described referring to a series of responses such as death, chromosomal instability or other abnormalities that occur in non-irradiated cells that came into contact with irradiated cells or medium from irradiated cells. In this work, we have developed a mathematical model via cellular automata, to quantify cell death induced by the bystander effect. The model is based on experiments with irradiated cells conditioned medium which suggests that irradiated cells secrete molecules in the medium that are capable of damaging other cells. The computational model consists of two-dimensional cellular automata which is able to simulate the transmission of bystander signals via extrinsic route and via Gap junctions. The model has been validated by experimental results in the literature. The time evolution of the effect and the dose-response curves were obtained in good accordance to them. Simulations were conducted for different values of bystander and irradiated cell densities with constant dose. From this work, we have obtained a relationship between cell density and effect. (author)
Lim, Ji-Hey; Piedrahita, Jorge A; Jackson, Lauren; Ghashghaei, Troy; Olby, Natasha J
2010-12-01
Research into transplantation strategies to treat spinal cord injury (SCI) is frequently performed in rodents, but translation of results to clinical patients can be poor and a large mammalian model of severe SCI is needed. The pig has been considered an optimal model species in which to perform preclinical testing, and the Yucatan minipig can be cloned successfully utilizing somatic cell nuclear transfer (SCNT). However, induction of paralysis in pigs poses significant welfare and nursing challenges. The present study was conducted to determine whether Yucatan SCNT clones could be used to develop an SCI animal model for cellular transplantation research. First, we demonstrated that transection of the sacrocaudal spinal cord in Yucatan SCNT clones produces profound, quantifiable neurological deficits restricted to the tail. We then established that neurospheres could be isolated from brain tissue of green fluorescence protein (GFP) transfected SCNT clones. Finally, we confirmed survival of transplanted GFP-expressing neural stem cells in the SCI lesion and their differentiation into glial and neuronal lineages for up to 4 weeks without immunosuppression. We conclude that this model of sacrocaudal SCI in Yucatan SCNT clones represents a powerful research tool to investigate the effect of cellular transplantation on axonal regeneration and functional recovery.
Institute of Scientific and Technical Information of China (English)
无
2000-01-01
This paper has attempted to simulate the microstructure formation based on fully coupling of temperature field, concentration field and velocity field with micro-kinetics. The authors presented a new way, wlich is the combination of FDM and cellular automata (CAFD) to visualize the microstructure formation of the thin complex superalloy turbine blades cast by the vacuum investment process. The distribution, orientation and mechanism of the heterogeneous nucleation, the growth kinetics of dendrites and the columnar to equiaxed transition (CET) are considered. Capitalizing on these simulating schemes, the comprehensive influence of key process variables on the scale and uniformity of grains has been investigated quantitatively. The simulated grain size and morphology agree well with the experimental results.
Stylized Facts Generated Through Cellular Automata Models. Case of Study: The Game of Life
Coronel-Brizio, H F; Rodriguez-Achach, M E; Stevens-Ramirez, G A
2007-01-01
In the present work, a geometrical method to generate a two dimensional random walk by means of a bidimensional Cellular Automaton is presented. We illustrate it by means of Conway's Game of Life with periodical borders, with a large lattice of 3000 x 3000 cells. The obtained random walk is of character anomalous, and its projection to a one dimensional random walk is analyzed, showing that it presents some statistical properties similar to the so-called stylized facts observed in financial time series. We consider that the procedure presented here is important not only because of its simplicity, but also because it could help us to understand and shed light on the stylized facts formation mechanism.
Institute of Scientific and Technical Information of China (English)
Jiang Rui; Jin Wen-Long; Wu Qing-Song
2008-01-01
Recently, a number of efforts are underway to investigate inter-vehicle communications (IVC). This paper studies the instantaneous information propagation behaviours based on IVC in three different traffic situations (free flow,synchronized flow and stop-and-go waves) in a cellular automaton model. It is shown that different behaviours appear in stop-and-go waves from those in free flow and synchronized flow. While the distribution of Multi-hop Communication Distance (MhCD) is either exponential or uniform in free flow and synchronized flow, the distribution of MhCD is either exponential or with a single peak in stop-and-go waves.
Investigation of cellular and molecular responses to pulsed focused ultrasound in a mouse model.
Directory of Open Access Journals (Sweden)
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.
Lee, C; Longo, V D
2011-07-28
The dietary recommendation for cancer patients receiving chemotherapy, as described by the American Cancer Society, is to increase calorie and protein intake. Yet, in simple organisms, mice, and humans, fasting--no calorie intake--induces a wide range of changes associated with cellular protection, which would be difficult to achieve even with a cocktail of potent drugs. In mammals, the protective effect of fasting is mediated, in part, by an over 50% reduction in glucose and insulin-like growth factor 1 (IGF-I) levels. Because proto-oncogenes function as key negative regulators of the protective changes induced by fasting, cells expressing oncogenes, and therefore the great majority of cancer cells, should not respond to the protective signals generated by fasting, promoting the differential protection (differential stress resistance) of normal and cancer cells. Preliminary reports indicate that fasting for up to 5 days followed by a normal diet, may also protect patients against chemotherapy without causing chronic weight loss. By contrast, the long-term 20 to 40% restriction in calorie intake (dietary restriction, DR), whose effects on cancer progression have been studied extensively for decades, requires weeks-months to be effective, causes much more modest changes in glucose and/or IGF-I levels, and promotes chronic weight loss in both rodents and humans. In this study, we review the basic as well as clinical studies on fasting, cellular protection and chemotherapy resistance, and compare them to those on DR and cancer treatment. Although additional pre-clinical and clinical studies are necessary, fasting has the potential to be translated into effective clinical interventions for the protection of patients and the improvement of therapeutic index.
Feng, Song; Ollivier, Julien F; Swain, Peter S; Soyer, Orkun S
2015-10-30
Systems biologists aim to decipher the structure and dynamics of signaling and regulatory networks underpinning cellular responses; synthetic biologists can use this insight to alter existing networks or engineer de novo ones. Both tasks will benefit from an understanding of which structural and dynamic features of networks can emerge from evolutionary processes, through which intermediary steps these arise, and whether they embody general design principles. As natural evolution at the level of network dynamics is difficult to study, in silico evolution of network models can provide important insights. However, current tools used for in silico evolution of network dynamics are limited to ad hoc computer simulations and models. Here we introduce BioJazz, an extendable, user-friendly tool for simulating the evolution of dynamic biochemical networks. Unlike previous tools for in silico evolution, BioJazz allows for the evolution of cellular networks with unbounded complexity by combining rule-based modeling with an encoding of networks that is akin to a genome. We show that BioJazz can be used to implement biologically realistic selective pressures and allows exploration of the space of network architectures and dynamics that implement prescribed physiological functions. BioJazz is provided as an open-source tool to facilitate its further development and use. Source code and user manuals are available at: http://oss-lab.github.io/biojazz and http://osslab.lifesci.warwick.ac.uk/BioJazz.aspx.
Dimastrogiovanni, Giorgio; Córdoba, Marlon; Navarro, Isabel; Jáuregui, Olga; Porte, Cinta
2015-08-01
This work investigates the suitability of the rainbow trout liver cell line (RTL-W1) as an in-vitro model to study the ability of model endocrine disrupters, namely TBT, TPT, 4-NP, BPA and DEHP, to act as metabolic disrupters by altering cellular lipids and markers of lipid metabolism. Among the tested compounds, BPA and DEHP significantly increased the intracellular accumulation of triacylglycerols (TAGs), while all the compounds -apart from TPT-, altered membrane lipids - phosphatidylcholines (PCs) and plasmalogen PCs - indicating a strong interaction of the toxicants with cell membranes and cell signaling. RTL-W1 expressed a number of genes involved in lipid metabolism that were modulated by exposure to BPA, TBT and TPT (up-regulation of FATP1 and FAS) and 4-NP and DEHP (down-regulation of FAS and LPL). Multiple and complex modes of action of these chemicals were observed in RTL-W1 cells, both in terms of expression of genes related to lipid metabolism and alteration of cellular lipids. Although further characterization is needed, this might be a useful model for the detection of chemicals leading to steatosis or other diseases associated with lipid metabolism in fish.
Directory of Open Access Journals (Sweden)
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.
DEFF Research Database (Denmark)
Osmanagic, Azra; Emamifar, Amir; Christian Bang, Jacob;
2016-01-01
BACKGROUND Pott's disease (PD) or spinal tuberculosis is a rare condition which accounts for less than 1% of total tuberculosis (TB) cases. The incidence of PD has recently increased in Europe and the United States, mainly due to immigration; however, it is still a rare diagnosis in Scandinavian...... was suggestive of PD. Polymerase chain reaction (PCR) of the patient's gastric fluid was positive for Mycobacterium tuberculosis (MT). Based on MRI and PCR findings, standard treatment for TB was initiated. Results of the spine biopsy and culture showed colonies of MT and confirmed the diagnosis afterwards. Due...... to the instability of the spine and severe and continuous pain, spine-stabilizing surgery was performed. Her TB was cured after nine months of treatment. CONCLUSIONS PD is an important differential diagnosis of malignancy that should be diagnosed instantly. History of exposure to TB and classic radiologic finding...
de la Cruz, Roberto; Spill, Fabian; Alarcón, Tomás
2016-01-01
We propose a modelling framework to analyse the stochastic behaviour of heterogeneous, multi-scale cellular populations. We illustrate our methodology with a particular example in which we study a population with an oxygen-regulated proliferation rate. Our formulation is based on an age-dependent stochastic process. Cells within the population are characterised by their age. The age-dependent (oxygen-regulated) birth rate is given by a stochastic model of oxygen-dependent cell cycle progression. We then formulate an age-dependent birth-and-death process, which dictates the time evolution of the cell population. The population is under a feedback loop which controls its steady state size: cells consume oxygen which in turns fuels cell proliferation. We show that our stochastic model of cell cycle progression allows for heterogeneity within the cell population induced by stochastic effects. Such heterogeneous behaviour is reflected in variations in the proliferation rate. Within this set-up, we have established...
Shi, Xiao-Qiu; Wu, Yi-Qi; Li, Hong; Zhong, Rui
2007-11-01
Two-dimensional cellular automaton model has been broadly researched for traffic flow, as it reveals the main characteristics of the traffic networks in cities. Based on the BML models, a first-order phase transition occurs between the low-density moving phase in which all cars move at maximal speed and the high-density jammed phase in which all cars are stopped. However, it is not a physical result of a realistic system. We propose a new traffic rule in a two-dimensional traffic flow model containing road sections, which reflects that a car cannot enter into a road crossing if the road section in front of the crossing is occupied by another car. The simulation results reveal a second-order phase transition that separates the free flow phase from the jammed phase. In this way the system will not be entirely jammed (“don’t block the box” as in New York City).
Institute of Scientific and Technical Information of China (English)
WANG Kuang-fei; LI Bang-sheng; MI Guo-fa; GUO Jing-jie; FU Heng-zhi
2008-01-01
Solute diffusion controlled solidification model was used to simulate the initial stage cellular to dendrite transition of Ti44AI alloys during directional solidification at different velocities. The simulation results show that during this process, a mixed structure composed of cells and dendrites was observed, where secondary dendrites are absent at facing surface with parallel closely spaced dendrites, which agrees with the previous experimental observa-tion. The dendrite spacings are larger than cellular spacings at a given rate, and the columnar grain spacing sharply increases to a maximum as solidification advance to coexistence zone. In addition, simulation also revealed that decreasing the numbers of the seed causes the trend of unstable dendrite transition to increase. Finally, the main influence factors affecting cell/dendrite transition were analyzed, which could be the change of growth rates resulting in slight fluctuations of liquid composition occurred at growth front. The simulation results are in reasonable agreement with the results of previous theoretical models and experimental observation at low cooling rates.
Directory of Open Access Journals (Sweden)
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.
Wang, Yang; Chen, Yan-Yan
2016-12-01
The signalized traffic is considerably complex due to the fact that various driving behaviors have emerged to respond to traffic signals. However, the existing cellular automaton models take the signal-vehicle interactions into account inadequately, resulting in a potential risk that vehicular traffic flow dynamics may not be completely explored. To remedy this defect, this paper proposes a more realistic cellular automaton model by incorporating a number of the driving behaviors typically observed when the vehicles are approaching a traffic light. In particular, the anticipatory behavior proposed in this paper is realized with a perception factor designed by considering the vehicle speed implicitly and the gap to its preceding vehicle explicitly. Numerical simulations have been performed based on a signal controlled road which is partitioned into three sections according to the different reactions of drivers. The effects of microscopic driving behaviors on Kerner's time-delayed traffic breakdown at signal (Kerner 2011, 2013) have been investigated with the assistance of spatiotemporal pattern and trajectory analysis. Furthermore, the contributions of the driving behaviors on the traffic breakdown have been statistically examined. Finally, with the activation of the anticipatory behavior, the influences of the other driving behaviors on the formation of platoon have been investigated in terms of the number of platoons, the averaged platoon size, and the averaged flow rate.
Guo, Fang; Li, Xingli; Kuang, Hua; Bai, Yang; Zhou, Huaguo
2016-11-01
The original cost potential field cellular automata describing normal pedestrian evacuation is extended to study more general evacuation scenarios. Based on the cost potential field function, through considering the psychological characteristics of crowd under emergencies, the quantitative formula of behavior variation is introduced to reflect behavioral changes caused by psychology tension. The numerical simulations are performed to investigate the effects of the magnitude of behavior variation, the different pedestrian proportions with different behavior variation and other factors on the evacuation efficiency and process in a room. The spatiotemporal dynamic characteristic during the evacuation process is also discussed. The results show that compared with the normal evacuation, the behavior variation under an emergency does not necessarily lead to the decrease of the evacuation efficiency. At low density, the increase of the behavior variation can improve the evacuation efficiency, while at high density, the evacuation efficiency drops significantly with the increasing amplitude of the behavior variation. In addition, the larger proportion of pedestrian affected by the behavior variation will prolong the evacuation time.
Hetherington, A. P.; Steacy, S.; McCloskey, J.
2007-12-01
Seismicity spatial and temporal patterns are strongly influenced by stress interaction between faults. However the effects of such interaction on earthquake statistics is not yet well understood. Computer models provide accurate, large and complete datasets to investigate this issue and also have the benefit of allowing direct comparison of seismicity behavior in time and space in networks, with and without fault interaction. We investigate the effect of such interaction on modeled real-world fault networks of varying complexity using a cellular-automata based model. Each 3-D fault within the fault network is modeled by a discrete cellular automaton. The cell size is 1 km square which allows for a minimum earthquake size of approximately Mw=4. The cell strength is distributed fractally across each fault and all cells are loaded by a remote tectonic stressing rate. When the stress on a cell exceeds its strength, the cell fails and stress is transferred to its nearest neighbors which may in turn cause them to break allowing the earthquake to grow. These stress transfer rules allow realistic stress concentrations to develop at the boundary of the rupture. If the extent of the rupture exceeds a user defined minimum length, and if interaction between faults is allowed, a boundary element method is used to calculate stress transfer to neighboring faults. Here we present results from four simulated fault networks based on active faults in the San Francisco Bay Area, California, the Northern Anatolian Fault, Turkey, Southern California, and the Marlborough Fault System, South Island, New Zealand. These are chosen for their varying level of fault complexity and we examine both interacting and non-interacting models in terms of their b-value and recurrence intervals for each region. Results will be compared and discussed.
Wang, Binyu; Xu, Haisong; Luo, M Ronnier; Guo, Jinyi
2011-07-01
The replacement of used-up ink cartridges is unavoidable, but it makes the existing characterization model far from accurate, while recharacterization is labor intensive. In this study, we propose a new correction method for cellular Yule-Nielsen spectral Neugebauer (CYNSN) models based on principal component analysis (PCA). First, a small set of correction samples are predicted, printed using new ink cartridges, and then measured. Second, the link between the predicted and measured reflectance weights, generated by PCA, is determined. The experimental results show that the proposed method provides a significant and robust improvement, since not only the color change between original and new inks but also the systemic error of CYNSN modelsis taken into account in the method.
Danila, Bogdan; Mocanu, Gabriela
2015-01-01
We investigate the transition to Self Organized Criticality in a two-dimensional model of a flux tube with a background flow. The magnetic induction equation, represented by a partial differential equation with a stochastic source term, is discretized and implemented on a two dimensional cellular automaton. The energy released by the automaton during one relaxation event is the magnetic energy. As a result of the simulations we obtain the time evolution of the energy release, of the system control parameter, of the event lifetime distribution and of the event size distribution, respectively, and we establish that a Self Organized Critical state is indeed reached by the system. Moreover, energetic initial impulses in the magnetohydrodynamic flow can lead to one dimensional signatures in the magnetic two dimensional system, once the Self Organized Critical regime is established. The applications of the model for the study of Gamma Ray Bursts is briefly considered, and it is shown that some astrophysical paramet...
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.
Directory of Open Access Journals (Sweden)
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.
Astrocytic gap junctional networks suppress cellular damage in an in vitro model of ischemia
Energy Technology Data Exchange (ETDEWEB)
Shinotsuka, Takanori; Yasui, Masato; Nuriya, Mutsuo, E-mail: mnuriya@z2.keio.jp
2014-02-07
Highlights: • Astrocytes exhibit characteristic changes in [Ca{sup 2+}]{sub i} under OGD. • Astrocytic [Ca{sup 2+}]{sub i} increase is synchronized with a neuronal anoxic depolarization. • Gap junctional couplings protect neurons as well as astrocytes during OGD. - Abstract: Astrocytes play pivotal roles in both the physiology and the pathophysiology of the brain. They communicate with each other via extracellular messengers as well as through gap junctions, which may exacerbate or protect against pathological processes in the brain. However, their roles during the acute phase of ischemia and the underlying cellular mechanisms remain largely unknown. To address this issue, we imaged changes in the intracellular calcium concentration ([Ca{sup 2+}]{sub i}) in astrocytes in mouse cortical slices under oxygen/glucose deprivation (OGD) condition using two-photon microscopy. Under OGD, astrocytes showed [Ca{sup 2+}]{sub i} oscillations followed by larger and sustained [Ca{sup 2+}]{sub i} increases. While the pharmacological blockades of astrocytic receptors for glutamate and ATP had no effect, the inhibitions of gap junctional intercellular coupling between astrocytes significantly advanced the onset of the sustained [Ca{sup 2+}]{sub i} increase after OGD exposure. Interestingly, the simultaneous recording of the neuronal membrane potential revealed that the onset of the sustained [Ca{sup 2+}]{sub i} increase in astrocytes was synchronized with the appearance of neuronal anoxic depolarization. Furthermore, the blockade of gap junctional coupling resulted in a concurrent faster appearance of neuronal depolarizations, which remain synchronized with the sustained [Ca{sup 2+}]{sub i} increase in astrocytes. These results indicate that astrocytes delay the appearance of the pathological responses of astrocytes and neurons through their gap junction-mediated intercellular network under OGD. Thus, astrocytic gap junctional networks provide protection against tissue damage
Modeling water sorption dynamics of cellular solid food systems using free volume theory
Meinders, M.B.J.; Vliet, van T.
2009-01-01
Water sorption and dynamical properties of bread crust were studied using gravimetric sorption experiments. Water uptake and loss were measured while relative humidity (RH) was step-wise in- or decreased. Experimental results were compared with Fickian diffusion models and empirical models like the
Modelling land-use effects of future urbanization using cellular automata
DEFF Research Database (Denmark)
Fuglsang, Morten; Münier, B.; Hansen, H.S.
2013-01-01
The modelling of land use change is a way to analyse future scenarios by modelling different pathways. Application of spatial data of different scales coupled with socio-economic data makes it possible to explore and test the understanding of land use change relations. In the EU-FP7 research...
Hateren, Hans van
2005-01-01
A model for the sensitivity regulation in the primate outer retina is developed and validated using horizontal cell measurements from the literature. The main conclusion is that the phototransduction of the cones is the key factor regulating sensitivity. The model consists of a nonlinearity cascaded
Optical imaging as a link between cellular neurophysiology and circuit modeling
Directory of Open Access Journals (Sweden)
Walther Akemann
2009-07-01
Full Text Available The relatively simple and highly modular circuitry of the cerebellum raised expectations decades ago that a realistic computational model of cerebellar circuit operations would be feasible, and prove insightful for unraveling cerebellar information processing. To this end, the biophysical properties of most cerebellar cell types and their synaptic connections have been well characterized and integrated into realistic single cell models. Furthermore, large scale models of cerebellar circuits that extrapolate from single cell properties to circuit dynamics have been constructed. While the development of single cell models have been constrained by microelectrode recordings, guidance and validation as these models are scaled up to study network interactions requires an experimental methodology capable of monitoring cerebellar dynamics at the population level. Here we review the potential of optical imaging techniques to serve this purpose.
Tucker, G. E.; Hobley, D. E. J.; Hutton, E.; Gasparini, N. M.; Istanbulluoglu, E.; Adams, J. M.; Nudurupati, S. S.
2015-11-01
CellLab-CTS 2015 is a Python-language software library for creating two-dimensional, continuous-time stochastic (CTS) cellular automaton models. The model domain consists of a set of grid nodes, with each node assigned an integer state-code that represents its condition or composition. Adjacent pairs of nodes may undergo transitions to different states, according to a user-defined average transition rate. A model is created by writing a Python code that defines the possible states, the transitions, and the rates of those transitions. The code instantiates, initializes, and runs one of four object classes that represent different types of CTS model. CellLab-CTS provides the option of using either square or hexagonal grid cells. The software provides the ability to treat particular grid-node states as moving particles, and to track their position over time. Grid nodes may also be assigned user-defined properties, which the user can update after each transition through the use of a callback function. As a component of the Landlab modeling framework, CellLab-CTS models take advantage of a suite of Landlab's tools and capabilities, such as support for standardized input and output.
Directory of Open Access Journals (Sweden)
Boyin Liu
Full Text Available Different toxicity tests for carbon nanotubes (CNT have been developed to assess their impact on human health and on aquatic and terrestrial animal and plant life. We present a new model, the fruit fly Drosophila embryo offering the opportunity for rapid, inexpensive and detailed analysis of CNTs toxicity during embryonic development. We show that injected DiI labelled multi-walled carbon nanotubes (MWCNTs become incorporated into cells in early Drosophila embryos, allowing the study of the consequences of cellular uptake of CNTs on cell communication, tissue and organ formation in living embryos. Fluorescently labelled subcellular structures showed that MWCNTs remained cytoplasmic and were excluded from the nucleus. Analysis of developing ectodermal and neural stem cells in MWCNTs injected embryos revealed normal division patterns and differentiation capacity. However, an increase in cell death of ectodermal but not of neural stem cells was observed, indicating stem cell-specific vulnerability to MWCNT exposure. The ease of CNT embryo injections, the possibility of detailed morphological and genomic analysis and the low costs make Drosophila embryos a system of choice to assess potential developmental and cellular effects of CNTs and test their use in future CNT based new therapies including drug delivery.
Wu, Ming J; O'Doherty, Patrick J; Murphy, Patricia A; Lyons, Victoria; Christophersen, Melinda; Rogers, Peter J; Bailey, Trevor D; Higgins, Vincent J
2011-01-01
Elemental uptake and export of the cell are tightly regulated thereby maintaining the ionomic homeostasis. This equilibrium can be disrupted upon exposure to exogenous reactive oxygen species (ROS), leading to reduction or elevation of the intracellular metal ions. In this study, the ionomic composition in the eukaryotic model organism Saccharomyces cerevisiae was profiled using the inductively-coupled plasma optical emission spectrometer (ICP-OES) following the treatment with individual ROS, including hydrogen peroxide, cumen hydroperoxide, linoleic acid hydroperoxide (LAH), the superoxide-generating agent menadione, the thiol-oxidising agent diamide [diazine-dicarboxylic acid-bis(dimethylamide)], dimedone and peroxynitrite. The findings demonstrated that different ROS resulted in distinct changes in cellular metal ions. Aluminium (Al(3+)) level rose up to 50-fold after the diamide treatment. Cellular potassium (K(+)) in LAH-treated cells was 26-fold less compared to the non-treated controls. The diamide-induced Al(3+) accumulation was further validated by the enhanced Al(3+) uptake along the time course and diamide doses. Pre-incubation of yeast with individual elements including iron, copper, manganese and magnesium failed to block diamide-induced Al(3+) uptake, suggesting Al(3+)-specific transporters could be involved in Al(3+) uptake. Furthermore, LAH-induced potassium depletion was validated by a rescue experiment in which addition of potassium increased yeast growth in LAH-containing media by 26% compared to LAH alone. Taken together, the data, for the first time, demonstrated the linkage between ionomic profiles and individual oxidative conditions.