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Sample records for cellular models based

  1. TRAFFIC FLOW MODEL BASED ON CELLULAR AUTOMATION WITH ADAPTIVE DECELERATION

    OpenAIRE

    Shinkarev, A. A.

    2016-01-01

    This paper describes continuation of the authors’ work in the field of traffic flow mathematical models based on the cellular automata theory. The refactored representation of the multifactorial traffic flow model based on the cellular automata theory is used for a representation of an adaptive deceleration step implementation. The adaptive deceleration step in the case of a leader deceleration allows slowing down smoothly but not instantly. Concepts of the number of time steps without confli...

  2. 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.

  3. 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.

  4. 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.  

  5. 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.

  6. Cellular-Based Statistical Model for Mobile Dispersion

    OpenAIRE

    Abdulla, Mouhamed; Shayan, Yousef R.

    2013-01-01

    While analyzing mobile systems we often approximate the actual coverage surface and assume an ideal cell shape. In a multi-cellular network, because of its tessellating nature, a hexagon is more preferred than a circular geometry. Despite this reality, perhaps due to the inherent simplicity, only a model for circular based random spreading is available. However, if used, this results an unfair terminal distribution for non-circular contours. Therefore, in this paper we specifically derived an...

  7. Mathematical model for flood routing based on cellular automaton

    Directory of Open Access Journals (Sweden)

    Xin CAI

    2014-04-01

    Full Text Available Increasing frequency and severity of flooding have caused tremendous damage in China, requiring more essential countermeasures to alleviate the damage. In this study, the dynamic simulation property of a cellular automaton was used to make further progress in flood routing. In consideration of terrain’s influence on flood routing, we regarded the terrain elevation as an auxiliary attribute of a two-dimensional cellular automaton in path selection for flood routing and developed a mathematical model based on a cellular automaton. A numerical case of propagation of an outburst flood in an area of the lower Yangtze River was analyzed with both the fixed-step and variable-step models. The results show that the flood does not spread simultaneously in all directions, but flows into the lower place first, and that the submerged area grows quickly at the beginning, but slowly later on. The final submerged areas obtained from the two different models are consistent, and the flood volume balance test shows that the flood volume meets the requirement of the total volume balance. The analysis of the case shows that the proposed model can be a valuable tool for flood routing.

  8. Fluctuation in option pricing using cellular automata based market models

    Science.gov (United States)

    Gao, Yuying; Beni, Gerardo

    2005-05-01

    A new agent-based Cellular Automaton (CA) computational algorithm for option pricing is proposed. CAs have been extensively used in modeling complex dynamical systems but not in modeling option prices. Compared with traditional tools, which rely on guessing volatilities to calculate option prices, the CA model is directly addressing market mechanisms and simulates price fluctuation from aggregation of actions made by interacting individual market makers in a large population. This paper explores whether CA models can provide reasonable good answers to pricing European options. The Black-Scholes model and the Binomial Tree model are used for comparison. Comparison reveals that CA models perform reasonably well in pricing options, reproducing overall characteristics of random walk based model, while at the same time providing plausible results for the 'fat-tail' phenomenon observed in many markets. We also show that the binomial tree model can be obtained from a CA rule. Thus, CA models are suitable tools to generalize the standard theories of option pricing.

  9. Global Network Model based on Earth Grid and Cellular

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    Dongqi Lu

    2014-06-01

    Full Text Available We aim to understand the current health state of the Earth and find how human activities influence it. Based on the theory of Earth’s Grid and Cellular Automata, we define and test a global network model, analyze the mutual interactions and feedbacks of ecosystem, hydrologic circle and atmosphere. In addition, we consult a lot of data to find a benchmark for the “Earth Health Map”, with the ecosystem distribution on it, which can be helpful for making a strategic decision for policy makers and prediction. Our model can be extended to other similar fields. In the end, we discuss the sensitivity of parameters selection, and the superiorities and weaknesses of our model.

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

    Science.gov (United States)

    Scianna, Marco; Preziosi, Luigi

    2016-09-01

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

  11. Motor Schema-Based Cellular Automaton Model for Pedestrian Dynamics

    Science.gov (United States)

    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.

  12. A cellular automata-based mathematical model for thymocyte development.

    Directory of Open Access Journals (Sweden)

    Hallan Souza-e-Silva

    Full Text Available Intrathymic T cell development is an important process necessary for the normal formation of cell-mediated immune responses. Importantly, such a process depends on interactions of developing thymocytes with cellular and extracellular elements of the thymic microenvironment. Additionally, it includes a series of oriented and tunely regulated migration events, ultimately allowing mature cells to cross endothelial barriers and leave the organ. Herein we built a cellular automata-based mathematical model for thymocyte migration and development. The rules comprised in this model take into account the main stages of thymocyte development, two-dimensional sections of the normal thymic microenvironmental network, as well as the chemokines involved in intrathymic cell migration. Parameters of our computer simulations with further adjusted to results derived from previous experimental data using sub-lethally irradiated mice, in which thymus recovery can be evaluated. The model fitted with the increasing numbers of each CD4/CD8-defined thymocyte subset. It was further validated since it fitted with the times of permanence experimentally ascertained in each CD4/CD8-defined differentiation stage. Importantly, correlations using the whole mean volume of young normal adult mice revealed that the numbers of cells generated in silico with the mathematical model fall within the range of total thymocyte numbers seen in these animals. Furthermore, simulations made with a human thymic epithelial network using the same mathematical model generated similar profiles for temporal evolution of thymocyte developmental stages. Lastly, we provided in silico evidence that the thymus architecture is important in the thymocyte development, since changes in the epithelial network result in different theoretical profiles for T cell development/migration. This model likely can be used to predict thymocyte evolution following therapeutic strategies designed for recovery of the

  13. The brittleness model of complex system based on cellular automata

    Institute of Scientific and Technical Information of China (English)

    LIN De-ming; JIN Hong-zhang; LI Qi; WU Hong-mei

    2004-01-01

    Now the research on the complex system is a hot spot. Brittleness is one of the basic characteristics of a complex system. In a complex system, after one of subsystems is struck to be collapsed, the whole system will collapse. Meanwhile, cellular automata is a discrete dynamic system. When the rule is given, the cellular automata could be defined. Then it can imitate the complex action. Cellular automata is used to simulate the brittleness action in this study. Entropy was used to analyze the action and get the rule. Then,three normal brittleness models were given. The result shows that the brittleness of complex system is existent and in addition some important behavior mode of complex system brittleness has been achieved.

  14. Occupant evacuation model based on cellular automata in fire

    Institute of Scientific and Technical Information of China (English)

    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.

  15. Network modeling of membrane-based artificial cellular systems

    Science.gov (United States)

    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.

  16. Markov Model Based CAC algorithms for Cellular Networks

    Directory of Open Access Journals (Sweden)

    PATLEVIČ Peter

    2010-05-01

    Full Text Available In this paper, we investigate using ofthe Hidden Markov Model philosophy for solvingconnection admission control (CAC problem incellular networks. For more effective bandwidthutilization and Quality of Service (QoS support itis necessary to solve the connection admissioncontrol with respect to minimizing blockingprobability of handoff and newly arrivedconnections. This paper looks into an thresholdoriented CAC scheme for operation with twoclasses of connections with a Markov model usedfor computation of the threshold value based oncurrent conditions in the network and so makesthe operation of the mobile network cell moreeffectively. In article we extrapolate Markov chainmodel based CAC for three classes of connectionsand sketch how to generalize problem for n classesof connections.

  17. Excellent approach to modeling urban expansion by fuzzy cellular automata: agent base model

    Science.gov (United States)

    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.

  18. 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.

  19. Equal Distribution Model of Epidemic Drugs Based on a Cellular Automata Model

    Directory of Open Access Journals (Sweden)

    Huang Xinyi

    2015-01-01

    Full Text Available The epidemic spreading of infectious disease is a process of evolution over time. Based on the cellular automata model[1], this paper analyzes the epidemic spreading rules, and establishes an efficient equal distribution model of drugs in a broad sense. For multiple regions, in case of demand of drugs exceeding supply, the drugs shall be distributed according to the proportion of a total number of people in each region, the number of patients, the number of the isolated, and the number of deaths. It is necessary to simulate based on these four schemes to obtain simulation results. The results show that, when the drugs are distributed by the proportion of the number of deaths, it is optimal for controlling over epidemic situations.

  20. 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.

  1. A Geometrical-Based Model for Cochannel Interference Analysis and Capacity Estimation of CDMA Cellular Systems

    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.

  2. A Geometrical-Based Model for Cochannel Interference Analysis and Capacity Estimation of CDMA Cellular Systems

    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.

  3. 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.

  4. Analysis on Traffic Conflicts of Two-lane Highway Based on Improved Cellular Automation Model

    Directory of Open Access Journals (Sweden)

    Xiru Tang

    2013-06-01

    Full Text Available Based on microscopic traffic characteristics of two-lane highway and different driving characteristics for drivers, the characteristics of drivers and vehicle structure are introduced into Cellular Automation model for establishing new Cellular Automation model of two-lane highway. Through computer simulation, the paper analyzes the effect of the promotion of different vehicles, drivers and arrival rates on traffic conflicts of two-lane highway, which gets the relationship between the parameters such as road traffic and velocity variance and collision. The results indicate that the frequency of traffic conflicts has close relationship with the product of traffic flow and velocity variation. When the traffic flow and velocity variation are great, the frequency of the conflict is the greatest, and when the traffic flow and velocity variation are little, the frequency of the conflict is the least.

  5. Antiproliferative Activity and Cellular Uptake of Evodiamine and Rutaecarpine Based on 3D Tumor Models

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    Hui Guo

    2016-07-01

    Full Text Available Evodiamine (EVO and rutaecarpine (RUT are promising anti-tumor drug candidates. The evaluation of the anti-proliferative activity and cellular uptake of EVO and RUT in 3D multicellular spheroids of cancer cells would better recapitulate the native situation and thus better reflect an in vivo response to the treatment. Herein, we employed the 3D culture of MCF-7 and SMMC-7721 cells based on hanging drop method and evaluated the anti-proliferative activity and cellular uptake of EVO and RUT in 3D multicellular spheroids, and compared the results with those obtained from 2D monolayers. The drugs’ IC50 values were significantly increased from the range of 6.4–44.1 μM in 2D monolayers to 21.8–138.0 μM in 3D multicellular spheroids, which may be due to enhanced mass barrier and reduced drug penetration in 3D models. The fluorescence of EVO and RUT was measured via fluorescence spectroscopy and the cellular uptake of both drugs was characterized in 2D tumor models. The results showed that the cellular uptake concentrations of RUT increased with increasing drug concentrations. However, the EVO concentrations uptaken by the cells showed only a small change with increasing drug concentrations, which may be due to the different solubility of EVO and Rut in solvents. Overall, this study provided a new vision of the anti-tumor activity of EVO and RUT via 3D multicellular spheroids and cellular uptake through the fluorescence of compounds.

  6. Simple Cellular Automata-Based Linear Models for the Shrinking Generator

    CERN Document Server

    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.

  7. Driver’s Awareness and Lane Changing Maneuver in Traffic Flow based on Cellular Automaton Model

    OpenAIRE

    Kohei Arai; Steven Ray Sentinuwo

    2015-01-01

    Effect of driver’s awareness (e.g., to estimate the speed and arrival time of another vehicle) on the lane changing maneuver is discussed. “Scope awareness” is defined as the visibility which is required for the driver to make a visual perception about road condition and the speed of vehicle that appears in the target lane for lane changing in the road. Cellular automaton based simulation model is created and applied to simulation studies for driver awareness behavior. This study clarifies re...

  8. 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.

  9. 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.

  10. Mathematical Modeling of Cellular Metabolism.

    Science.gov (United States)

    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.

  11. 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.

  12. A nanoflare based cellular automaton model and the observed properties of the coronal plasma

    CERN Document Server

    Fuentes, Marcelo López

    2016-01-01

    We use the cellular automaton model described in L\\'opez Fuentes \\& Klimchuk (2015, ApJ, 799, 128) to study the evolution of coronal loop plasmas. The model, based on the idea of a critical misalignment angle in tangled magnetic fields, produces nanoflares of varying frequency with respect to the plasma cooling time. We compare the results of the model with active region (AR) observations obtained with the Hinode/XRT and SDO/AIA instruments. The comparison is based on the statistical properties of synthetic and observed loop lightcurves. Our results show that the model reproduces the main observational characteristics of the evolution of the plasma in AR coronal loops. The typical intensity fluctuations have an amplitude of 10 to 15\\% both for the model and the observations. The sign of the skewness of the intensity distributions indicates the presence of cooling plasma in the loops. We also study the emission measure (EM) distribution predicted by the model and obtain slopes in log(EM) versus log(T) betw...

  13. Driver’s Awareness and Lane Changing Maneuver in Traffic Flow based on Cellular Automaton Model

    Directory of Open Access Journals (Sweden)

    Kohei Arai

    2015-08-01

    Full Text Available Effect of driver’s awareness (e.g., to estimate the speed and arrival time of another vehicle on the lane changing maneuver is discussed. “Scope awareness” is defined as the visibility which is required for the driver to make a visual perception about road condition and the speed of vehicle that appears in the target lane for lane changing in the road. Cellular automaton based simulation model is created and applied to simulation studies for driver awareness behavior. This study clarifies relations between the lane changing behavior and the scope awareness parameter that reflects driver behavior. Simulation results show that the proposed model is valid for investigation of the important features of lane changing maneuver.

  14. Model of Handover and Traffic Based on Cellular Geometry with Smart Antenna

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    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.

  15. 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.

  16. An empirical Bayesian approach for model-based inference of cellular signaling networks

    Directory of Open Access Journals (Sweden)

    Klinke David J

    2009-11-01

    Full Text Available Abstract Background A common challenge in systems biology is to infer mechanistic descriptions of biological process given limited observations of a biological system. Mathematical models are frequently used to represent a belief about the causal relationships among proteins within a signaling network. Bayesian methods provide an attractive framework for inferring the validity of those beliefs in the context of the available data. However, efficient sampling of high-dimensional parameter space and appropriate convergence criteria provide barriers for implementing an empirical Bayesian approach. The objective of this study was to apply an Adaptive Markov chain Monte Carlo technique to a typical study of cellular signaling pathways. Results As an illustrative example, a kinetic model for the early signaling events associated with the epidermal growth factor (EGF signaling network was calibrated against dynamic measurements observed in primary rat hepatocytes. A convergence criterion, based upon the Gelman-Rubin potential scale reduction factor, was applied to the model predictions. The posterior distributions of the parameters exhibited complicated structure, including significant covariance between specific parameters and a broad range of variance among the parameters. The model predictions, in contrast, were narrowly distributed and were used to identify areas of agreement among a collection of experimental studies. Conclusion In summary, an empirical Bayesian approach was developed for inferring the confidence that one can place in a particular model that describes signal transduction mechanisms and for inferring inconsistencies in experimental measurements.

  17. Modelling cellular behaviour

    Science.gov (United States)

    Endy, Drew; Brent, Roger

    2001-01-01

    Representations of cellular processes that can be used to compute their future behaviour would be of general scientific and practical value. But past attempts to construct such representations have been disappointing. This is now changing. Increases in biological understanding combined with advances in computational methods and in computer power make it possible to foresee construction of useful and predictive simulations of cellular processes.

  18. Cellular systems biology profiling applied to cellular models of disease.

    Science.gov (United States)

    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.

  19. Antiproliferative Activity and Cellular Uptake of Evodiamine and Rutaecarpine Based on 3D Tumor Models

    OpenAIRE

    Hui Guo; Dongmei Liu; Bin Gao; Xiaohui Zhang; Minli You; Hui Ren; Hongbo Zhang; Santos, Hélder A.; Feng Xu

    2016-01-01

    Evodiamine (EVO) and rutaecarpine (RUT) are promising anti-tumor drug candidates. The evaluation of the anti-proliferative activity and cellular uptake of EVO and RUT in 3D multicellular spheroids of cancer cells would better recapitulate the native situation and thus better reflect an in vivo response to the treatment. Herein, we employed the 3D culture of MCF-7 and SMMC-7721 cells based on hanging drop method and evaluated the anti-proliferative activity and cellular uptake of EVO and RUT i...

  20. Modeling and Simulation of Polarization in Internet Group Opinions Based on Cellular Automata

    Directory of Open Access Journals (Sweden)

    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.

  1. Fuzzy Case-Based Reasoning in Product Style Acquisition Incorporating Valence-Arousal-Based Emotional Cellular Model

    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.

  2. Analyzing the Influence of Mobile Phone Use of Drivers on Traffic Flow Based on an Improved Cellular Automaton Model

    OpenAIRE

    Yao Xiao; Jing Shi

    2015-01-01

    This paper aimed to analyze the influence of drivers’ behavior of phone use while driving on traffic flow, including both traffic efficiency and traffic safety. An improved cellular automaton model was proposed to simulate traffic flow with distracted drivers based on the Nagel-Schreckenberg model. The driving characters of drivers using a phone were first discussed and a value representing the probability to use a phone while driving was put into the CA model. Simulation results showed that ...

  3. A trans-well-based cellular model for the rapid pre-evaluation of tympanic membrane repair materials.

    Science.gov (United States)

    Hung, Shih-Han; Su, Chin-Hui; Tseng, How

    2016-08-01

    It is important to have a standardized tympanic membrane (TM) perforation platform to evaluate the various myringoplasty materials that have been studied and developed extensively during recent years. However, currently there are no cellular models specifically designed for this purpose, and animal models remain unsatisfactory. The purpose of this study is to propose an inexpensive, readily available, well-controlled, and easy-to-create cellular model as a substitute for use in the evaluation of TM repairing materials. A trans-well model was created using a cell culture insert with a round hole created at the center of the polycarbonate membrane. HaCaT cells were cultured on the fenestrated culture insert, and the desired myringoplasty graft was placed at the center of the window for one week and observed by fluorescent microscopy under vital staining. Under this cellular model, there was notable migration of HaCaT cells onto the positive control graft (rabbit fascia), while only a few cell clusters were observed on the negative control graft (paper). Model validation showed that the cell migration ratio for the PLLA + 1% hyaluronic acid (HA) graft is significantly higher than using myringoplasty paper, poly L-lactide (PLLA), or PLLA + 0.5% HA (p < 0.05). This trans-well-based cellular model might be a useful pre-evaluation platform for the evaluation of TM repairing materials. The model is inexpensive, readily available, easy to create, and standardized for use. PMID:26335291

  4. Treatment Analysis in a Cancer Stem Cell Context Using a Tumor Growth Model Based on Cellular Automata.

    Directory of Open Access Journals (Sweden)

    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.

  5. 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.

  6. 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.

  7. Cellular automata model based on GIS and urban sprawl dynamics simulation

    Science.gov (United States)

    Mu, Fengyun; Zhang, Zengxiang

    2005-10-01

    The simulation of land use change process needs the support of Geographical Information System (GIS) and other relative technologies. While the present commercial GIS lack capabilities of distribution, prediction, and simulation of spatial-temporal data. Cellular automata (CA) provide dynamically modeling "from bottom-to-top" framework and posses the capability of modeling spatial-temporal evolvement process of a complicated geographical system, which is composed of a fourfold: cells, states, neighbors and rules. The simplicity and flexibility make CA have the ability to simulate a variety of behaviors of complex systems. One of the most potentially useful applications of cellular automata from the point of view of spatial planning is their use in simulations of urban sprawl at local and regional level. The paper firstly introduces the principles and characters of the cellular automata, and then discusses three methods of the integration of CA and GIS. The paper analyses from a practical point of view the factors that effect urban activities in the science of spatial decision-making. The status of using CA to dynamic simulates of urban expansion at home and abroad is analyzed. Finally, the problems and tendencies that exist in the application of CA model are detailed discussed, such as the quality of the data that the CA needs, the self-organization of the CA roots in the mutual function among the elements of the system, the partition of the space scale, the time calibration of the CA and the integration of the CA with other modular such as artificial nerve net modular and population modular etc.

  8. 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.

  9. Fatigue design of a cellular phone folder using regression model-based multi-objective optimization

    Science.gov (United States)

    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.

  10. Cellular based cancer vaccines

    DEFF Research Database (Denmark)

    Hansen, Morten; Met, O; Svane, I M;

    2012-01-01

    Cancer vaccines designed to re-calibrate the existing host-tumour interaction, tipping the balance from tumor acceptance towards tumor control holds huge potential to complement traditional cancer therapies. In general, limited success has been achieved with vaccines composed of tumor...... in vitro migration via autocrine receptor-mediated endocytosis of CCR7. In the current review, we discuss optimal design of DC maturation focused on pre-clinical as well as clinical results from standard and polarized dendritic cell based cancer vaccines....

  11. Modeling on dynamic recrystallization of aluminium alloy 7050 during hot compression based on cellular automaton

    Institute of Scientific and Technical Information of China (English)

    LI Jun-chao; XIE Zhi-yuan; LI Song-pu; ZANG Yan-yan

    2016-01-01

    The dynamic recrystallization (DRX) process of hot compressed aluminium alloy 7050 was predicted using cellular automaton (CA) combined with topology deformation. The hot deformatation characteristics of aluminium alloy 7050 were investigated by hot uniaxial compression tests in order to obtain the material parameters used in the CA model. The influences of process parameters (strain, strain rate and temperature) on the fraction of DRX and the average recrystallization grain (R-grain) size were investigated and discussed. It is found that larger stain, higher temperature and lower strain rate (less than 0.1 s–1) are beneficial to the increasing fraction of DRX. And the deformation temperature affects the mean R-grain size much more greatly than other parameters. It is also noted that there is a critical strain for the occurrence of DRX which is related to strain rate and temperature. In addition, it is shown that the CA model with topology deformation is able to simulate the microstructural evolution and the flow behavior of aluminium alloy 7050 material under various deformation conditions.

  12. A cardiac electrical activity model based on a cellular automata system in comparison with neural network model.

    Science.gov (United States)

    Khan, Muhammad Sadiq Ali; Yousuf, Sidrah

    2016-03-01

    Cardiac Electrical Activity is commonly distributed into three dimensions of Cardiac Tissue (Myocardium) and evolves with duration of time. The indicator of heart diseases can occur randomly at any time of a day. Heart rate, conduction and each electrical activity during cardiac cycle should be monitor non-invasively for the assessment of "Action Potential" (regular) and "Arrhythmia" (irregular) rhythms. Many heart diseases can easily be examined through Automata model like Cellular Automata concepts. This paper deals with the different states of cardiac rhythms using cellular automata with the comparison of neural network also provides fast and highly effective stimulation for the contraction of cardiac muscles on the Atria in the result of genesis of electrical spark or wave. The specific formulated model named as "States of automaton Proposed Model for CEA (Cardiac Electrical Activity)" by using Cellular Automata Methodology is commonly shows the three states of cardiac tissues conduction phenomena (i) Resting (Relax and Excitable state), (ii) ARP (Excited but Absolutely refractory Phase i.e. Excited but not able to excite neighboring cells) (iii) RRP (Excited but Relatively Refractory Phase i.e. Excited and able to excite neighboring cells). The result indicates most efficient modeling with few burden of computation and it is Action Potential during the pumping of blood in cardiac cycle. PMID:27087101

  13. Evaluation of adamantane hydroxamates as botulinum neurotoxin inhibitors: synthesis, crystallography, modeling, kinetic and cellular based studies

    OpenAIRE

    Šilhár, Peter; Silvaggi, Nicholas R; Pellett, Sabine; Čapková, Kateřina; Johnson, Eric A.; Allen, Karen N.; Janda, Kim D.

    2012-01-01

    Botulinum neurotoxins (BoNTs) are the most lethal biotoxins known to mankind and are responsible for the neuroparalytic disease botulism. Current treatments for botulinum poisoning are all protein based and thus have a limited window of treatment opportunity. Inhibition of the BoNT light chain protease (LC) has emerged as a therapeutic strategy for the treatment of botulism as it may provide an effective post exposure remedy. Using a combination of crystallographic and modeling studies a seri...

  14. Mechanistic model of radon-induced lung cancer risk at low exposure levels based on cellular alpha particle hits

    Energy Technology Data Exchange (ETDEWEB)

    Werner, Hofmann; Hatim, Fakir [Salzburg Univ., Div. of Physics and Biophysics, Dept. of Material Science (Austria); Lucia-Adina, Truta-Popa [Babes-Bolyai Univ., Faculty of Physics (Romania)

    2006-07-01

    To explore the role of the multiplicity of cellular hits by radon progeny alpha particles for lung cancer incidence, the number of single and multiple alpha particle hits were computed for basal and secretory cells in the bronchial epithelium of human airway bifurcations employing Monte Carlo methods. Hot spots of alpha particle hits were observed at the branching points of bronchial airway bifurcations, suggesting that multiple alpha particle hits may occur primarily at carinal ridges. Random alpha particle intersections of bronchial cells during a given exposure period, selected from a Poisson distribution, were simulated by an initiation-promotion model, based on experimentally observed cellular transformation and survival functions. To consider potential bystander effects, which have been observed in cellular in vitro studies, alpha particle interactions were also simulated for larger sensitive target volumes in bronchial epithelium, consisting of a collection of cells. Lung cancer risk simulations indicated that cancer induction for continuous exposures is related to the cycle time of an irradiated cell, thus exhibiting a distinct dose-rate effect. While the dominant role of single hits leads to a linear dose-response relationship at low radon exposure levels, predicted lung cancer risk for a collection of interacting cells exhibits a linear-quadratic response, suggesting that bystander effects, if operating at all under in vivo irradiations, may be restricted to a small number of adjacent cells. (author)

  15. Analyzing the Influence of Mobile Phone Use of Drivers on Traffic Flow Based on an Improved Cellular Automaton Model

    Directory of Open Access Journals (Sweden)

    Yao Xiao

    2015-01-01

    Full Text Available This paper aimed to analyze the influence of drivers’ behavior of phone use while driving on traffic flow, including both traffic efficiency and traffic safety. An improved cellular automaton model was proposed to simulate traffic flow with distracted drivers based on the Nagel-Schreckenberg model. The driving characters of drivers using a phone were first discussed and a value representing the probability to use a phone while driving was put into the CA model. Simulation results showed that traffic flow rate was significantly reduced if some drivers used a phone compared to no phone use. The flow rate and velocity decreased as the proportion of drivers using a phone increased. While, under low density, the risk of traffic decreased first and then increased as the distracted drivers increased, the distracted behavior of drivers, like using a phone, could reduce the flow rate by 5 percent according to the simulation.

  16. BioJazz: in silico evolution of cellular networks with unbounded complexity using rule-based modeling.

    Science.gov (United States)

    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.

  17. Analytical Models for Dimensioning of OFDMA-based Cellular Networks Carrying VoIP and Best-Effort Traffic

    Directory of Open Access Journals (Sweden)

    Bruno Baynat

    2012-10-01

    Full Text Available The last years have seen an exponentially growing interest for mobile telecommunication services. As a consequence, a great diversity of applications is expected to be supported by cellular networks. To answer this ever increasing demand, the ITU-R defined the requirements that the fourth generation (4G of mobile standards must fulfill. Today, two especially promising candidates for 4G stand out: WiMAX and LTE. However, 4G cellular networks are still far from being implemented, and the high deployment costs render over-provisioning out of question. We thus propose in this paper accurate and convenient analytical models well-suited for the complex dimensioning of these promising access networks. Our main interest is WiMAX, yet, we show how our models can be easily used to consider LTE cells since both technologies are based on OFDMA. Generic Markovian models are developed specifically for three service classes defined in the WiMAX standard: UGS, ertPS and BE, respectively corresponding to VoIP, VoIP with silence suppression and best-effort traffic. First, we consider cells carrying either UGS, ertPS or BE traffic. Three methods to combine the previous models are then proposed to assume both UGS and BE traffic in the studied cell. Finally, we provide a way to easily integrate the ertPS traffic and obtain a UGS/ertPS/BE model able to account for multiple traffic profiles in each service class while keeping an instantaneous resolution. The proposed models are compared in depth with realistic simulations that show their accuracy. Lastly, we demonstrate through different examples how our models can be used to answer dimensioning issues which would be intractable with simulations.

  18. Cellular automata a parallel model

    CERN Document Server

    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.

  19. Developing an effective 2-D urban flood inundation model for city emergency management based on cellular automata

    Science.gov (United States)

    Liu, L.; Liu, Y.; Wang, X.; Yu, D.; Liu, K.; Huang, H.; Hu, G.

    2015-03-01

    Flash floods have occurred frequently in the urban areas of southern China. An effective process-oriented urban flood inundation model is urgently needed for urban storm-water and emergency management. This study develops an efficient and flexible cellular automaton (CA) model to simulate storm-water runoff and the flood inundation process during extreme storm events. The process of infiltration, inlets discharge and flow dynamics can be simulated with little preprocessing on commonly available basic urban geographic data. In this model, a set of gravitational diverging rules are implemented to govern the water flow in a rectangular template of three cells by three cells of a raster layer. The model is calibrated by one storm event and validated by another in a small urban catchment in Guangzhou of southern China. The depth of accumulated water at the catchment outlet is interpreted from street-monitoring closed-circuit television (CCTV) videos and verified by on-site survey. A good level of agreement between the simulated process and the reality is reached for both storm events. The model reproduces the changing extent and depth of flooded areas at the catchment outlet with an accuracy of 4 cm in water depth. Comparisons with a physically based 2-D model (FloodMap) show that the model is capable of effectively simulating flow dynamics. The high computational efficiency of the CA model can meet the needs of city emergency management.

  20. Cloud computing models and their application in LTE based cellular systems

    NARCIS (Netherlands)

    Staring, A.J.; Karagiannis, G.

    2013-01-01

    As cloud computing emerges as the next novel concept in computer science, it becomes clear that the model applied in large data storage systems used to resolve issues coming forth from an increasing demand, could also be used to resolve the very high bandwidth requirements on access network, core ne

  1. A cellular automaton based model simulating HVAC fluid and heat transport in a building. Modeling approach and comparison with experimental results

    Energy Technology Data Exchange (ETDEWEB)

    Saiz, A. [Department of Applied Mathematics, Polytechnic University of Valencia, ETSGE School, Camino de Vera s/n, 46022 Valencia (Spain); Urchueguia, J.F. [Department of Applied Physics, Polytechnic University of Valencia, ETSII School, Camino de Vera s/n, 46022 Valencia (Spain); Martos, J. [Superior Technical School of Engineering, Department of Electronic Engineering, University of Valencia, Vicente Andres Estelles s/n, Burjassot 46100, Valencia (Spain)

    2010-09-15

    A discrete model characterizing heat and fluid flow in connection with thermal fluxes in a building is described and tested against experiment in this contribution. The model, based on a cellular automaton approach, relies on a set of a few quite simple rules and parameters in order to simulate the dynamic evolution of temperatures and energy flows in any water or brine based thermal energy distribution network in a building or system. Using an easy-to-record input, such as the instantaneous electrical power demand of the heating or cooling system, our model predicts time varying temperatures in characteristic spots and the related enthalpy flows whose simulation usually requires heavy computational tools and detailed knowledge of the network elements. As a particular example, we have applied our model to simulate an existing fan coil based hydronic heating system driven by a geothermal heat pump. When compared to the experimental temperature and thermal energy records, the outcome of the model coincides. (author)

  2. Spatiotemporal Simulation of Tourist Town Growth Based on the Cellular Automata Model: The Case of Sanpo Town in Hebei Province

    Directory of Open Access Journals (Sweden)

    Jun Yang

    2013-01-01

    Full Text Available Spatiotemporal simulation of tourist town growth is important for research on land use/cover change under the influence of urbanization. Many scholars have shown great interest in the unique pattern of driving urban development with tourism development. Based on the cellular automata (CA model, we simulated and predicted the spatiotemporal growth of Sanpo town in Hebei Province, using the tourism urbanization growth model. Results showed that (1 average annual growth rate of the entire region was 1.5 Ha2 per year from 2005 to 2010, 4 Ha2 per year from 2010 to 2015, and 2.5 Ha2 per year from 2015 to 2020; (2 urban growth rate increased yearly, with regional differences, and had a high degree of correlation with the Euclidean distance of town center, traffic route, attractions, and other factors; (3 Gougezhuang, an important village center in the west of the town, demonstrated traffic advantages and increased growth rate since 2010; (4 Magezhuang village has the largest population in the region, so economic advantages have driven the development of rural urbanization. It showed that CA had high reliability in simulating the spatiotemporal evolution of tourist town, which assists the study of spatiotemporal growth under urbanization and rational protection of tourism resources.

  3. 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.

  4. Differential expression proteomics of human colorectal cancer based on a syngeneic cellular model for the progression of adenoma to carcinoma.

    Science.gov (United States)

    Roth, Udo; Razawi, Hanieh; Hommer, Julia; Engelmann, Katja; Schwientek, Tilo; Müller, Stefan; Baldus, Stephan E; Patsos, Georgios; Corfield, Anthony P; Paraskeva, Christos; Hanisch, Franz-Georg

    2010-01-01

    This is the first differential expression proteomics study on a human syngeneic cellular in vitro progression model of the colorectal adenoma-to-carcinoma sequence, the anchorage-dependent non-tumorigenic adenoma derived cell line AA/C1 and the derived anchorage-independent and tumorigenic carcinoma cell line AA/C1/SB10C. The study is based on quantitative 2-DE and is complemented by Western blot validation. Excluding redundancies due to proteolysis and post-translational modified isoforms of over 2000 protein spots, 13 proteins were revealed as regulated with statistical variance being within the 95th confidence level and were identified by peptide mass fingerprinting in MALDI MS. Progression-associated proteins belong to the functional complexes of anaerobic glycolysis/gluconeogenesis, steroid biosynthesis, prostaglandin biosynthesis, the regulation and maintenance of the cytoskeleton, protein biosynthesis and degradation, the regulation of apoptosis or other functions. Partial but significant overlap was revealed with previous proteomics and transcriptomics studies in colorectal carcinoma. Among upregulated proteins we identified 3-HMG-CoA synthase, protein phosphatase 1, prostaglandin E synthase 2, villin 1, annexin A1, triosephosphate isomerase, phosphoserine aminotransferase 1, fumarylacetoacetate hydrolase and pyrroline-5-carboxylate reductase 1 (PYCR1), while glucose-regulated protein 78, cathepsin D, lamin A/C and quinolate phosphoribosyltransferase were downregulated.

  5. Understanding cisplatin resistance using cellular models.

    OpenAIRE

    STORDAL, BRITTA KRISTINA

    2007-01-01

    PUBLISHED Many mechanisms of cisplatin resistance have been proposed from studies of cellular models of resistance including changes in cellular drug accumulation, detoxification of the drug, inhibition of apoptosis and repair of the DNA adducts. A series of resistant models were developed from CCRF-CEM leukaemia cells with increasing doses of cisplatin from 100 ng/ml. This produced increasing resistance up to 7-fold with a treatment dose of 1.6 ?g/ml. Cisplatin resistance i...

  6. Understanding cisplatin resistance using cellular models

    OpenAIRE

    Stordal, Britta; Davey, Mary

    2007-01-01

    Many mechanisms of cisplatin resistance have been proposed from studies of cellular models of resistance including changes in cellular drug accumulation, detoxification of the drug, inhibition of apoptosis and repair of the DNA adducts. A series of resistant models were developed from CCRF-CEM leukaemia cells with increasing doses of cisplatin from 100 ng/ml. This produced increasing resistance up to 7-fold with a treatment dose of 1.6 microg/ml. Cisplatin resistance in these cells correlated...

  7. An Option Pricing Model Based on Cellular Automaton%基于元胞自动机的期权定价模型

    Institute of Scientific and Technical Information of China (English)

    李捷

    2011-01-01

    Option pricing is one of the most difficult problems in financial research. The key to the problem is how to simulate the randomness of the underlying asset price. This paper designs and implements an option pricing model based on the cellular automaton, which treats market participants as the cells in the cellular automaton. The model uses cellular automaton rules to simulate the interactions between traders and the changes of underlying asset prices. The paper compares the output data of the model with the calculation results of the Black-Scholes model, tests the normality of the model's output data, and finds that the option pricing model based on the cellular automaton is not only feasible, but also more effective than the Black-Scholes model.%针对期权定价难于模拟基础资产价格波动随机性的问题,设计了基于元胞自动机的期权定价模型.该模型将市场参与者看作一个个的元胞,使用元胞规则来模拟金融市场中交易者之间的交互行为。从而在总体上模拟出基础资产价格的变化.比较了模型产出的数据和Black-Scholes模型的计算结果,检验了模型产出数据的正态性,发现基于元胞自动机的期权定价模型不仅具有可行性,而且比Black-Scholes模型更有效.

  8. Analytical Modeling of Uplink Cellular Networks

    CERN Document Server

    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...

  9. Modeling the topological organization of cellular processes.

    Science.gov (United States)

    Giavitto, Jean-Louis; Michel, Olivier

    2003-07-01

    The cell as a dynamical system presents the characteristics of having a dynamical structure. That is, the exact phase space of the system cannot be fixed before the evolution and integrative cell models must state the evolution of the structure jointly with the evolution of the cell state. This kind of dynamical systems is very challenging to model and simulate. New programming concepts must be developed to ease their modeling and simulation. In this context, the goal of the MGS project is to develop an experimental programming language dedicated to the simulation of this kind of systems. MGS proposes a unified view on several computational mechanisms (CHAM, Lindenmayer systems, Paun systems, cellular automata) enabling the specification of spatially localized computations on heterogeneous entities. The evolution of a dynamical structure is handled through the concept of transformation which relies on the topological organization of the system components. An example based on the modeling of spatially distributed biochemical networks is used to illustrate how these notions can be used to model the spatial and temporal organization of intracellular processes. PMID:12915272

  10. Fate of PLA and PCL-Based Polymeric Nanocarriers in Cellular and Animal Models of Triple-Negative Breast Cancer.

    Science.gov (United States)

    Sitia, Leopoldo; Ferrari, Raffaele; Violatto, Martina B; Talamini, Laura; Dragoni, Luca; Colombo, Claudio; Colombo, Laura; Lupi, Monica; Ubezio, Paolo; D'Incalci, Maurizio; Morbidelli, Massimo; Salmona, Mario; Moscatelli, Davide; Bigini, Paolo

    2016-03-14

    An integrated platform to assess the interaction between nanocarriers and biological matrices has been developed by our group using poly methyl-methacrylate nanoparticles. In this study, we exploited this platform to evaluate the behavior of two biodegradable formulations, poly-ε-caprolactone (PCL3) and poly lactic-acid (PLA8), respectively, in cellular and animal models of triple-negative breast cancer (TNBC). Both NPs shared the main physicochemical parameters (size, shape, ζ-potential) and exclusively differentiated on the material on which they are composed. Our results showed that (1) PLA8 NPs, systemically injected in mice, underwent rapid degradation without penetration into tumors; (2) PLA8 NPs were not internalized in the human TNBC cell line (MDA-MB-231); (3) PCL3 NPs had a longer bioavailability, reached the tumor parenchyma, and efficiently penetrated in MDA-MB-231 cells. Our data highlight the relevance of the material selection to both improve bioavailability and target tropism, and make PCL3 NPs an interesting tool for the development of nanodrugs against TNBC. PMID:26791775

  11. Cellular automata modelling of biomolecular networks dynamics.

    Science.gov (United States)

    Bonchev, D; Thomas, S; Apte, A; Kier, L B

    2010-01-01

    The modelling of biological systems dynamics is traditionally performed by ordinary differential equations (ODEs). When dealing with intracellular networks of genes, proteins and metabolites, however, this approach is hindered by network complexity and the lack of experimental kinetic parameters. This opened the field for other modelling techniques, such as cellular automata (CA) and agent-based modelling (ABM). This article reviews this emerging field of studies on network dynamics in molecular biology. The basics of the CA technique are discussed along with an extensive list of related software and websites. The application of CA to networks of biochemical reactions is exemplified in detail by the case studies of the mitogen-activated protein kinase (MAPK) signalling pathway, the FAS-ligand (FASL)-induced and Bcl-2-related apoptosis. The potential of the CA method to model basic pathways patterns, to identify ways to control pathway dynamics and to help in generating strategies to fight with cancer is demonstrated. The different line of CA applications presented includes the search for the best-performing network motifs, an analysis of importance for effective intracellular signalling and pathway cross-talk. PMID:20373215

  12. Animal and cellular models of human disease

    OpenAIRE

    Arends, Mark; White, Eric; Whitelaw, Christopher

    2016-01-01

    In this eighteenth (2016) Annual Review Issue of The Journal of Pathology, we present a collection of 19 invited review articles that cover different aspects of cellular and animal models of disease. These include genetically-engineered models, chemically-induced models, naturally-occurring models, and combinations thereof, with the focus on recent methodological and conceptual developments across a wide range of human diseases.

  13. 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.

  14. Body composition analysis: Cellular level modeling of body component ratios

    OpenAIRE

    Z. Wang; Heymsfield, S. B.; PI-SUNYER, F.X.; Gallagher, D.; PIERSON, R.N.

    2008-01-01

    During the past two decades, a major outgrowth of efforts by our research group at St. Luke’s-Roosevelt Hospital is the development of body composition models that include cellular level models, models based on body component ratios, total body potassium models, multi-component models, and resting energy expenditure-body composition models. This review summarizes these models with emphasis on component ratios that we believe are fundamental to understanding human body composition during growt...

  15. 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.

  16. Antenna modeling considerations for accurate SAR calculations in human phantoms in close proximity to GSM cellular base station antennas.

    Science.gov (United States)

    van Wyk, Marnus J; Bingle, Marianne; Meyer, Frans J C

    2005-09-01

    International bodies such as International Commission on Non-Ionizing Radiation Protection (ICNIRP) and the Institute for Electrical and Electronic Engineering (IEEE) make provision for human exposure assessment based on SAR calculations (or measurements) and basic restrictions. In the case of base station exposure this is mostly applicable to occupational exposure scenarios in the very near field of these antennas where the conservative reference level criteria could be unnecessarily restrictive. This study presents a variety of critical aspects that need to be considered when calculating SAR in a human body close to a mobile phone base station antenna. A hybrid FEM/MoM technique is proposed as a suitable numerical method to obtain accurate results. The verification of the FEM/MoM implementation has been presented in a previous publication; the focus of this study is an investigation into the detail that must be included in a numerical model of the antenna, to accurately represent the real-world scenario. This is accomplished by comparing numerical results to measurements for a generic GSM base station antenna and appropriate, representative canonical and human phantoms. The results show that it is critical to take the disturbance effect of the human phantom (a large conductive body) on the base station antenna into account when the antenna-phantom spacing is less than 300 mm. For these small spacings, the antenna structure must be modeled in detail. The conclusion is that it is feasible to calculate, using the proposed techniques and methodology, accurate occupational compliance zones around base station antennas based on a SAR profile and basic restriction guidelines. PMID:15931680

  17. A Versatile Dependent Model for Heterogeneous Cellular Networks

    OpenAIRE

    Haenggi, Martin

    2013-01-01

    We propose a new model for heterogeneous cellular networks that incorporates dependencies between the layers. In particular, it places lower-tier base stations at locations that are poorly covered by the macrocells, and it includes a small-cell model for the case where the goal is to enhance network capacity.

  18. Cellular automaton-based position sensitive detector equalization

    Energy Technology Data Exchange (ETDEWEB)

    Ferrando, Nestor [Grupo de Diseno de Sistemas Digitales, Instituto de Aplicaciones de las Tecnologias de la Informacion y de las Comunicaciones Avanzadas, Universidad Politecnica de Valencia, Camino de Vera s/n, 46022 Valencia (Spain)], E-mail: nesferjo@upvnet.upv.es; Herrero, V.; Cerda, J.; Lerche, C.W.; Colom, R.J.; Gadea, R.; Martinez, J.D.; Monzo, J.M.; Mateo, F.; Sebastia, A.; Benlloch, J.M. [Grupo de Diseno de Sistemas Digitales, Instituto de Aplicaciones de las Tecnologias de la Informacion y de las Comunicaciones Avanzadas, Universidad Politecnica de Valencia, Camino de Vera s/n, 46022 Valencia (Spain)

    2009-06-01

    Indirect position detectors based on scintillator crystals lack of spacial uniformity in their response. This happens due to crystal inhomogeneities and gain differences among the photomultiplier anodes. In order to solve this, PESIC, an integrated front-end for multianode photomultiplier based nuclear imaging devices was created. One of its main features is the digitally programmable gain adjustment for every photomultiplier output. On another front, cellular automata have been proved to be a useful method for dynamic system modeling. In this paper, a cellular automaton which emulates the behavior of the scintillator crystal, the photomultiplier and the front-end is introduced. Thanks to this model, an automatic energy-based calibration of the detector can be done by configuring the cellular automaton with experimental data and making it evolve up to an stable state. This can be useful as a precalibration method of the detector.

  19. Light weight cellular structures based on aluminium

    Energy Technology Data Exchange (ETDEWEB)

    Prakash, O. [Indian Inst. of Tech., Kanpur (India); Embury, J.D.; Sinclair, C. [McMaster Univ., Hamilton, ON (Canada); Sang, H. [Queen`s Univ., Kingston, ON (Canada); Silvetti, P. [Cordoba Univ. Nacional (Argentina). Facultad de Ciencias Exactas, Fisicas y Naturales

    1997-02-01

    An interesting form of lightweight material which has emerged in the past 2 decades is metallic foam. This paper deals with the basic concepts of making metallic foams and a detailed study of foams produced from Al-SiC. In addition, some aspects of cellular solids based on honeycomb structures are outlined including the concept of producing both two-phase foams and foams with composite walls.

  20. 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.

  1. A Mathematical Model for Cisplatin Cellular Pharmacodynamics

    Directory of Open Access Journals (Sweden)

    Ardith W. El-Kareh

    2003-03-01

    Full Text Available A simple theoretical model for the cellular pharmacodynamics of cisplatin is presented. The model, which takes into account the kinetics of cisplatin uptake by cells and the intracellular binding of the drug, can be used to predict the dependence of survival (relative to controls on the time course of extracellular exposure. Cellular pharmacokinetic parameters are derived from uptake data for human ovarian and head and neck cancer cell lines. Survival relative to controls is assumed to depend on the peak concentration of DNA-bound intracellular platinum. Model predictions agree well with published data on cisplatin cytotoxicity for three different cancer cell lines, over a wide range of exposure times. In comparison with previously published mathematical models for anticancer drug pharmacodynamics, the present model provides a better fit to experimental data sets including long exposure times (∼100 hours. The model provides a possible explanation for the fact that cell kill correlates well with area under the extracellular concentration-time curve in some data sets, but not in others. The model may be useful for optimizing delivery schedules and for the dosing of cisplatin for cancer therapy.

  2. 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.

  3. Cellular worlds: a framework for modeling micro - macro dynamics

    OpenAIRE

    H Couclelis

    1985-01-01

    Cellular spaces have recently received a lot of attention in computer science and elsewhere as models capable of bridging the gap between disaggregate and aggregate description. Despite their obvious spatial interpretation, standard cell-space models are too constrained by their background conventions to be useful in realistic geographic applications. In this paper, a generalization of the cell-space principle is presented, based on discrete model theory, and then applied to a hypothetical bu...

  4. 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

  5. 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.

  6. 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.

  7. 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.

  8. Simulation of changes in heavy metal contamination in farmland soils of a typical manufacturing center through logistic-based cellular automata modeling.

    Science.gov (United States)

    Qiu, Menglong; Wang, Qi; Li, Fangbai; Chen, Junjian; Yang, Guoyi; Liu, Liming

    2016-01-01

    A customized logistic-based cellular automata (CA) model was developed to simulate changes in heavy metal contamination (HMC) in farmland soils of Dongguan, a manufacturing center in Southern China, and to discover the relationship between HMC and related explanatory variables (continuous and categorical). The model was calibrated through the simulation and validation of HMC in 2012. Thereafter, the model was implemented for the scenario simulation of development alternatives for HMC in 2022. The HMC in 2002 and 2012 was determined through soil tests and cokriging. Continuous variables were divided into two groups by odds ratios. Positive variables (odds ratios >1) included the Nemerow synthetic pollution index in 2002, linear drainage density, distance from the city center, distance from the railway, slope, and secondary industrial output per unit of land. Negative variables (odds ratios polluting enterprises, distance from the town center, soil pH, and distance from bodies of water. Categorical variables, including soil type, parent material type, organic content grade, and land use type, also significantly influenced HMC according to Wald statistics. The relative operating characteristic and kappa coefficients were 0.91 and 0.64, respectively, which proved the validity and accuracy of the model. The scenario simulation shows that the government should not only implement stricter environmental regulation but also strengthen the remediation of the current polluted area to effectively mitigate HMC.

  9. Crowd evacuation model for large sports venues based on multi-Agent and Cellular Automata technology%Agent-CA的体育场馆人群疏散模型

    Institute of Scientific and Technical Information of China (English)

    曹爱春; 杨晓艇; 侯旭东

    2013-01-01

    A crowd evacuation model for large sports venues based on multi-agent and cellular automata technology according to the behavior characteristics and rules of evacuation is proposed. The cell in the cellular space occupied by virtual individuals is taken as an independent agent, and cellular and state are encapsulated and extended to the autonomy agent, and then individual differences are realized through the design of evacuation behavior strategy as the evolution rules to reflect the individual character, physical strength, mental effect on evacuation behavior. The evacuation simulation are carried out in sports venues. The results show that the proposed model fully considers the factors. Case evacuation is closer to the reality of large sports venues shortening the time of evacuation.%根据体育场馆人群疏散的特点与规律,提出一种基于多智能体和元胞自动机相融合的大型体育场馆人群疏散模型(Agent-CA)。将元胞空间中被虚拟人个体占据的元胞视为一个独立的智能体,将元胞及其状态进行封装,扩展为具有自主性的智能体,通过设计各种人群疏散行为策略做为演化规则,实现个体的差异性以体现个人个性、体力、心理等对疏散行为的影响,对体育场馆的人群疏散进行仿真实验。结果表明,Agent-CA综合了多智能体和元胞自动机的优点,充分考虑了个体内在因素,更接近现实大型体育场馆的人群疏散情形,缩短了疏散时间。

  10. Cellular Automata Models for Diffusion of Innovations

    CERN Document Server

    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).

  11. 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.

  12. Mosquito population dynamics from cellular automata-based simulation

    Science.gov (United States)

    Syafarina, Inna; Sadikin, Rifki; Nuraini, Nuning

    2016-02-01

    In this paper we present an innovative model for simulating mosquito-vector population dynamics. The simulation consist of two stages: demography and dispersal dynamics. For demography simulation, we follow the existing model for modeling a mosquito life cycles. Moreover, we use cellular automata-based model for simulating dispersal of the vector. In simulation, each individual vector is able to move to other grid based on a random walk. Our model is also capable to represent immunity factor for each grid. We simulate the model to evaluate its correctness. Based on the simulations, we can conclude that our model is correct. However, our model need to be improved to find a realistic parameters to match real data.

  13. 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

  14. Modelling Nonlinear Sequence Generators in terms of Linear Cellular Automata

    CERN Document Server

    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.

  15. Preliminary Analysis of the efficacy of Artificial neural Network (ANN) and Cellular Automaton (CA) based Land Use Models in Urban Land-Use Planning

    Science.gov (United States)

    Harun, R.

    2013-05-01

    This research provides an opportunity of collaboration between urban planners and modellers by providing a clear theoretical foundations on the two most widely used urban land use models, and assessing the effectiveness of applying the models in urban planning context. Understanding urban land cover change is an essential element for sustainable urban development as it affects ecological functioning in urban ecosystem. Rapid urbanization due to growing inclination of people to settle in urban areas has increased the complexities in predicting that at what shape and size cities will grow. The dynamic changes in the spatial pattern of urban landscapes has exposed the policy makers and environmental scientists to great challenge. But geographic science has grown in symmetry to the advancements in computer science. Models and tools are developed to support urban planning by analyzing the causes and consequences of land use changes and project the future. Of all the different types of land use models available in recent days, it has been found by researchers that the most frequently used models are Cellular Automaton (CA) and Artificial Neural Networks (ANN) models. But studies have demonstrated that the existing land use models have not been able to meet the needs of planners and policy makers. There are two primary causes identified behind this prologue. First, there is inadequate understanding of the fundamental theories and application of the models in urban planning context i.e., there is a gap in communication between modellers and urban planners. Second, the existing models exclude many key drivers in the process of simplification of the complex urban system that guide urban spatial pattern. Thus the models end up being effective in assessing the impacts of certain land use policies, but cannot contribute in new policy formulation. This paper is an attempt to increase the knowledge base of planners on the most frequently used land use model and also assess the

  16. Car Deceleration Considering Its Own Velocity in Cellular Automata Model

    Institute of Scientific and Technical Information of China (English)

    LI Ke-Ping

    2006-01-01

    In this paper, we propose a new cellular automaton model, which is based on NaSch traffic model. In our method, when a car has a larger velocity, if the gap between the car and its leading car is not enough large, it will decrease. The aim is that the following car has a buffer space to decrease its velocity at the next time, and then avoid to decelerate too high. The simulation results show that using our model, the car deceleration is realistic, and is closer to thefield measure than that of NaSch model.

  17. Cellular automata modeling of cooperative eutectic growth

    Directory of Open Access Journals (Sweden)

    E. Olejnik

    2010-01-01

    Full Text Available The model and results of the 2D simulation of the cooperative growth of two phases in the lamellar eutectic are presented. The pro-posed model takes into account heat transfer, components diffusion and nonstationary concentration distribution in the liquid and solid phases, non-equlibrium nature of the phase transformation and kinetics of the growth, influence of the surface energy and interface curva-ture on the conditions of the thermodynamic equilibrium. For the determination of the phase interface shape the Cellular Automata tech-nique (CA was used. For the calculation of temperature and concentration distribution the numerical solution of the Fourier equation was used. The partial differential equations were solved by Finite Differences Method (FDM. The spatial position and cell sizes of CA lattice and FDM mesh are equal.Proposed model can predict the steady state growth with a constant interlamellar spacing in the regular plate eutectic, as well as some transient processes that bring to the changes of that parameters. Obtained simulation data show the solid-liquid interface changes result in the termination of lamella and enlargement of interlamellar spacing. Another simulation results illustrate a pocket formation in the center of one phase that forestalls nucleation (or intergrowth of the new lamellae of another phase. The data of the solidification study of the transparent material (CBr4 – 8,4% C2Cl6 obtained in the thin layer demonstrate the qualita-tive agreement of the simulation.

  18. An efficient Cellular Potts Model algorithm that forbids cell fragmentation

    Science.gov (United States)

    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.

  19. Modeling cellular effects of coal pollutants

    International Nuclear Information System (INIS)

    The goal of this project is to develop and test models for the dose and dose-rate dependence of biological effects of coal pollutants on mammalian cells in tissue culture. Particular attention is given to the interaction of pollutants with the genetic material (deoxyribonucleic acid, or NDA) in the cell. Unlike radiation, which can interact directly with chromatin, chemical pollutants undergo numerous changes before the ultimate carcinogen becomes covalently bound to the DNA. Synthetic vesicles formed from a phospholipid bilayer are being used to investigate chemical transformations that may occur during the transport of pollutants across cellular membranes. The initial damage to DNA is rapidly modified by enzymatic repair systems in most living organisms. A model has been developed for predicting the effects of excision repair on the survival of human cells exposed to chemical carcinogens. In addition to the excision system, normal human cells also have tolerance mechanisms that permit continued growth and division of cells without removal of the damage. We are investigating the biological effect of damage passed to daughter cells by these tolerance mechanisms

  20. 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.

  1. Parallelizing the Cellular Potts Model on graphics processing units

    Science.gov (United States)

    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.

  2. 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.

  3. Unified Stochastic Geometry Model for MIMO Cellular Networks with Retransmissions

    KAUST Repository

    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.

  4. Coverage and Economy of Cellular Networks with Many Base Stations

    CERN Document Server

    Lee, Seunghyun

    2012-01-01

    The performance of a cellular network can be significantly improved by employing many base stations (BSs), which shortens transmission distances. However, there exist no known results on quantifying the performance gains from deploying many BSs. To address this issue, we adopt a stochastic-geometry model of the downlink cellular network and analyze the mobile outage probability. Specifically, given Poisson distributed BSs, the outage probability is shown to diminish inversely with the increasing ratio between the BS and mobile densities. Furthermore, we analyze the optimal tradeoff between the performance gain from increasing the BS density and the resultant network cost accounting for energy consumption, BS hardware and backhaul cables. The optimal BS density is proved to be proportional to the square root of the mobile density and the inverse of the square root of the cost factors considered.

  5. 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.

  6. 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.

  7. Integrating cellular metabolism into a multiscale whole-body model.

    Directory of Open Access Journals (Sweden)

    Markus Krauss

    Full Text Available Cellular metabolism continuously processes an enormous range of external compounds into endogenous metabolites and is as such a key element in human physiology. The multifaceted physiological role of the metabolic network fulfilling the catalytic conversions can only be fully understood from a whole-body perspective where the causal interplay of the metabolic states of individual cells, the surrounding tissue and the whole organism are simultaneously considered. We here present an approach relying on dynamic flux balance analysis that allows the integration of metabolic networks at the cellular scale into standardized physiologically-based pharmacokinetic models at the whole-body level. To evaluate our approach we integrated a genome-scale network reconstruction of a human hepatocyte into the liver tissue of a physiologically-based pharmacokinetic model of a human adult. The resulting multiscale model was used to investigate hyperuricemia therapy, ammonia detoxification and paracetamol-induced toxication at a systems level. The specific models simultaneously integrate multiple layers of biological organization and offer mechanistic insights into pathology and medication. The approach presented may in future support a mechanistic understanding in diagnostics and drug development.

  8. A Snaking and Interweaving Bicycle Flow Model Based on Cellular Automata%基于元胞自动机的自行车流蛇行、穿插模型

    Institute of Scientific and Technical Information of China (English)

    邓建华

    2011-01-01

    通过重新定义元胞尺寸、状态值及元胞邻域,建立了自行车元胞自动机基本模型,并在基本模型中引入随机偏移概率来表达自行车不遵循车道行驶的特性.通过模型模拟运行,并对获得的自行车流参数进行分析,结果表明引入随机偏移概率能很好地描述自行车不遵循车道随机蛇行、穿插的特性.%Through the re-definition of cellular size, cellular state value and the neighborhood, The paper establishs a bicycle basic cellular automata model and introduc the stochastic offset probability in bicycle’s base cellular automata model innovatively to express the property of riding not following with one lane.Through models simulation, the paper analyzs the result of the bicycle flow-parameters of simulated models and shows that the stochastic offset probability is corresponding sufficiently to describe the bicycle’s snaking and interweaving property.

  9. The Research of Image Encryption Algorithm Based on Chaos Cellular Automata

    OpenAIRE

    Shuiping Zhang; Huijune Luo

    2012-01-01

    The Research presents an image encryption algorithm which bases on chaotic cellular automata. This algorithm makes use of features that extreme sensitivity of chaotic system to initial conditions, the cellular automaton with a high degree of parallel processing. The encryption algorithm uses two-dimensional chaotic system to Encrypt image, Then establish a cellular automaton model on the initial encrypted image. Encryption key of this algorithm is made up of the initial value by the two-dimen...

  10. A Fluid Model for Performance Analysis in Cellular Networks

    Directory of Open Access Journals (Sweden)

    Coupechoux Marceau

    2010-01-01

    Full Text Available We propose a new framework to study the performance of cellular networks using a fluid model and we derive from this model analytical formulas for interference, outage probability, and spatial outage probability. The key idea of the fluid model is to consider the discrete base station (BS entities as a continuum of transmitters that are spatially distributed in the network. This model allows us to obtain simple analytical expressions to reveal main characteristics of the network. In this paper, we focus on the downlink other-cell interference factor (OCIF, which is defined for a given user as the ratio of its outer cell received power to its inner cell received power. A closed-form formula of the OCIF is provided in this paper. From this formula, we are able to obtain the global outage probability as well as the spatial outage probability, which depends on the location of a mobile station (MS initiating a new call. Our analytical results are compared to Monte Carlo simulations performed in a traditional hexagonal network. Furthermore, we demonstrate an application of the outage probability related to cell breathing and densification of cellular networks.

  11. Cellular telephone-based radiation detection instrument

    Science.gov (United States)

    Craig, William W.; Labov, Simon E.

    2011-06-14

    A network of radiation detection instruments, each having a small solid state radiation sensor module integrated into a cellular phone for providing radiation detection data and analysis directly to a user. The sensor module includes a solid-state crystal bonded to an ASIC readout providing a low cost, low power, light weight compact instrument to detect and measure radiation energies in the local ambient radiation field. In particular, the photon energy, time of event, and location of the detection instrument at the time of detection is recorded for real time transmission to a central data collection/analysis system. The collected data from the entire network of radiation detection instruments are combined by intelligent correlation/analysis algorithms which map the background radiation and detect, identify and track radiation anomalies in the region.

  12. Cellular-automata model of the dwarf shrubs populations and communities dynamics

    OpenAIRE

    A. S. Komarov; E. V. Zubkova; P. V. Frolov

    2015-01-01

    The probabilistic cellular-automata model of development and long-time dynamics of dwarf shrub populations and communities is developed. It is based on the concept of discrete description of the plant ontogenesis and joint model approaches in terms of probabilistic cellular automata and L-systems by Lindenmayer. Short representation of the basic model allows evaluation of the approach and software implementation. The main variables of the model are a number of partial bushes in clones or area...

  13. 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.

  14. 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}).

  15. Simulation of root forms using cellular automata model

    International Nuclear Information System (INIS)

    This research aims to produce a simulation program for root forms using cellular automata model. Stephen Wolfram in his book entitled “A New Kind of Science” discusses the formation rules based on the statistical analysis. In accordance with Stephen Wolfram’s investigation, the research will develop a basic idea of computer program using Delphi 7 programming language. To best of our knowledge, there is no previous research developing a simulation describing root forms using the cellular automata model compared to the natural root form with the presence of stone addition as the disturbance. The result shows that (1) the simulation used four rules comparing results of the program towards the natural photographs and each rule had shown different root forms; (2) the stone disturbances prevent the root growth and the multiplication of root forms had been successfully modeled. Therefore, this research had added some stones, which have size of 120 cells placed randomly in the soil. Like in nature, stones cannot be penetrated by plant roots. The result showed that it is very likely to further develop the program of simulating root forms by 50 variations

  16. 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.

  17. 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.

  18. Mapping of cellular iron using hyperspectral fluorescence imaging in a cellular model of Parkinson's disease

    Science.gov (United States)

    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.

  19. Cellular Automata Model Based on Safety Distance%基于安全距离的元胞自动机交通流模型研究

    Institute of Scientific and Technical Information of China (English)

    邱小平; 于丹; 孙若晓; 杨达

    2015-01-01

    With the traffic congestion increasing significantly, traffic safety level declines and traffic accident rate increases gradually. To improve driving safety, the length of the cellular cells is fined, and the Gipps’safe distance rule is introduced to improve the NaSch model, further, a new cellular automata traffic flow model is proposed. The Gipps’safe distance rule is widely proved to have good performance in describing the vehicle driving behavior. In addition, we use the field data to calibrate and evaluate the proposed model. The numerical simulation analysis is carried out to analyze the model. Model evaluation results show that the performance of the new model is better than NaSch model. The simulation results show that the improved model can describe the traffic flow characteristics well and can reproduce free flow, synchronized flow, congestion and other traffic phenomenon in the real traffic flow. Furthermore, the study also found that the drivers’overestimation of the maximum deceleration of vehicle ahead will lead to decreased road capacity. However, the drivers’overestimation of their own vehicle maximum deceleration will increase the capacity of the road, but is likely to cause unsafe driving behaviors and increase accident rate.%随着交通拥堵状况日益显著,整体交通安全性下降,交通事故率逐渐增大。基于提高驾驶安全性考虑,细化元胞长度,引入被广泛证明在描述车辆驾驶行为方面具有很高精度的Gipps安全距离规则,对NaSch模型进行改进,提出一个新的基于安全距离的元胞自动机交通流模型。采用实测数据对模型进行标定和评估,进一步对模型进行数值模拟分析。模型评估结果显示,新建立的模型相对NaSch模型精度更高。数值模拟结果表明,改进模型能够很好地表现交通流特性,再现实际交通中的自由流、同步流及拥堵流等交通现象。此外,还发现驾驶员对前车最大

  20. Computational model of cellular metabolic dynamics

    DEFF Research Database (Denmark)

    Li, Yanjun; Solomon, Thomas; Haus, Jacob M;

    2010-01-01

    Identifying the mechanisms by which insulin regulates glucose metabolism in skeletal muscle is critical to understanding the etiology of insulin resistance and type 2 diabetes. Our knowledge of these mechanisms is limited by the difficulty of obtaining in vivo intracellular data. To quantitatively...... cytosol and mitochondria. The model simulated skeletal muscle metabolic responses to insulin corresponding to human hyperinsulinemic-euglycemic clamp studies. Insulin-mediated rate of glucose disposal was the primary model input. For model validation, simulations were compared with experimental data...... type 2 diabetes....

  1. Cellular Phone Base Stations: Technology and Exposures (invited paper)

    International Nuclear Information System (INIS)

    The principles and practice of cellular radio systems for mobile communications are presented using GSM 1800 as a reference system. In particular, the concepts of small cells and frequency re-use and the components of radio base station technology are described. Public and cellular broadcasting have been widely available for many years and a brief history is given to indicate length of exposure from these sources. National and international guidelines for safe exposure to non-ionising radiation are used by cellular operators to define exclusion zones around transmitting antennas. A methodology for calculating an exclusion zone is described, together with an example for a typical antenna configuration. Estimated levels of exposure near practical base stations are given and comparisons made with other sources of RF radiation. Finally, the digital nature of today's cellular radio systems, such as GSM, are explained and the implications described. (author)

  2. Cellular automata modeling of cooperative eutectic growth

    OpenAIRE

    E. Olejnik; E. Fraś; D. Gurgul; A. Burbelko

    2010-01-01

    The model and results of the 2D simulation of the cooperative growth of two phases in the lamellar eutectic are presented. The pro-posed model takes into account heat transfer, components diffusion and nonstationary concentration distribution in the liquid and solid phases, non-equlibrium nature of the phase transformation and kinetics of the growth, influence of the surface energy and interface curva-ture on the conditions of the thermodynamic equilibrium. For the determination of the phase ...

  3. Modeling cellular deformations using the level set formalism

    Directory of Open Access Journals (Sweden)

    Yang Liu

    2008-07-01

    Full Text Available Abstract Background Many cellular processes involve substantial shape changes. Traditional simulations of these cell shape changes require that grids and boundaries be moved as the cell's shape evolves. Here we demonstrate that accurate cell shape changes can be recreated using level set methods (LSM, in which the cellular shape is defined implicitly, thereby eschewing the need for updating boundaries. Results We obtain a viscoelastic model of Dictyostelium cells using micropipette aspiration and show how this viscoelastic model can be incorporated into LSM simulations to recreate the observed protrusion of cells into the micropipette faithfully. We also demonstrate the use of our techniques by simulating the cell shape changes elicited by the chemotactic response to an external chemoattractant gradient. Conclusion Our results provide a simple but effective means of incorporating cellular deformations into mathematical simulations of cell signaling. Such methods will be useful for simulating important cellular events such as chemotaxis and cytokinesis.

  4. Emergence, Competition and Dynamical Stabilization of Dissipative Rotating Spiral Waves in an Excitable Medium: A Computational Model Based on Cellular Automata

    CERN Document Server

    Makovetskiy, S D

    2008-01-01

    We report some qualitatively new features of emergence, competition and dynamical stabilization of dissipative rotating spiral waves (RSWs) in the cellular-automaton model of laser-like excitable media proposed in arXiv:cond-mat/0410460v2 ; arXiv:cond-mat/0602345 . Part of the observed features are caused by unusual mechanism of excitation vorticity when the RSW's core get into the surface layer of an active medium. Instead of the well known scenario of RSW collapse, which takes place after collision of RSW's core with absorbing boundary, we observed complicated transformations of the core leading to regeneration (nonlinear "reflection" from the boundary) of the RSW or even to birth of several new RSWs in the surface layer. Computer experiments on bottlenecked evolution of such the RSW-ensembles (vortex matter) are reported and a possible explanation of real experiments on spin-lattice relaxation in dilute paramagnets is proposed on the basis of an analysis of the RSWs dynamics. Chimera states in RSW-ensemble...

  5. Modeling cellular deformations using the level set formalism

    OpenAIRE

    Yang Liu; Effler Janet C; Kutscher Brett L; Sullivan Sarah E; Robinson Douglas N; Iglesias Pablo A

    2008-01-01

    Abstract Background Many cellular processes involve substantial shape changes. Traditional simulations of these cell shape changes require that grids and boundaries be moved as the cell's shape evolves. Here we demonstrate that accurate cell shape changes can be recreated using level set methods (LSM), in which the cellular shape is defined implicitly, thereby eschewing the need for updating boundaries. Results We obtain a viscoelastic model of Dictyostelium cells using micropipette aspiratio...

  6. Minimal model for complex dynamics in cellular processes.

    Science.gov (United States)

    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.

  7. Metadata Standard and Data Exchange Specifications to Describe, Model, and Integrate Complex and Diverse High-Throughput Screening Data from the Library of Integrated Network-based Cellular Signatures (LINCS).

    Science.gov (United States)

    Vempati, Uma D; Chung, Caty; Mader, Chris; Koleti, Amar; Datar, Nakul; Vidović, Dušica; Wrobel, David; Erickson, Sean; Muhlich, Jeremy L; Berriz, Gabriel; Benes, Cyril H; Subramanian, Aravind; Pillai, Ajay; Shamu, Caroline E; Schürer, Stephan C

    2014-06-01

    The National Institutes of Health Library of Integrated Network-based Cellular Signatures (LINCS) program is generating extensive multidimensional data sets, including biochemical, genome-wide transcriptional, and phenotypic cellular response signatures to a variety of small-molecule and genetic perturbations with the goal of creating a sustainable, widely applicable, and readily accessible systems biology knowledge resource. Integration and analysis of diverse LINCS data sets depend on the availability of sufficient metadata to describe the assays and screening results and on their syntactic, structural, and semantic consistency. Here we report metadata specifications for the most important molecular and cellular components and recommend them for adoption beyond the LINCS project. We focus on the minimum required information to model LINCS assays and results based on a number of use cases, and we recommend controlled terminologies and ontologies to annotate assays with syntactic consistency and semantic integrity. We also report specifications for a simple annotation format (SAF) to describe assays and screening results based on our metadata specifications with explicit controlled vocabularies. SAF specifically serves to programmatically access and exchange LINCS data as a prerequisite for a distributed information management infrastructure. We applied the metadata specifications to annotate large numbers of LINCS cell lines, proteins, and small molecules. The resources generated and presented here are freely available.

  8. The importance of volume exclusion in modelling cellular migration.

    Science.gov (United States)

    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.

  9. Cellular Automaton Model for Immunology of Tumor Growth

    CERN Document Server

    Voitikova, M

    1998-01-01

    The stochastic discrete space-time model of an immune response on tumor spreading in a two-dimensional square lattice has been developed. The immunity-tumor interactions are described at the cellular level and then transferred into the setting of cellular automata (CA). The multistate CA model for system, in which all statesoflattice sites, composing of both immune and tumor cells populations, are the functions of the states of the 12 nearest neighbors. The CA model incorporates the essential featuresof the immunity-tumor system. Three regimes of neoplastic evolution including metastatic tumor growth and screen effect by inactive immune cells surrounding a tumor have been predicted.

  10. 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.

  11. Modeling diffusion of innovations with probabilistic cellular automata

    CERN Document Server

    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.

  12. Modeling and Analysis of Cellular Networks using Stochastic Geometry: A Tutorial

    KAUST Repository

    ElSawy, Hesham

    2016-03-22

    This paper presents a tutorial on stochastic geometry (SG) based analysis for cellular networks. This tutorial is distinguished by its depth with respect to wireless communication details and its focus on cellular networks. The paper starts by modeling and analyzing the baseband interference in a basic cellular network model. Then, it characterizes signal-tointerference- plus-noise-ratio (SINR) and its related performance metrics. In particular, a unified approach to conduct error probability, outage probability, and rate analysis is presented. Although the main focus of the paper is on cellular networks, the presented unified approach applies for other types of wireless networks that impose interference protection around receivers. The paper then extends the baseline unified approach to capture cellular network characteristics (e.g., frequency reuse, multiple antenna, power control, etc.). It also presents numerical examples associated with demonstrations and discussions. Finally, we point out future research directions.

  13. A Computational model for compressed sensing RNAi cellular screening

    Directory of Open Access Journals (Sweden)

    Tan Hua

    2012-12-01

    Full Text Available Abstract Background RNA interference (RNAi becomes an increasingly important and effective genetic tool to study the function of target genes by suppressing specific genes of interest. This system approach helps identify signaling pathways and cellular phase types by tracking intensity and/or morphological changes of cells. The traditional RNAi screening scheme, in which one siRNA is designed to knockdown one specific mRNA target, needs a large library of siRNAs and turns out to be time-consuming and expensive. Results In this paper, we propose a conceptual model, called compressed sensing RNAi (csRNAi, which employs a unique combination of group of small interfering RNAs (siRNAs to knockdown a much larger size of genes. This strategy is based on the fact that one gene can be partially bound with several small interfering RNAs (siRNAs and conversely, one siRNA can bind to a few genes with distinct binding affinity. This model constructs a multi-to-multi correspondence between siRNAs and their targets, with siRNAs much fewer than mRNA targets, compared with the conventional scheme. Mathematically this problem involves an underdetermined system of equations (linear or nonlinear, which is ill-posed in general. However, the recently developed compressed sensing (CS theory can solve this problem. We present a mathematical model to describe the csRNAi system based on both CS theory and biological concerns. To build this model, we first search nucleotide motifs in a target gene set. Then we propose a machine learning based method to find the effective siRNAs with novel features, such as image features and speech features to describe an siRNA sequence. Numerical simulations show that we can reduce the siRNA library to one third of that in the conventional scheme. In addition, the features to describe siRNAs outperform the existing ones substantially. Conclusions This csRNAi system is very promising in saving both time and cost for large-scale RNAi

  14. A Computational model for compressed sensing RNAi cellular screening

    Science.gov (United States)

    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

  15. Targeted cellular ablation based on the morphology of malignant cells

    Science.gov (United States)

    Ivey, Jill W.; Latouche, Eduardo L.; Sano, Michael B.; Rossmeisl, John H.; Davalos, Rafael V.; Verbridge, Scott S.

    2015-11-01

    Treatment of glioblastoma multiforme (GBM) is especially challenging due to a shortage of methods to preferentially target diffuse infiltrative cells, and therapy-resistant glioma stem cell populations. Here we report a physical treatment method based on electrical disruption of cells, whose action depends strongly on cellular morphology. Interestingly, numerical modeling suggests that while outer lipid bilayer disruption induced by long pulses (~100 μs) is enhanced for larger cells, short pulses (~1 μs) preferentially result in high fields within the cell interior, which scale in magnitude with nucleus size. Because enlarged nuclei represent a reliable indicator of malignancy, this suggested a means of preferentially targeting malignant cells. While we demonstrate killing of both normal and malignant cells using pulsed electric fields (PEFs) to treat spontaneous canine GBM, we proposed that properly tuned PEFs might provide targeted ablation based on nuclear size. Using 3D hydrogel models of normal and malignant brain tissues, which permit high-resolution interrogation during treatment testing, we confirmed that PEFs could be tuned to preferentially kill cancerous cells. Finally, we estimated the nuclear envelope electric potential disruption needed for cell death from PEFs. Our results may be useful in safely targeting the therapy-resistant cell niches that cause recurrence of GBM tumors.

  16. Lattice gas cellular automata and lattice Boltzmann models an introduction

    CERN Document Server

    Wolf-Gladrow, Dieter A

    2000-01-01

    Lattice-gas cellular automata (LGCA) and lattice Boltzmann models (LBM) are relatively new and promising methods for the numerical solution of nonlinear partial differential equations. The book provides an introduction for graduate students and researchers. Working knowledge of calculus is required and experience in PDEs and fluid dynamics is recommended. Some peculiarities of cellular automata are outlined in Chapter 2. The properties of various LGCA and special coding techniques are discussed in Chapter 3. Concepts from statistical mechanics (Chapter 4) provide the necessary theoretical background for LGCA and LBM. The properties of lattice Boltzmann models and a method for their construction are presented in Chapter 5.

  17. 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.

  18. Modeling evolution and immune system by cellular automata

    International Nuclear Information System (INIS)

    In this review the behavior of two different biological systems is investigated using cellular automata. Starting from this spatially extended approach it is also tried, in some cases, to reduce the complexity of the system introducing mean-field approximation, and solving (or trying to solve) these simplified systems. It is discussed the biological meaning of the results, the comparison with experimental data (if available) and the different features between spatially extended and mean-field versions. The biological systems considered in this review are the following: Darwinian evolution in simple ecosystems and immune system response. In the first section the main features of molecular evolution are introduced, giving a short survey of genetics for physicists and discussing some models for prebiotic systems and simple ecosystems. It is also introduced a cellular automaton model for studying a set of evolving individuals in a general fitness landscape, considering also the effects of co-evolution. In particular the process of species formation (speciation) is described in sect. 5. The second part deals with immune system modeling. The biological features of immune response are discussed, as well as it is introduced the concept of shape space and of idiotypic network. More detailed reviews which deal with immune system models (mainly focused on idiotypic network models) can be found. Other themes here discussed: the applications of CA to immune system modeling, two complex cellular automata for humoral and cellular immune response. Finally, it is discussed the biological data and the general conclusions are drawn in the last section

  19. 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.

  20. Four Dimensional (4-D BioChemInfoPhysics Models of Cardiac Cellular and Sub-Cellular Vibrations (Oscillations

    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

  1. 基于元胞自动机理论的协同设计任务调度模型%Collaboration Design Tasks Scheduling Model Based on Cellular Automaton

    Institute of Scientific and Technical Information of China (English)

    徐鸿翔; 吴晶华; 张向华

    2011-01-01

    分析了设计任务调度的特点,提出了基于元胞自动机理论的调度模型。对元胞自动机任务调度模型进行了数学描述,对设计任务调度的策略进行了分析,建立了元胞自动机目标调度模型,通过具体算例对所提出的模型进行了验证,表明元胞自动机模型可以有效地进行任务调度的优化。%The characteristic of design tasks scheduling was analyzed,and a collaborative tasks scheduling model based on Cellular Automaton(CA) was put forward.Firstly,mathematics description was done for design tasks scheduling model based on Cellular Automaton.Secondly,the strategy for design tasks scheduling was analyzed.And so,the scheduling target model was established.Finally,a simulation experiment was carried out by using the proposed algorithm.The convergent velocity would be fast and the ability to optimize would be better.

  2. 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.

  3. Simulation Modeling by Classification of Problems: A Case of Cellular Manufacturing

    Science.gov (United States)

    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.

  4. 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.

  5. Vehicle Speed Estimation and Forecasting Methods Based on Cellular Floating Vehicle Data

    OpenAIRE

    Wei-Kuang Lai; Ting-Huan Kuo; Chi-Hua Chen

    2016-01-01

    Traffic information estimation and forecasting methods based on cellular floating vehicle data (CFVD) are proposed to analyze the signals (e.g., handovers (HOs), call arrivals (CAs), normal location updates (NLUs) and periodic location updates (PLUs)) from cellular networks. For traffic information estimation, analytic models are proposed to estimate the traffic flow in accordance with the amounts of HOs and NLUs and to estimate the traffic density in accordance with the amounts of CAs and PL...

  6. Bases of Schur algebras associated to cellularly stratified diagram algebras

    CERN Document Server

    Bowman, C

    2011-01-01

    We examine homomorphisms between induced modules for a certain class of cellularly stratified diagram algebras, including the BMW algebra, Temperley-Lieb algebra, Brauer algebra, and (quantum) walled Brauer algebra. We define the `permutation' modules for these algebras, these are one-sided ideals which allow us to study the diagrammatic Schur algebras of Hartmann, Henke, Koenig and Paget. We construct bases of these Schur algebras in terms of modified tableaux. On the way we prove that the (quantum) walled Brauer algebra and the Temperley-Lieb algebra are both cellularly stratified and therefore have well-defined Specht filtrations.

  7. Particle acceleration in a complex solar active region modelled by a Cellular automata model

    Science.gov (United States)

    Dauphin, C.; Vilmer, N.; Anastasiadis, A.

    2004-12-01

    The models of cellular automat allowed to reproduce successfully several statistical properties of the solar flares. We use a cellular automat model based on the concept of self-organised critical system to model the evolution of the magnetic energy released in an eruptive active area. Each burst of magnetic energy released is assimilated to a process of magnetic reconnection. We will thus generate several current layers (RCS) where the particles are accelerated by a direct electric field. We calculate the energy gain of the particles (ions and electrons) for various types of magnetic configuration. We calculate the distribution function of the kinetic energy of the particles after their interactions with a given number of RCS for each type of configurations. We show that the relative efficiency of the acceleration of the electrons and the ions depends on the selected configuration.

  8. Ion beam analysis based on cellular nonlinear networks

    OpenAIRE

    Senger, V.; R. Tetzlaff; H. Reichau; Ratzinger, U.

    2011-01-01

    The development of a non- destructive measurement method for ion beam parameters has been treated in various projects. Although results are promising, the high complexity of beam dynamics has made it impossible to implement a real time process control up to now. In this paper we will propose analysing methods based on the dynamics of Cellular Nonlinear Networks (CNN) that can be implemented on pixel parallel CNN based architectures and yield satisfying results even at low re...

  9. A cellular automata model of Ebola virus dynamics

    Science.gov (United States)

    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.

  10. A New Cellular Automaton Model for Traffic Flow

    Institute of Scientific and Technical Information of China (English)

    YongtaoHU

    1999-01-01

    Establishment of effective traffic models to reveal fundamental traffic characteristics is an essential requirement in the design,planning and operation of transportation systems .In 1992 Nagel and Schreckenberg presented a cellular automaton model describing traffic flow of N cars on a single lane and applied it in the famous project TRANSIMS on transportation simulation.In this paper,the author proposes a new model for the same problem and gives a comparison of simulation results with the former ones.The comparison shows that the new model works better under the condition of high traffic density.

  11. Relationship between cellular response models and biochemical mechanisms

    International Nuclear Information System (INIS)

    In most cellular response experiments, survival reflects the kinetics of a variety of damage and repair processes. Unfortunately, biochemical studies of molecular repair deal with mechanisms which cannot be readily correlated with these kinetic observations. The difference in these approaches sometimes leads to confusion over terms such as potentially-lethal and sublethal damage. These terms were introduced with operation definitions, derived from kinetic studies of cell survival, but some researchers have since attempted to associate them with specific biochemical mechanisms. Consequently, the terms are often used in totally different ways be different investigators. The use of carefully constructed models originating either out of assumptions based on mechanisms, or on kinetics, can be used to design experiments to eliminate some alternative kinetic schemes. In turn, some mechanisms may also be eliminated, resulting in a reduction in the number of mechanisms which must be investigated biochemically. One must take advantage of a wide range of specialized radiation procedures in order to accomplish this. Examples of the use of such specialized experimental designs, which have led to a more detailed understanding of the kinetics of both algal and mammalian cell responses, are discussed

  12. Finite Field Arithmetic Architecture Based on Cellular Array

    Directory of Open Access Journals (Sweden)

    Kee-Won Kim

    2015-05-01

    Full Text Available Recently, various finite field arithmetic structures are introduced for VLSI circuit implementation on cryptosystems and error correcting codes. In this study, we present an efficient finite field arithmetic architecture based on cellular semi-systolic array for Montgomery multiplication by choosing a proper Montgomery factor which is highly suitable for the design on parallel structures. Therefore, our architecture has reduced a time complexity by 50% compared to typical architecture.

  13. A Cellular Model for Screening Neuronal Nitric Oxide Synthase Inhibitors

    OpenAIRE

    Fang, Jianguo; Silverman, Richard B.

    2009-01-01

    Nitric oxide synthase (NOS) inhibitors are potential drug candidates because it has been well demonstrated that excessive production of NO critically contributes to a range of diseases. Most inhibitors have been screened in vitro using recombinant enzymes, leading to the discovery of a variety of potent compounds. To make inhibition studies more physiologically relevant and bridge the gap between the in vitro assay and in vivo studies, we report here a cellular model for screening NOS inhibit...

  14. The Research of Image Encryption Algorithm Based on Chaos Cellular Automata

    Directory of Open Access Journals (Sweden)

    Shuiping Zhang

    2012-02-01

    Full Text Available The Research presents an image encryption algorithm which bases on chaotic cellular automata. This algorithm makes use of features that extreme sensitivity of chaotic system to initial conditions, the cellular automaton with a high degree of parallel processing. The encryption algorithm uses two-dimensional chaotic system to Encrypt image, Then establish a cellular automaton model on the initial encrypted image. Encryption key of this algorithm is made up of the initial value by the two-dimensional chaotic systems, parameters, two-dimensional cellular automata local evolution rules f and iterations n. Experimental results shows that the algorithm has features that high efficiency, better security, sensitivity to the key and so on.

  15. Shape Memory Alloy-Based Periodic Cellular Structures Project

    Data.gov (United States)

    National Aeronautics and Space Administration — This SBIR Phase I effort will develop and demonstrate an innovative shape memory alloy (SMA) periodic cellular structural technology. Periodic cellular structures...

  16. Cellular Automata-Based Parallel Random Number Generators Using FPGAs

    Directory of Open Access Journals (Sweden)

    David H. K. Hoe

    2012-01-01

    Full Text Available Cellular computing represents a new paradigm for implementing high-speed massively parallel machines. Cellular automata (CA, which consist of an array of locally connected processing elements, are a basic form of a cellular-based architecture. The use of field programmable gate arrays (FPGAs for implementing CA accelerators has shown promising results. This paper investigates the design of CA-based pseudo-random number generators (PRNGs using an FPGA platform. To improve the quality of the random numbers that are generated, the basic CA structure is enhanced in two ways. First, the addition of a superrule to each CA cell is considered. The resulting self-programmable CA (SPCA uses the superrule to determine when to make a dynamic rule change in each CA cell. The superrule takes its inputs from neighboring cells and can be considered itself a second CA working in parallel with the main CA. When implemented on an FPGA, the use of lookup tables in each logic cell removes any restrictions on how the super-rules should be defined. Second, a hybrid configuration is formed by combining a CA with a linear feedback shift register (LFSR. This is advantageous for FPGA designs due to the compactness of the LFSR implementations. A standard software package for statistically evaluating the quality of random number sequences known as Diehard is used to validate the results. Both the SPCA and the hybrid CA/LFSR were found to pass all the Diehard tests.

  17. Basalt fiber reinforced porous aggregates-geopolymer based cellular material

    Science.gov (United States)

    Luo, Xin; Xu, Jin-Yu; Li, Weimin

    2015-09-01

    Basalt fiber reinforced porous aggregates-geopolymer based cellular material (BFRPGCM) was prepared. The stress-strain curve has been worked out. The ideal energy-absorbing efficiency has been analyzed and the application prospect has been explored. The results show the following: fiber reinforced cellular material has successively sized pore structures; the stress-strain curve has two stages: elastic stage and yielding plateau stage; the greatest value of the ideal energy-absorbing efficiency of BFRPGCM is 89.11%, which suggests BFRPGCM has excellent energy-absorbing property. Thus, it can be seen that BFRPGCM is easy and simple to make, has high plasticity, low density and excellent energy-absorbing features. So, BFRPGCM is a promising energy-absorbing material used especially in civil defense engineering.

  18. Infinity computations in cellular automaton forest-fire model

    Science.gov (United States)

    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.

  19. Modelling of detonation cellular structure in aluminium suspensions

    Science.gov (United States)

    Briand, A.; Veyssiere, B.; Khasainov, B. A.

    2010-12-01

    Heterogeneous detonations involving aluminium suspensions have been studied for many years for industrial safety policies, and for military and propulsion applications. Owing to their weak detonability and to the lack of available experimental results on the detonation cellular structure, numerical simulations provide a convenient way to improve the knowledge of such detonations. One major difficulty arising in numerical study of heterogeneous detonations involving suspensions of aluminium particles in oxidizing atmospheres is the modelling of aluminium combustion. Our previous two-step model provided results on the effect on the detonation cellular structure of particle diameter and characteristic chemical lengths. In this study, a hybrid model is incorporated in the numerical code EFAE, combining both kinetic and diffusion regimes in parallel. This more realistic model provides good agreement with the previous two-step model and confirms the correlations found between the detonation cell width, and particle diameter and characteristic lengths. Moreover, the linear dependence found between the detonation cell width and the induction length remains valid with the hybrid model.

  20. Cellular automata model of magnetospheric-ionospheric coupling

    OpenAIRE

    Kozelov, B. V.; Kozelova, T. V.

    2003-01-01

    We propose a cellular automata model (CAM) to describe the substorm activity of the magnetospheric-ionospheric system. The state of each cell in the model is described by two numbers that correspond to the energy content in a region of the current sheet in the magnetospheric tail and to the conductivity of the ionospheric domain that is magnetically connected with this region. The driving force of the system is supposed to be provided by the solar wind that is convected along the two b...

  1. 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.

  2. 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.

  3. A Cellular Automata Model for the Study of Landslides

    Science.gov (United States)

    Liucci, Luisa; Suteanu, Cristian; Melelli, Laura

    2016-04-01

    Power-law scaling has been observed in the frequency distribution of landslide sizes in many regions of the world, for landslides triggered by different factors, and in both multi-temporal and post-event datasets, thus indicating the universal character of this property of landslides and suggesting that the same mechanisms drive the dynamics of mass wasting processes. The reasons for the scaling behavior of landslide sizes are widely debated, since their understanding would improve our knowledge of the spatial and temporal evolution of this phenomenon. Self-Organized Critical (SOC) dynamics and the key role of topography have been suggested as possible explanations. The scaling exponent of the landslide size-frequency distribution defines the probability of landslide magnitudes and it thus represents an important parameter for hazard assessment. Therefore, another - still unanswered - important question concerns the factors on which its value depends. This paper investigates these issues using a Cellular Automata (CA) model. The CA uses a real topographic surface acquired from a Digital Elevation Model to represent the initial state of the system, where the states of cells are defined in terms of altitude. The stability criterion is based on the slope gradient. The system is driven to instability through a temporal decrease of the stability condition of cells, which may be thought of as representing the temporal weakening of soil caused by factors like rainfall. A transition rule defines the way in which instabilities lead to discharge from unstable cells to the neighboring cells, deciding upon the landslide direction and the quantity of mass involved. Both the direction and the transferred mass depend on the local topographic features. The scaling properties of the area-frequency distributions of the resulting landslide series are investigated for several rates of weakening and for different time windows, in order to explore the response of the system to model

  4. Cellular Automata Models Applied to the Study of Landslide Dynamics

    Science.gov (United States)

    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

  5. 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.

  6. Structural modeling of sandwich structures with lightweight cellular cores

    Science.gov (United States)

    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.

  7. 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.

  8. Robustness of a Cellular Automata Model for the HIV Infection

    CERN Document Server

    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...

  9. Membrane-Based Functions in the Origin of Cellular Life

    Science.gov (United States)

    Chipot, Christophe; New, Michael H.; Schweighofer, Karl; Pohorille, Andrew; Wilson, Michael A.

    1999-01-01

    Our objective is to help explain how the earliest ancestors of contemporary cells (protocells) performed their essential functions employing only the molecules available in the protobiological milieu. Our hypothesis is that vesicles, built of amphiphilic, membrane-forming materials, emerged early in protobiological evolution and served as precursors to protocells. We further assume that the cellular functions associated with contemporary membranes, such as capturing and, transducing of energy, signaling, or sequestering organic molecules and ions, evolved in these membrane environments. An alternative hypothesis is that these functions evolved in different environments and were incorporated into membrane-bound structures at some later stage of evolution. We focus on the application of the fundamental principles of physics and chemistry to determine how they apply to the formation of a primitive, functional cell. Rather than attempting to develop specific models for cellular functions and to identify the origin of the molecules which perform these functions, our goal is to define the structural and energetic conditions that any successful model must fulfill, therefore providing physico-chemical boundaries for these models. We do this by carrying out large-scale, molecular level computer simulations on systems of interest.

  10. Bilayer Beams and Relay Sharing based OFDMA Cellular Architecture

    Directory of Open Access Journals (Sweden)

    Yanxiong Pan

    2011-08-01

    Full Text Available Over the past decade, researchers have been putting a lot of energy on co-channel interference suppression in the forthcoming fourth generation (4G wireless networks. Existing approaches to interference suppression are mainly based on signal processing, cooperative communication or coordination techniques. Though good performance has been attained already, a more complex receiver is needed, and there is still room for improvement through other ways.Considering spatial frequency reuse, which provides an easier way to cope with the co-channel interference, this paper proposed a bilayer beams and relay sharing based (BBRS OFDMA cellular architecture and corresponding frequency planning scheme. The main features of the novel architecture are as follows. Firstly, the base station (BS uses two beams, one composed of six wide beams providing coverage to mobile stations (MSs that access to the BS, and the other composed of six narrow beams communicating with fixed relay stations (FRSs. Secondly, in the corresponding frequency planning scheme, soft frequency reuse is considered on all FRSs further. System-level simulation results demonstrate that better coverage performance is obtained and the mean data rate of MSs near the cell edge is improved significantly. The BBRS cellular architecture provides a practical method to interference suppression in 4G networks since a better tradeoff between performance and complexity is achieved.

  11. Measurements of Electromagnetic Fields Emitted from Cellular Base Stations in

    Directory of Open Access Journals (Sweden)

    K. J. Ali

    2013-05-01

    Full Text Available With increasing the usage of mobile communication devices and internet network information, the entry of private telecommunications companies in Iraq has been started since 2003. These companies began to build up cellular towers to accomplish the telecommunication works but they ignore the safety conditions imposed for the health and environment that are considered in random way. These negative health effects which may cause a health risk for life beings and environment pollution. The aim of this work is to determine the safe and unsafe ranges and discuss damage caused by radiation emitted from Asia cell base stations in Shirqat city and discuses the best ways in which can be minimize its exposure level to avoid its negative health effects. Practical measurements of power density around base stations has been accomplished by using a radiation survey meter type (Radio frequency EMF Strength Meter 480846 in two ways. The first way of measurements has been accomplished at a height of 2 meters above ground for different distances from (0-300 meters .The second way is at a distance of 150 meters for different levels from (2-15 meters above ground level. The maximum measured power density is about (3 mW/m2. Results indicate that the levels of power density are far below the RF radiation exposure of USSR safety standards levels. And that means these cellular base station don't cause negative the health effect for life being if the exposure is within the acceptable international standard levels.

  12. Research in dynamic evolution of software architectures based on cellular automata model%软件体系结构动态演化的元胞自动机模型研究

    Institute of Scientific and Technical Information of China (English)

    刘晓斌; 杨贯中; 欧阳柳波; 李勇军

    2015-01-01

    目前软件体系结构动态演化的元胞自动机模型存在描述单一、元胞间关系不明确、没有详细阐述动态演化过程应用约束条件的缺点。针对这些不足进行相关的研究,重新定义了软件体系结构动态演化的扩展元胞自动机模型,基于扩展元胞自动机模型结合演化应用约束条件,分析了软件体系结构的动态演化过程,运用元胞间控制约束条件和行为相关约束条件来正确地指导SA动态演化。提出了动点稳态转移的概念,对演化程度和一致性进行定义分析,此方法比以往的元胞自动机模型更能准确指导SA动态演化,促进SA动态演化的进一步研究。通过案例验证了该方法的应用价值和可行性,可以更全面地应用于软件体系结构的动态演化。%There are some defects in dynamic evolution of software architecture based on cellular automata model in recent research, including that specification is not detailed and relationship between cellular is not clear, that it can’t describe the constraints in process of dynamic evolution. In regard to these deficiencies, this paper refines the extend-cellular automata model of dynamic evolution of software architecture, which is based on the combination of evolutionary constraints applied to analyze the dynamic evolution of software architecture process, and SA dynamic evolution is correctly guided by applying both inter-cell behavior related constraints and control constraints. Besides, it puts forward the concept of steady-state transfer of moving-point for charactering the degree and consistency of evolution and can more exactly guide SA dynamic evolution than ever on cellular automata model, which advances the further study on dynamic evolution of software archi-tecture. The case study shows that the proposed method is valuable and feasible, which can be more fully applied to the dynamic evolution of software architecture.

  13. Exploring Quantum Dot Cellular Automata Based Reversible Circuit

    Directory of Open Access Journals (Sweden)

    Saroj Kumar Chandra

    2012-03-01

    Full Text Available Quantum-dot Cellular Automata (QCA is a new technology for development of logic circuits based on nanotechnology, and it is an one of the alternative for designing high performance computing over existing CMOS technology. The basic logic in QCA does not use voltage level for logic representation rather it represent binary state by polarization of electrons on the Quantum Cell which is basic building block of QCA. Extensive work is going on QCA for circuit design due to low power consumption and regularity in the circuit.. Clocking is used in QCA circuit to synchronize and control the information flow and to provide the power to run the circuit. Reversible logic design is a well-known paradigm in digital computation, and if circuit developed is reversible then it consumes very low power . Here, in this paper we are presenting a Reversible Universal Gate (RUG based on Quantum-dot Cellular Automata (QCA. The RUG implemented by QCA Designer tool and also its behavior is simulated by it.

  14. An Asynchronous Cellular Automata-Based Adaptive Illumination Facility

    Science.gov (United States)

    Bandini, Stefania; Bonomi, Andrea; Vizzari, Giuseppe; Acconci, Vito

    The term Ambient Intelligence refers to electronic environments that are sensitive and responsive to the presence of people; in the described scenario the environment itself is endowed with a set of sensors (to perceive humans or other physical entities such as dogs, bicycles, etc.), interacting with a set of actuators (lights) that choose their actions (i.e. state of illumination) in an attempt improve the overall experience of these users. The model for the interaction and action of sensors and actuators is an asynchronous Cellular Automata (CA) with memory, supporting a self-organization of the system as a response to the presence and movements of people inside it. The paper will introduce the model, as well as an ad hoc user interface for the specification of the relevant parameters of the CA transition rule that determines the overall system behaviour.

  15. Shape Memory Alloy-Based Periodic Cellular Structures Project

    Data.gov (United States)

    National Aeronautics and Space Administration — This SBIR Phase II effort will continue to develop and demonstrate an innovative shape memory alloy (SMA) periodic cellular structural technology. Periodic cellular...

  16. Modeling Recrystallization of Austenite for C-Mn Steels during Hot Deformation by Cellular Automaton

    Institute of Scientific and Technical Information of China (English)

    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.

  17. Critical Behavior in a Cellular Automata Animal Disease Transmission Model

    CERN Document Server

    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...

  18. One-Dimensional Traffic Cellular Automaton Model Based on Selective Random Deceleration%基于选择性随机减速的元胞自动机交通流模型

    Institute of Scientific and Technical Information of China (English)

    杨奕; 施帮利; 徐鹏

    2011-01-01

    在一维元胞自动机交通流SDNS模型的基础上,建立了基于选择性随机减速的元胞自动机模型(Select-CA模型).驾驶员可根据与前车的间距变化选择不同的随机减速方式,并定义了不同随机减速方式的选择条件.通过计算机数值模拟发现,当减速方式可变时,模型模拟得到的交通流流量较大,且流量、速度和车辆比例与随机减速概率密切相关.与SDNS模型相比,Select-CA模型减少了车流的阻塞现象,提高了道路的通行能力.%Based on the SDNS cellular automata(CA) traffic model,an improved single-lane traffic CA model with consideration of selectivity random deceleration is proposed.The model considers the vehicles adopting different random deceleration rules under the mutative traffic condition and introduces the rules of deceleration probability change.Numerical simulations show a complicated evolution process of traffic flow.Different values of deceleration probability have different effects on the mixed traffic flow.In the evolution process,the traffic flow is higher in the new model than in the SDNS model,indicating that the stop status of the whole traffic flow has been improved.

  19. Facilitating arrhythmia simulation: the method of quantitative cellular automata modeling and parallel running

    Directory of Open Access Journals (Sweden)

    Mondry Adrian

    2004-08-01

    Full Text Available Abstract Background Many arrhythmias are triggered by abnormal electrical activity at the ionic channel and cell level, and then evolve spatio-temporally within the heart. To understand arrhythmias better and to diagnose them more precisely by their ECG waveforms, a whole-heart model is required to explore the association between the massively parallel activities at the channel/cell level and the integrative electrophysiological phenomena at organ level. Methods We have developed a method to build large-scale electrophysiological models by using extended cellular automata, and to run such models on a cluster of shared memory machines. We describe here the method, including the extension of a language-based cellular automaton to implement quantitative computing, the building of a whole-heart model with Visible Human Project data, the parallelization of the model on a cluster of shared memory computers with OpenMP and MPI hybrid programming, and a simulation algorithm that links cellular activity with the ECG. Results We demonstrate that electrical activities at channel, cell, and organ levels can be traced and captured conveniently in our extended cellular automaton system. Examples of some ECG waveforms simulated with a 2-D slice are given to support the ECG simulation algorithm. A performance evaluation of the 3-D model on a four-node cluster is also given. Conclusions Quantitative multicellular modeling with extended cellular automata is a highly efficient and widely applicable method to weave experimental data at different levels into computational models. This process can be used to investigate complex and collective biological activities that can be described neither by their governing differentiation equations nor by discrete parallel computation. Transparent cluster computing is a convenient and effective method to make time-consuming simulation feasible. Arrhythmias, as a typical case, can be effectively simulated with the methods

  20. 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.

  1. Computer Modeling of the Earliest Cellular Structures and Functions

    Science.gov (United States)

    Pohorille, Andrew

    2000-03-01

    In the absence of extinct or extant record of protocells (the earliest ancestors of contemporary cells), the most direct way to test ourunderstanding of the origin of cellular life is to construct laboratory models of protocells. Such efforts are currently underway in the NASA Astrobiology Program. They are accompanied by computational studies aimed at explaining self-organization of simple molecules into ordered structures and developing designs for molecules that perform protocellular functions. Many of these functions, such as import of nutrients, capture and storage of energy, and response to changes in the environment are carried out by proteins bound to membranes. We will discuss a series of large-scale, molecular-level computer simulations which demonstrate (a) how small proteins (peptides)organize themselves into ordered structures at water-membrane interfaces and insert into membranes, (b) how these peptides aggregate to form membrane-spanning structures (e.g. channels), and (c) by what mechanisms such aggregates perform essential protocellular functions, such as proton transport of protons across cell walls, a key step in cellular bioenergetics. The simulations were performed using the molecular dynamics method, in which Newton's equations of motion for each atom in the system are solved iteratively. The problems of interest required simulations on multi-nanosecond time scales, which corresponded to 10^6-10^8 time steps.

  2. A Computational Model of Cellular Response to Modulated Radiation Fields

    International Nuclear Information System (INIS)

    Purpose: To develop a model to describe the response of cell populations to spatially modulated radiation exposures of relevance to advanced radiotherapies. Materials and Methods: A Monte Carlo model of cellular radiation response was developed. This model incorporated damage from both direct radiation and intercellular communication including bystander signaling. The predictions of this model were compared to previously measured survival curves for a normal human fibroblast line (AGO1522) and prostate tumor cells (DU145) exposed to spatially modulated fields. Results: The model was found to be able to accurately reproduce cell survival both in populations which were directly exposed to radiation and those which were outside the primary treatment field. The model predicts that the bystander effect makes a significant contribution to cell killing even in uniformly irradiated cells. The bystander effect contribution varies strongly with dose, falling from a high of 80% at low doses to 25% and 50% at 4 Gy for AGO1522 and DU145 cells, respectively. This was verified using the inducible nitric oxide synthase inhibitor aminoguanidine to inhibit the bystander effect in cells exposed to different doses, which showed significantly larger reductions in cell killing at lower doses. Conclusions: The model presented in this work accurately reproduces cell survival following modulated radiation exposures, both in and out of the primary treatment field, by incorporating a bystander component. In addition, the model suggests that the bystander effect is responsible for a significant portion of cell killing in uniformly irradiated cells, 50% and 70% at doses of 2 Gy in AGO1522 and DU145 cells, respectively. This description is a significant departure from accepted radiobiological models and may have a significant impact on optimization of treatment planning approaches if proven to be applicable in vivo.

  3. Modeling of solidification grain structure for Ti-45%Al alloy ingot by cellular automaton

    Institute of Scientific and Technical Information of China (English)

    WU Shi-ping; LIU Dong-rong; GUO Jing-jie; FU Heng-zhi

    2005-01-01

    A cellular automaton model for simulating grain structure formation during solidification processes of Ti45%Al(mole fraction) alloy ingot was developed, based on finite differential method for macroscopic modeling of heat transfer and a cellular automaton technique for microscopic modeling of nucleation, growth, solute redistribution and solute diffusion. The relation between the growth velocity of a dendrite tip and the local undercooling,which consists of constitutional, thermal, curvature and attachment kinetics undercooling is calculated according to the Kurz-Giovanola-Trivedi model. The effect of solidification contraction is taken into consideration. The influence of process variables upon the resultant grain structures was investigated. Special moving allocation technique was designed to minimize the computation time and memory size associated with a large number of cells. The predicted grain structures are in good agreement with the experimental results.

  4. COMPARATIVE ANALYSIS OF CONGESTION CONTROL MODELS FOR CELLULAR WIRELESS NETWORK

    Directory of Open Access Journals (Sweden)

    Falade A. J

    2015-08-01

    Full Text Available Cellular wireless systems like GSM suffer from congestion resulting in overall system degradation and poor service delivery. When the traffic demand in a geographical area is high, the input traffic rate will exceed thecapacity of the output lines. This work focused on homogenous wireless network (the network traffic and resource dimensioning that are statistically identical such that the network performance evaluation can be reduced to a system with single cell and a single traffic type. Such system can employa queuing model to evaluate the performance metric of a cell in terms of blocking probability. Five congestion control models were compared in the work to ascertain their peculiarities, they are Erlang B, Erlang C, Engset (cleared, Engset (buffered, and Bernoulli. To analyze the system, an aggregate onedimensional Markov chain wasderived, such that it describes a call arrival process under the assumption that it is Poisson distributed. The models were simulated and their results show varying performances, however the Bernoulli model (Pb5 tends to show a situation that allows more users access to the system and the congestion level remain unaffected despite increase in the number of users and the offered traffic into the system.

  5. Modeling dynamics of HIV infected cells using stochastic cellular automaton

    Science.gov (United States)

    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.

  6. Cellular automaton model of mass transport with chemical reactions

    International Nuclear Information System (INIS)

    The transport and chemical reactions of solutes are modelled as a cellular automaton in which molecules of different species perform a random walk on a regular lattice and react according to a local probabilistic rule. The model describes advection and diffusion in a simple way, and as no restriction is placed on the number of particles at a lattice site, it is also able to describe a wide variety of chemical reactions. Assuming molecular chaos and a smooth density function, we obtain the standard reaction-transport equations in the continuum limit. Simulations on one-and two-dimensional lattices show that the discrete model can be used to approximate the solutions of the continuum equations. We discuss discrepancies which arise from correlations between molecules and how these discrepancies disappear as the continuum limit is approached. Of particular interest are simulations displaying long-time behaviour which depends on long-wavelength statistical fluctuations not accounted for by the standard equations. The model is applied to the reactions a + b ↔ c and a + b → c with homogeneous and inhomogeneous initial conditions as well as to systems subject to autocatalytic reactions and displaying spontaneous formation of spatial concentration patterns. (author) 9 figs., 34 refs

  7. Cellular automaton model of crowd evacuation inspired by slime mould

    Science.gov (United States)

    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

  8. A novel fluorescence-based cellular permeability assay.

    Science.gov (United States)

    Chandra, Ankur; Barillas, Samuel; Suliman, Ahmed; Angle, Niren

    2007-04-10

    Vascular permeability is a pathologic process in many disease states ranging from metastatic progression of malignancies to ischemia-reperfusion injury. In order to more precisely study tissue, and more specifically cell layer permeability, our goal was to create a fluorescence-based assay which could quantify permeability without radioactivity or electrical impedance measurements. Human aortic endothelial cells were grown in monolayer culture on Costar-Transwell clear polyester membrane 6-well cell culture inserts. After monolayer integrity was confirmed, vascular endothelial growth factor (VEGF(165)) at varying concentrations with a fixed concentration of yellow-green fluorescent 0.04 microm carboxylate-modified FluoSpheres microspheres were placed in the luminal chamber and incubated for 24 h. When stimulated with VEGF(165) at 20, 40, 80, and 100 ng/ml, this assay system was able to detect increases in trans-layer flux of 8.2+/-2.4%, 16.0+/-3.7%, 41.5+/-4.9%, and 58.6+/-10.1% for each concentration, respectively. This represents the first fluorescence-based permeability assay with the sensitivity to detect changes in the permeability of a cell layer to fluid flux independent of protein flux; as well as being simpler and safer than previous radioactive-and impedance-based permeability assays. With the application of this in vitro assay to a variety of pathologic conditions, both the dynamics and physiology relating to cellular permeability can be more fully investigated. PMID:16962665

  9. Measurement of oxidatively generated base damage in cellular DNA

    Energy Technology Data Exchange (ETDEWEB)

    Cadet, Jean, E-mail: jean.cadet@cea.fr [Laboratoire ' Lesions des Acides Nucleiques' , SCIB-UMR-E no3 (CEA/UJF), FRE CNRS 3200, Departement de Recherche Fondamentale sur la Matiere Condensee, CEA/Grenoble, F-38054 Grenoble Cedex 9 (France); Douki, Thierry; Ravanat, Jean-Luc [Laboratoire ' Lesions des Acides Nucleiques' , SCIB-UMR-E no3 (CEA/UJF), FRE CNRS 3200, Departement de Recherche Fondamentale sur la Matiere Condensee, CEA/Grenoble, F-38054 Grenoble Cedex 9 (France)

    2011-06-03

    This survey focuses on the critical evaluation of the main methods that are currently available for monitoring single and complex oxidatively generated damage to cellular DNA. Among chromatographic methods, HPLC-ESI-MS/MS and to a lesser extent HPLC-ECD which is restricted to a few electroactive nucleobases and nucleosides are appropriate for measuring the formation of single and clustered DNA lesions. Such methods that require optimized protocols for DNA extraction and digestion are sensitive enough for measuring base lesions formed under conditions of severe oxidative stress including exposure to ionizing radiation, UVA light and high intensity UVC laser pulses. In contrast application of GC-MS and HPLC-MS methods that are subject to major drawbacks have been shown to lead to overestimated values of DNA damage. Enzymatic methods that are based on the use of DNA repair glycosylases in order to convert oxidized bases into strand breaks are suitable, even if they are far less specific than HPLC methods, to deal with low levels of single modifications. Several other methods including immunoassays and {sup 32}P-postlabeling methods that are still used suffer from drawbacks and therefore are not recommended. Another difficult topic is the measurement of oxidatively generated clustered DNA lesions that is currently achieved using enzymatic approaches and that would necessitate further investigations.

  10. Cellular Neural Network-Based Methods for Distributed Network Intrusion Detection

    OpenAIRE

    Kang Xie; Yixian Yang; Yang Xin; Guangsheng Xia

    2015-01-01

    According to the problems of current distributed architecture intrusion detection systems (DIDS), a new online distributed intrusion detection model based on cellular neural network (CNN) was proposed, in which discrete-time CNN (DTCNN) was used as weak classifier in each local node and state-controlled CNN (SCCNN) was used as global detection method, respectively. We further proposed a new method for design template parameters of SCCNN via solving Linear Matrix Inequality. Experimental resul...

  11. An Exact Path-Loss Density Model for Mobiles in a Cellular System

    OpenAIRE

    Abdulla, Mouhamed; Shayan, Yousef R.

    2013-01-01

    In trying to emulate the spatial position of wireless nodes for purpose of analysis, we rely on stochastic simulation. And, it is customary, for mobile systems, to consider a base-station radiation coverage by an ideal cell shape. For cellular analysis, a hexagon contour is always preferred mainly because of its tessellating nature. Despite this fact, largely due to its intrinsic simplicity, in literature only random dispersion model for a circular shape is known. However, if considered, this...

  12. Power System Self-organized Criticality Simulation Model Based on Cellular Automata%基于元胞自动机的电力系统自组织临界特性仿真模型

    Institute of Scientific and Technical Information of China (English)

    于群; 曹娜; 郭剑波

    2011-01-01

    将元胞自动机理论应用到电力系统大停电机理研究中,提出并建立了用元胞自动机来模拟电网故障演化的电网故障元胞自动机模型,定义了电网故障元胞自动机模型中元胞、元胞空间、规则和邻居等的构成方法。利用电网故障元胞自动机模型,仿真研究了电网故障的传播演化过程,并对电网故障的自组织临界性(SOC)进行了验证。%By applying the theory of cellular automata in the evolutionary mechanism of the power system blackout,a model for simulating power failure with cellular automata is presented.The model defines the composing method of cells,cellular space,rules,neighbors,etc.The spread and evolution of power failure is investigated using proposed model and the self-organized criticality(SOC) of the power grid failure is verified. This work is supported by State Administration of Work Safety Project(No.10-052) and State Grid Corporation of China.

  13. GIM3E: Condition-specific Models of Cellular Metabolism Developed from Metabolomics and Expression Data

    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/

  14. 基于Fisher判别和元胞自动机模型的微电网格局计算方法%An Approach to Calculate Micro-Grid's Configuration Based on Fisher Discriminant and Cellular Automata Model

    Institute of Scientific and Technical Information of China (English)

    王砚帛; 谭永东; 文菓; 杨佳

    2012-01-01

    Based on Fisher discriminant and cellular automata model an approach to calculate the configuration of micro-grid is proposed. The cell space of micro-grid is established and Fisher discriminant is utilized to obtain the macroscopic evolution rules for cell space of micro-grid. According to the diversity of micro-grid user's electricity demands and decision-making uncertainty of power transaction a local evolution rule considering neighbors' relationship is drafted, and a concept of role transition's probability is also proposed. Using Matlab, a model to simulate the time-space dynamic evolution process of micro-grid configuration is built. The availability and effectiveness of the proposed method in the calculation of micro-grid's configuration and in the simulation of time-space dynamic evolution process of micro-grid configuration are verified by simulation results.%基于Fisher判别方法和元胞自动机模型提出了一种微电网格局计算方法.建立了微电网元胞空间,运用Fisher判别方法获取微电网元胞空间的宏观演化规则,并根据微电网用户角色的多样化和电力交易决策的不确定性,制定了考虑领域关系的局部演化规则,提出了角色转化概率的概念.在Matlab环境下建立了仿真算例模拟微电网格局的时空动态演化过程.仿真结果验证了该方法对于微电网格局计算以及模拟微电网格局时空动态演化过程的可行性和有效性.

  15. Critical Behavior in Cellular Automata Animal Disease Transmission Model

    Science.gov (United States)

    Morley, P. D.; Chang, Julius

    Using 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 in a farm, there is mandatory slaughter (culling) of all livestock in an infected premise (IP). Those farms in the neighboring of 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 interactions 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 nonlocal disease transport probability can be as low as 0.01% 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 fission cascade. Finally, we calculate that the percentage of culled animals that are actually healthy is ≈30%.

  16. Modeling chemical systems using cellular automata a textbook and laboratory manual

    CERN Document Server

    Kier, Lemont B; Cheng, Chao-Kun

    2006-01-01

    Provides a practical introduction to an exciting modeling paradigm for complex systems. This book discusses the nature of scientific inquiry using models and simulations, and describes the nature of cellular automata models. It gives descriptions of how cellular automata models can be used in the study of a variety of phenomena.

  17. 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.

  18. Membrane-Based Functions in the Origin of Cellular Life

    Science.gov (United States)

    Wilson, Michael A.

    2003-01-01

    How simple membrane peptides performed such essential proto-cellular functions as transport of ions and organic matter across membranes separating the interior of the cell from the environment, capture and utilization of energy, and transduction of environmental signals, is a key question in protobiological evolution. On the basis of detailed, molecular-level computer simulations we investigate how these peptides insert into membranes, self-assemble into higher-order structures and acquire functions. We have studied the insertion of an a-helical peptide containing leucine (L) and serine (S) of the form (LSLLLSL)S into a model membrane. The transmembrane state is metastable, and approximately 15 kcal/mol is required to insert the peptide into the membrane. Investigations of dimers formed by (LSLLLSL)S and glycophorin A demonstrate how the favorable free energy of helix association can offset the unfavorable free energy of insertion, leading to self- assembly of peptide helices in the membrane. An example of a self-assembled structure is the tetrameric transmembrane pore of the influenza virus M2 protein, which is an efficient and selective voltage-gated proton channel. Our simulations explain the gating mechanism and provide guidelines how to reengineering the channel to act as a simple proton pump. In general, emergence of integral membrane proteins appears to be quite feasible and may be easier to envision than the emergence of water-soluble proteins.

  19. Opinion evolution based on cellular automata rules in small world networks

    Science.gov (United States)

    Shi, Xiao-Ming; Shi, Lun; Zhang, Jie-Fang

    2010-03-01

    In this paper, we apply cellular automata rules, which can be given by a truth table, to human memory. We design each memory as a tracking survey mode that keeps the most recent three opinions. Each cellular automata rule, as a personal mechanism, gives the final ruling in one time period based on the data stored in one's memory. The key focus of the paper is to research the evolution of people's attitudes to the same question. Based on a great deal of empirical observations from computer simulations, all the rules can be classified into 20 groups. We highlight the fact that the phenomenon shown by some rules belonging to the same group will be altered within several steps by other rules in different groups. It is truly amazing that, compared with the last hundreds of presidential voting in America, the eras of important events in America's history coincide with the simulation results obtained by our model.

  20. Ethical Perspectives on Stem Cell-based Cellular Therapies for Neurodegenerative Diseases

    DEFF Research Database (Denmark)

    Ebbesen, Mette; Pedersen, Finn Skou; Andersen, Svend;

    2012-01-01

    The effect of stem cell-based therapies for neurodegenerative diseases such as Alzheimer disease, Huntington disease, and Parkinson disease are currently being investigated. Here we specify possible therapeutic effects and possible side effects for patients and conclude that cellular therapies may....... Beauchamp and James F. Childress is based on these principles. We show that this theory is useful for analyzing complex ethical cases of biomedicine by using cellular therapy for neurodegenerative diseases as a model system. We go through the three steps in an ethical case analysis using Beauchamp...... and Childress’ principles. We explain that the ethical issues of using stem cells for therapies for neurodegenerative diseases often referred to in the literature are related to the moral status of the blastocyst and the developing embryo. We believe that these are to be seen as potential human life...

  1. 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

  2. Pickering Emulsion-Based Marbles for Cellular Capsules

    Directory of Open Access Journals (Sweden)

    Guangzhao Zhang

    2016-07-01

    Full Text Available The biodegradable cellular capsule, being prepared from simple vaporization of liquid marbles, is an ideal vehicle for the potential application of drug encapsulation and release. This paper reports the fabrication of cellular capsules via facile vaporization of Pickering emulsion marbles in an ambient atmosphere. Stable Pickering emulsion (water in oil was prepared while utilizing dichloromethane (containing poly(l-lactic acid and partially hydrophobic silica particles as oil phase and stabilizing agents respectively. Then, the Pickering emulsion marbles were formed by dropping emulsion into a petri dish containing silica particles with a syringe followed by rolling. The cellular capsules were finally obtained after the complete vaporization of both oil and water phases. The technique of scanning electron microscope (SEM was employed to research the microstructure and surface morphology of the prepared capsules and the results showed the cellular structure as expected. An in vitro drug release test was implemented which showed a sustained release property of the prepared cellular capsules. In addition, the use of biodegradable poly(l-lactic acid and the biocompatible silica particles also made the fabricated cellular capsules of great potential in the application of sustained drug release.

  3. Cellular automata model of magnetospheric-ionospheric coupling

    Directory of Open Access Journals (Sweden)

    B. V. Kozelov

    Full Text Available We propose a cellular automata model (CAM to describe the substorm activity of the magnetospheric-ionospheric system. The state of each cell in the model is described by two numbers that correspond to the energy content in a region of the current sheet in the magnetospheric tail and to the conductivity of the ionospheric domain that is magnetically connected with this region. The driving force of the system is supposed to be provided by the solar wind that is convected along the two boundaries of the system. The energy flux inside is ensured by the penetration of the energy from the solar wind into the array of cells (magnetospheric tail with a finite velocity. The third boundary (near to the Earth is closed and the fourth boundary is opened, thereby modeling the flux far away from the tail. The energy dissipation in the system is quite similar to other CAM models, when the energy in a particular cell exceeds some pre-defined threshold, and the part of the energy excess is redistributed between the neighbouring cells. The second number attributed to each cell mimics ionospheric conductivity that can allow for a part of the energy to be shed on field-aligned currents. The feedback between "ionosphere" and "magnetospheric tail" is provided by the change in a part of the energy, which is redistributed in the tail when the threshold is surpassed. The control parameter of the model is the z-component of the interplanetary magnetic field (Bz IMF, "frozen" into the solar wind. To study the internal dynamics of the system at the beginning, this control parameter is taken to be constant. The dynamics of the system undergoes several bifurcations, when the constant varies from - 0.6 to - 6.0. The Bz IMF input results in the periodic transients (activation regions and the inter-transient period decreases with the decrease of Bz. At the same time the onset of activations in the array shifts towards the "Earth". When the modulus of the Bz IMF exceeds some

  4. Realistic multi-cellular dosimetry for 177Lu-labelled antibodies: model and application

    Science.gov (United States)

    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.

  5. Unified tractable model for downlink MIMO cellular networks using stochastic geometry

    KAUST Repository

    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.

  6. 2D cellular automaton model for the evolution of active region coronal plasmas

    CERN Document Server

    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...

  7. Cellular neural network-based hybrid approach toward automatic image registration

    Science.gov (United States)

    Arun, Pattathal VijayaKumar; Katiyar, Sunil Kumar

    2013-01-01

    Image registration is a key component of various image processing operations that involve the analysis of different image data sets. Automatic image registration domains have witnessed the application of many intelligent methodologies over the past decade; however, inability to properly model object shape as well as contextual information has limited the attainable accuracy. A framework for accurate feature shape modeling and adaptive resampling using advanced techniques such as vector machines, cellular neural network (CNN), scale invariant feature transform (SIFT), coreset, and cellular automata is proposed. CNN has been found to be effective in improving feature matching as well as resampling stages of registration and complexity of the approach has been considerably reduced using coreset optimization. The salient features of this work are cellular neural network approach-based SIFT feature point optimization, adaptive resampling, and intelligent object modelling. Developed methodology has been compared with contemporary methods using different statistical measures. Investigations over various satellite images revealed that considerable success was achieved with the approach. This system has dynamically used spectral and spatial information for representing contextual knowledge using CNN-prolog approach. This methodology is also illustrated to be effective in providing intelligent interpretation and adaptive resampling.

  8. Mechanistic Modelling of DNA Repair and Cellular Survival Following Radiation-Induced DNA Damage.

    Science.gov (United States)

    McMahon, Stephen J; Schuemann, Jan; Paganetti, Harald; Prise, Kevin M

    2016-01-01

    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 R(2) > 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. PMID:27624453

  9. 基于元胞自动机模型的开采沉陷模拟%Simulation of Coal Mining Subsidence Based on the Model of Cellular Automata

    Institute of Scientific and Technical Information of China (English)

    陈秋计

    2013-01-01

    The simulation of mining subsidence plays an important role in mining environmental management and ecological restoration. Based on the GIS platform, the mining subsidence theory and geographical Cellular Automata (CA) are combined with each other, and then the mining subsidence cellular space is constructed by using the development tool of object-oriented method with the help of software of VS2010. The mining subsidence frame structure of CA model and realization method is discussed, and the mining subsidence simulation object relation graph is constructed. The evolution model of CA for mining subsidence is established based on the research result. Finally, the prototype system of mining subsidence CA is developed by taking a coal mine in Shanxi Province as an example. Based on the coal seam condition and mining method of the study area, the evolution of mining subsidence in the future is simulated usi ng the prototype system in order to provide the basis for land reclamation and ecological restoration. The results show that object-oriented method is good for the analysis and exploitation of mining subsidence simulation system, and mining subsidence simulation based on GIS and CA, which is facilitated to the development of the system and has good compatibility, is able to show more spatiotemporal information, facilitating data management. In space division, the CA model could organically integrate into traditional method, and is able to accurately predict the future of surface subsidence damage, providing the basis for the treatment for subsidence area. Since mining subsidence relates to many subjects, there are many works need to be down in the future for further perfecting evolution model, exploring the evolution process of system in three-dimensional space, and enhancing the reality and practicability of simulation.%开采沉陷模拟对矿区的环境治理和生态恢复具有重要意义.本文将开采沉陷理论与地理元胞自动

  10. CELLULAR AUTOMATA MODELLING OF GRAIN COARSENING DURING REIHEATING AND VALIDATION WITH THE EXPERIMENTAL RESULTS

    Institute of Scientific and Technical Information of China (English)

    W.H. Yu; E.J. Palmiere; S.P. Banks; J.T. Han

    2005-01-01

    A novel 2D cellular automata (CA) model has been developed for description of normal grain coarsening and abnormal grain coarsening process. The program reflects the grain coarsening quite well even through the average grain size becomes very large. Follow results have been obtained: (a) The model reflect the normal grain growth kinetics gradually increase with probability and grain growth speed can be controlled. Based on this result, temperature can be coupled in the model. (b) Abnormal grain growth is modelled successfully. (c) Methodology has been put forward to find the relationship between the experiment results and modelling results. The experimental work on the grain coarsening has been carried out. Graphical output matched the realistic microstructure in every detail. Because many physical parameters can be taken into account in the CA programme, this CA model could not only qualitatively demonstrate the grain growth process, but also quantitatively predict and analyse the grain coarsening process.

  11. Genetic Algorithm Calibration of Probabilistic Cellular Automata for Modeling Mining Permit Activity

    Science.gov (United States)

    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.

  12. A self-modifying cellular automaton model of historical urbanization in the San Francisco Bay area

    Science.gov (United States)

    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.

  13. Bioinspired Collagen/Glycosaminoglycan-Based Cellular Microenvironments for Tuning Osteoclastogenesis.

    Science.gov (United States)

    Rother, Sandra; Salbach-Hirsch, Juliane; Moeller, Stephanie; Seemann, Thomas; Schnabelrauch, Matthias; Hofbauer, Lorenz C; Hintze, Vera; Scharnweber, Dieter

    2015-10-28

    Replicating the biocomplexity of native extracellular matrices (ECM) is critical for a deeper understanding of biochemical signals influencing bone homeostasis. This will foster the development of bioinspired biomaterials with adjustable bone-inducing properties. Collagen-based coatings containing single HA derivatives have previously been reported to promote osteogenic differentiation and modulate osteoclastogenesis and resorption depending on their sulfation degree. However, the potential impact of different GAG concentrations as well as the interplay of multiple GAGs in these coatings is not characterized in detail to date. These aspects were addressed in the current study by integrating HA and different sulfate-modified HA derivatives (sHA) during collagen in vitro fibrillogenesis. Besides cellular microenvironments with systematically altered single-GAG concentrations, matrices containing both low and high sHA (sHA1, sHA4) were characterized by biochemical analysis such as agarose gel electrophoresis, performed for the first time with sHA derivatives. The morphology and composition of the collagen coatings were altered in a GAG sulfation- and concentration-dependent manner. In multi-GAG microenvironments, atomic force microscopy revealed intermediate collagen fibril structures with thin fibrils and microfibrils. GAG sulfation altered the surface charge of the coatings as demonstrated by ζ-potential measurements revealed for the first time as well. This highlights the prospect of GAG-containing matrices to adjust defined surface charge properties. The sHA4- and the multi-GAG coatings alike significantly enhanced the viability of murine osteoclast-precursor-like RAW264.7 cells. Although in single-GAG matrices there was no dose-dependent effect on cell viability, osteoclastogenesis was significantly suppressed only on sHA4-coatings in a dose-dependent fashion. The multi-GAG coatings led to an antiosteoclastogenic effect in-between those with single-GAGs which

  14. 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.

  15. 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.

  16. Accurate assessment of cell density in low cellular liquid-based cervical cytology

    NARCIS (Netherlands)

    Siebers, A.G.; Laak, J.A.W.M. van der; Huberts-Manders, R.; Vedder, J.E.M.; Bulten, J.

    2013-01-01

    A. G. Siebers, J. A. W. M. van der Laak, R. Huberts-Manders, J. E. M. Vedder and J. Bulten Accurate assessment of cell density in low cellular liquid-based cervical cytology Objective: Scant cellularity is the most important source of unsatisfactory liquid-based cytology. Although still being debate

  17. Transfer matrix modeling and experimental validation of cellular porous material with resonant inclusions.

    Science.gov (United States)

    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.

  18. Cellular models and therapies for age-related macular degeneration

    Directory of Open Access Journals (Sweden)

    David L. Forest

    2015-05-01

    Full Text Available Age-related macular degeneration (AMD is a complex neurodegenerative visual disorder that causes profound physical and psychosocial effects. Visual impairment in AMD is caused by the loss of retinal pigmented epithelium (RPE cells and the light-sensitive photoreceptor cells that they support. There is currently no effective treatment for the most common form of this disease (dry AMD. A new approach to treating AMD involves the transplantation of RPE cells derived from either human embryonic or induced pluripotent stem cells. Multiple clinical trials are being initiated using a variety of cell therapies. Although many animal models are available for AMD research, most do not recapitulate all aspects of the disease, hampering progress. However, the use of cultured RPE cells in AMD research is well established and, indeed, some of the more recently described RPE-based models show promise for investigating the molecular mechanisms of AMD and for screening drug candidates. Here, we discuss innovative cell-culture models of AMD and emerging stem-cell-based therapies for the treatment of this vision-robbing disease.

  19. Evolutionary Computational Method of Facial Expression Analysis for Content-based Video Retrieval using 2-Dimensional Cellular Automata

    CERN Document Server

    Geetha, P

    2010-01-01

    In this paper, Deterministic Cellular Automata (DCA) based video shot classification and retrieval is proposed. The deterministic 2D Cellular automata model captures the human facial expressions, both spontaneous and posed. The determinism stems from the fact that the facial muscle actions are standardized by the encodings of Facial Action Coding System (FACS) and Action Units (AUs). Based on these encodings, we generate the set of evolutionary update rules of the DCA for each facial expression. We consider a Person-Independent Facial Expression Space (PIFES) to analyze the facial expressions based on Partitioned 2D-Cellular Automata which capture the dynamics of facial expressions and classify the shots based on it. Target video shot is retrieved by comparing the similar expression is obtained for the query frame's face with respect to the key faces expressions in the database video. Consecutive key face expressions in the database that are highly similar to the query frame's face, then the key faces are use...

  20. Stochastic Models of Vesicular Sorting in Cellular Organelles

    CERN Document Server

    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...

  1. A material optimization model to approximate energy bounds for cellular materials under multiload conditions

    DEFF Research Database (Denmark)

    Guedes, J.M.; Rodrigues, H.C.; Bendsøe, Martin P.

    2003-01-01

    This paper describes a computational model, based on inverse homogenization and topology design, for approximating energy bounds for two-phase composites under multiple load cases. The approach allows for the identification of possible single-scale cellular materials that give rise to the optimal...... bounds within this class of composites. A comparison of the computational results with the globally optimal bounds given via rank-N layered composites illustrates the behaviour for tension and shear load situations, as well as the importance of considering the shape of the basic unit cell as part...

  2. Empirical results for pedestrian dynamics and their implications for cellular automata models

    CERN Document Server

    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.

  3. Modelling of Eutectic Saturation Influence on Microstructure in Thin Wall Ductile Iron Casting Using Cellular Automata

    Directory of Open Access Journals (Sweden)

    M. Górny

    2012-12-01

    Full Text Available The mathematical model of the globular eutectic solidification in 2D was designed. Proposed model is based on the Cellular AutomatonFinite Differences (CA-FD calculation method. Model has been used for studies of the primary austenite and of globular eutectic grainsgrowth during the ductile iron solidification in the thin wall casting. Model takes into account, among other things, non-uniformtemperature distribution in the casting wall cross-section, kinetics of the austenite and graphite grains nucleation, and non-equilibriumnature of the interphase boundary migration. Calculation of eutectic saturation influence (Sc = 0.9 - 1.1 on microstructure (austenite and graphite fraction, density of austenite and graphite grains and temperature curves in 2 mm wall ductile iron casting has been done.

  4. The Algorithm of Continuous Optimization Based on the Modified Cellular Automaton

    Directory of Open Access Journals (Sweden)

    Oleg Evsutin

    2016-08-01

    Full Text Available This article is devoted to the application of the cellular automata mathematical apparatus to the problem of continuous optimization. The cellular automaton with an objective function is introduced as a new modification of the classic cellular automaton. The algorithm of continuous optimization, which is based on dynamics of the cellular automaton having the property of geometric symmetry, is obtained. The results of the simulation experiments with the obtained algorithm on standard test functions are provided, and a comparison between the analogs is shown.

  5. Convergence and attractivity of memristor-based cellular neural networks with time delays.

    Science.gov (United States)

    Qin, Sitian; Wang, Jun; Xue, Xiaoping

    2015-03-01

    This paper presents theoretical results on the convergence and attractivity of memristor-based cellular neural networks (MCNNs) with time delays. Based on a realistic memristor model, an MCNN is modeled using a differential inclusion. The essential boundedness of its global solutions is proven. The state of MCNNs is further proven to be convergent to a critical-point set located in saturated region of the activation function, when the initial state locates in a saturated region. It is shown that the state convergence time period is finite and can be quantitatively estimated using given parameters. Furthermore, the positive invariance and attractivity of state in non-saturated regions are also proven. The simulation results of several numerical examples are provided to substantiate the results. PMID:25562569

  6. Simulation of emotional contagion using modified SIR model: A cellular automaton approach

    Science.gov (United States)

    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.

  7. A new cellular automata model of traffic flow with negative exponential weighted look-ahead potential

    Science.gov (United States)

    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).

  8. Predictive model to describe water migration in cellular solid foods during storage

    NARCIS (Netherlands)

    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

  9. 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...

  10. Effect of morphology on water sorption in cellular solid foods. Part I: Pore scale network model

    NARCIS (Netherlands)

    Esveld, D.C.; Sman, van der R.G.M.; Dalen, van G.; Duynhoven, van J.P.M.; Meinders, M.B.J.

    2012-01-01

    A pore scale network model is developed to predict the dynamics of moisture diffusion into complex cellular solid foods like bread, crackers, and cereals. The morphological characteristics of the sample, including the characteristics of each cellular void and the open pore connections between them a

  11. Predictive model to describe water migration in cellular solid foods during storage

    NARCIS (Netherlands)

    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

  12. Rapid detection of biothreat agents based on cellular machinery.

    Energy Technology Data Exchange (ETDEWEB)

    Lane, Todd W.; Gantt, Richard W.

    2004-12-01

    This research addresses rapid and sensitive identification of biological agents in a complex background. We attempted to devise a method by which the specificity of the cellular transcriptional machinery could be used to detect and identify bacterial bio-terror agents in a background of other organisms. Bacterial cells contain RNA polymerases and transcription factors that transcribe genes into mRNA for translation into proteins. RNA polymerases in conjunction with transcription factors recognize regulatory elements (promoters) upstream of the gene. These promoters are, in many cases, recognized by the polymerase and transcription factor combinations of one species only. We have engineered a plasmid, for Escherichia coli, containing the virA promoter from the target species Shigella flexneri. This promoter was fused to a reporter gene Green Fluorescent Protein (GFP). In theory the indicator strain (carrying the plasmid) is mixed with the target strain and the two are lysed. The cellular machinery from both cells mixes and the GFP is produced. This report details the results of testing this system.

  13. Modeling of the competition life cycle using the software complex of cellular automata PyCAlab

    Science.gov (United States)

    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.

  14. 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.

  15. Medical image segmentation based on cellular neural network

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The application of cellular neural network (CNN) has made great progress in image processing. When the selected objects extraction (SOE) CNN is applied to gray scale images, its effects depend on the choice of initial points. In this paper, we take medical images as an example to analyze this limitation. Then an improved algorithm is proposed in which we can segment any gray level objects regardless of the limitation stated above. We also use the gradient information and contour detection CNN to determine the contour and ensure the veracity of segmentation effectively. Finally, we apply the improved algorithm to tumor segmentation of the human brain MR image. The experimental results show that the algorithm is practical and effective.

  16. Cellular-automata model of the dwarf shrubs populations and communities dynamics

    Directory of Open Access Journals (Sweden)

    A. S. Komarov

    2015-06-01

    Full Text Available The probabilistic cellular-automata model of development and long-time dynamics of dwarf shrub populations and communities is developed. It is based on the concept of discrete description of the plant ontogenesis and joint model approaches in terms of probabilistic cellular automata and L-systems by Lindenmayer. Short representation of the basic model allows evaluation of the approach and software implementation. The main variables of the model are a number of partial bushes in clones or area projective cover. The model allows us to investigate the conditions of self-maintenance and sustainability population under different environmental conditions (inaccessibility of the territory for settlement, mosaic moisture conditions of soil and wealth. The model provides a forecast of the total biomass dynamics shrubs and their fractions (stems, leaves, roots, fine roots, fruits on the basis of the data obtained in the discrete description of ontogenesis and further information on the productivity of the plant fractions. The inclusion of the joint dynamics of biomass of shrubs and soil in EFIMOD models cycle of carbon and nitrogen to evaluate the role of shrubs in these circulations, especially at high impact, such as forest fires and clear cutting, allow forecasting of the dynamics of populations and ecosystem functions of shrubs (regulation of biogeochemical cycles maintaining biodiversity, participation in the creation of non-wood products with changing climatic conditions and strong damaging effects (logging, fires; and application of the models developed to investigate the stability and productivity of shrubs and their participation in the cycle of carbon and nitrogen in different climatic and edaphic conditions.

  17. 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.

  18. Transition between immune and disease states in a cellular automaton model of clonal immune response

    CERN Document Server

    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...

  19. Modeling collective & intelligent decision making of multi-cellular populations.

    Science.gov (United States)

    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.

  20. An event-driven model simulating fundamental seismic characteristics with the use of cellular automata

    Science.gov (United States)

    Pavlou, L.; Georgoudas, I. G.; Sirakoulis, G. Ch.; Scordilis, E. M.; Andreadis, I.

    This paper presents an extensive simulation tool based on a Cellular Automata (CA) system that models fundamental seismic characteristics of a region. The CA-based dynamic model consists of cells-charges and it is used for the simulation of the earthquake process. The simulation tool has remarkably accelerated the response of the model by incorporating principles of the High Performance Computing (HPC). Extensive programming features of parallel computing have been applied, thus improving its processing effectiveness. The tool implements an enhanced (or hyper-) 2-dimensional version of the proposed CA model. Regional characteristics that depend on the seismic background of the area under study are assigned to the model with the application of a user-friendly software environment. The model is evaluated with real data that correspond to a circular region around Skyros Island, Greece, for different time periods, as for example one of 45 years (1901-1945). The enhanced 2-dimensional version of the model incorporates all principal characteristics of the 2-dimensional one, also including groups of CA cells that interact with others, located to a considerable distance in an attempt to simulate long-range interaction. The advanced simulation tool has been thoroughly evaluated. Several measurements have been made for different critical states, as well as for various cascade (earthquake) sizes, cell activities and different neighbourhood sizes. Simulation results qualitatively approach the Gutenberg-Richter (GR) scaling law and reveal fundamental characteristics of the system.

  1. Computational models of atrial cellular electrophysiology and calcium handling, and their role in atrial fibrillation.

    Science.gov (United States)

    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

  2. In vivo and in vitro cellular response to PEG-based hydrogels for wound repair

    Science.gov (United States)

    Waldeck, Heather

    Biomaterials are continuously being explored as a means to support, improve, or influence wound healing processes. Understanding the determining factors controlling the host response to biomaterials is crucial in developing strategies to employ materials for biomedical uses. In order to evaluate the host response to poly(ethylene glycol) (PEG)-based hydrogels, both in vivo and in vitro studies were performed to determine its efficacy as a dermal wound treatment and to investigate the mechanisms controlling cell-material interaction, respectively. The results of an in vivo study using a full thickness wound in a rat model demonstrated that both soluble and immobilized bioactive factors could be incorporated into a PEG-based semi-interpenetrating network (sIPN) to enhance the rate and the quality of dermal wound healing. To gain a better understanding of the results observed in vivo, in vitro studies were then conducted to examine the dynamics and mechanisms of the cell-material interaction. Degradation of the sIPN was explored as an influential factor in both mediating cellular response and controlling solute transport from the material. As degradation through gelatin dissolution could be influenced by simple alterations to the material formulation, these results provide facile guidelines to control the delivery of high molecular weight compounds. Further investigation of the cellular response to PEG-based biomaterials focused on key factors influencing cell-material interaction. Specifically, the role of the beta1 integrin subunit and several serum proteins (TGF-aalpha, IL-1beta and PDGF-BB) in mediating cellular response was explored. As cell-material interactions are based on commonly occurring interfaces between cells and molecules of the native extracellular environment, these studies provided insight into the mechanisms controlling the observed cellular response. Finally, the inflammatory response of primary monocytes to biomaterials was examined. Monocytes

  3. The natural alternative: protozoa as cellular models for Legionella infection.

    Science.gov (United States)

    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.

  4. A federation of simulations based on cellular automata in cyber-physical systems

    Directory of Open Access Journals (Sweden)

    Hoang Van Tran

    2016-02-01

    Full Text Available In cyber-physical system (CPS, cooperation between a variety of computational and physical elements usually poses difficulties to current modelling and simulation tools. Although much research has proposed to address those challenges, most solutions do not completely cover uncertain interactions in CPS. In this paper, we present a new approach to federate simulations for CPS. A federation is a combination of, and coordination between simulations upon a standard of communication. In addition, a mixed simulation is defined as several parallel simulations federated in a common time progress. Such simulations run on the models of physical systems, which are built based on cellular automata theory. The experimental results are performed on a federation of three simulations of forest fire spread, river pollution diffusion and wireless sensor network. The obtained results can be utilized to observe and predict the behaviours of physical systems in their interactions.

  5. Cellular automata-based artificial life system of horizontal gene transfer

    Directory of Open Access Journals (Sweden)

    Ji-xin Liu

    2016-02-01

    Full Text Available Mutation and natural selection is the core of Darwin's idea about evolution. Many algorithms and models are based on this idea. However, in the evolution of prokaryotes, more and more researches have indicated that horizontal gene transfer (HGT would be much more important and universal than the authors had imagined. Owing to this mechanism, the prokaryotes not only become adaptable in nearly any environment on Earth, but also form a global genetic bank and a super communication network with all the genes of the prokaryotic world. Under this background, they present a novel cellular automata model general gene transfer to simulate and study the vertical gene transfer and HGT in the prokaryotes. At the same time, they use Schrodinger's life theory to formulate some evaluation indices and to discuss the intelligence and cognition of prokaryotes which is derived from HGT.

  6. An Analysis of Base Station Location Accuracy within Mobile-Cellular Networks

    Directory of Open Access Journals (Sweden)

    Liam Smit

    2015-05-01

    Full Text Available An important feature within a mobile-cellular net- work is that the location of a cellphone can be determined. As long as the cellphone is powered on, the location of the cellphone can always be traced to at least the cell from which it is receiving, or last received, signal from the cellular network. Such network-based methods of estimating the location of a cellphone is useful in cases where the cellphone user is unable or unwilling to reveal his or her location, and have practical value in digital forensic investigations. This study investigates the accuracy of using mobile-cellular network base station information for estimating the location of cellphones. Through quantitative analysis of mobile-cellular network base station data, large variations between the best and worst accuracy of recorded location information is exposed. Thus, depending on the requirements, base station locations may or may not be accurate enough for a particular application.

  7. Symbolic Computation Using Cellular Automata-Based Hyperdimensional Computing.

    Science.gov (United States)

    Yilmaz, Ozgur

    2015-12-01

    This letter introduces a novel framework of reservoir computing that is capable of both connectionist machine intelligence and symbolic computation. A cellular automaton is used as the reservoir of dynamical systems. Input is randomly projected onto the initial conditions of automaton cells, and nonlinear computation is performed on the input via application of a rule in the automaton for a period of time. The evolution of the automaton creates a space-time volume of the automaton state space, and it is used as the reservoir. The proposed framework is shown to be capable of long-term memory, and it requires orders of magnitude less computation compared to echo state networks. As the focus of the letter, we suggest that binary reservoir feature vectors can be combined using Boolean operations as in hyperdimensional computing, paving a direct way for concept building and symbolic processing. To demonstrate the capability of the proposed system, we make analogies directly on image data by asking, What is the automobile of air?

  8. The cellular bases of antibody responses during dengue virus infection

    Directory of Open Access Journals (Sweden)

    Juan Carlos Yam-Puc

    2016-06-01

    Full Text Available Dengue virus (DENV is one of the most significant human viral pathogens transmitted by mosquitoes and can cause from an asymptomatic disease to mild undifferentiated fever, classical dengue, and severe dengue. Neutralizing memory antibody (Ab responses are one of the most important mechanisms that counteract reinfections and are therefore the main aim of vaccination. However, it has also been proposed that in dengue, some of these class-switched (IgG memory Abs might worsen the disease. Although these memory Abs derive from B cells by T-cell dependent processes, we know rather little about the (acute, chronic or memory B cell responses and the complex cellular mechanisms generating these Abs during DENV infections.This review aims to provide an updated and comprehensive perspective of the B cell responses during DENV infection, starting since the very early events like the cutaneous DENV entrance and the arrival into draining lymph nodes, to the putative B cell activation, proliferation and germinal centers (GCs formation (the source of affinity-matured class-switched memory Abs, till the outcome of GC reactions such as the generation of plasmablasts, Ab-secreting plasma cells and memory B cells. We discuss topics very poorly explored such as the possibility of B cell infection by DENV or even activation-induced B cell death. The current information about the nature of the Ab responses to DENV is also illustrated.

  9. The Cellular Bases of Antibody Responses during Dengue Virus Infection

    Science.gov (United States)

    Yam-Puc, Juan Carlos; Cedillo-Barrón, Leticia; Aguilar-Medina, Elsa Maribel; Ramos-Payán, Rosalío; Escobar-Gutiérrez, Alejandro; Flores-Romo, Leopoldo

    2016-01-01

    Dengue virus (DENV) is one of the most significant human viral pathogens transmitted by mosquitoes and can cause from an asymptomatic disease to mild undifferentiated fever, classical dengue, and severe dengue. Neutralizing memory antibody (Ab) responses are one of the most important mechanisms that counteract reinfections and are therefore the main aim of vaccination. However, it has also been proposed that in dengue, some of these class-switched (IgG) memory Abs might worsen the disease. Although these memory Abs derive from B cells by T-cell-dependent processes, we know rather little about the (acute, chronic, or memory) B cell responses and the complex cellular mechanisms generating these Abs during DENV infections. This review aims to provide an updated and comprehensive perspective of the B cell responses during DENV infection, starting since the very early events such as the cutaneous DENV entrance and the arrival into draining lymph nodes, to the putative B cell activation, proliferation, and germinal centers (GCs) formation (the source of affinity-matured class-switched memory Abs), till the outcome of GC reactions such as the generation of plasmablasts, Ab-secreting plasma cells, and memory B cells. We discuss topics very poorly explored such as the possibility of B cell infection by DENV or even activation-induced B cell death. The current information about the nature of the Ab responses to DENV is also illustrated. PMID:27375618

  10. The Cellular Bases of Antibody Responses during Dengue Virus Infection.

    Science.gov (United States)

    Yam-Puc, Juan Carlos; Cedillo-Barrón, Leticia; Aguilar-Medina, Elsa Maribel; Ramos-Payán, Rosalío; Escobar-Gutiérrez, Alejandro; Flores-Romo, Leopoldo

    2016-01-01

    Dengue virus (DENV) is one of the most significant human viral pathogens transmitted by mosquitoes and can cause from an asymptomatic disease to mild undifferentiated fever, classical dengue, and severe dengue. Neutralizing memory antibody (Ab) responses are one of the most important mechanisms that counteract reinfections and are therefore the main aim of vaccination. However, it has also been proposed that in dengue, some of these class-switched (IgG) memory Abs might worsen the disease. Although these memory Abs derive from B cells by T-cell-dependent processes, we know rather little about the (acute, chronic, or memory) B cell responses and the complex cellular mechanisms generating these Abs during DENV infections. This review aims to provide an updated and comprehensive perspective of the B cell responses during DENV infection, starting since the very early events such as the cutaneous DENV entrance and the arrival into draining lymph nodes, to the putative B cell activation, proliferation, and germinal centers (GCs) formation (the source of affinity-matured class-switched memory Abs), till the outcome of GC reactions such as the generation of plasmablasts, Ab-secreting plasma cells, and memory B cells. We discuss topics very poorly explored such as the possibility of B cell infection by DENV or even activation-induced B cell death. The current information about the nature of the Ab responses to DENV is also illustrated. PMID:27375618

  11. Combined Base Station Association and Power Control in Multi-channel Cellular Networks

    CERN Document Server

    Singh, Chandramani; Sundaresan, Rajesh

    2011-01-01

    A combined base station association and power control problem is studied for the uplink of multichannel multicell cellular networks, in which each channel is used by exactly one cell (i.e., base station). A distributed association and power update algorithm is proposed and shown to converge to a Nash equilibrium of a noncooperative game. We consider network models with discrete mobiles (yielding an atomic congestion game), as well as a continuum of mobiles (yielding a population game). We find that the equilibria need not be Pareto efficient, nor need they be system optimal. To address the lack of system optimality, we propose pricing mechanisms. It is shown that these mechanisms can be implemented in a distributed fashion.

  12. Cellular Neural Network-Based Methods for Distributed Network Intrusion Detection

    Directory of Open Access Journals (Sweden)

    Kang Xie

    2015-01-01

    Full Text Available According to the problems of current distributed architecture intrusion detection systems (DIDS, a new online distributed intrusion detection model based on cellular neural network (CNN was proposed, in which discrete-time CNN (DTCNN was used as weak classifier in each local node and state-controlled CNN (SCCNN was used as global detection method, respectively. We further proposed a new method for design template parameters of SCCNN via solving Linear Matrix Inequality. Experimental results based on KDD CUP 99 dataset show its feasibility and effectiveness. Emerging evidence has indicated that this new approach is affordable to parallelism and analog very large scale integration (VLSI implementation which allows the distributed intrusion detection to be performed better.

  13. Vehicle Speed Estimation and Forecasting Methods Based on Cellular Floating Vehicle Data

    Directory of Open Access Journals (Sweden)

    Wei-Kuang Lai

    2016-02-01

    Full Text Available Traffic information estimation and forecasting methods based on cellular floating vehicle data (CFVD are proposed to analyze the signals (e.g., handovers (HOs, call arrivals (CAs, normal location updates (NLUs and periodic location updates (PLUs from cellular networks. For traffic information estimation, analytic models are proposed to estimate the traffic flow in accordance with the amounts of HOs and NLUs and to estimate the traffic density in accordance with the amounts of CAs and PLUs. Then, the vehicle speeds can be estimated in accordance with the estimated traffic flows and estimated traffic densities. For vehicle speed forecasting, a back-propagation neural network algorithm is considered to predict the future vehicle speed in accordance with the current traffic information (i.e., the estimated vehicle speeds from CFVD. In the experimental environment, this study adopted the practical traffic information (i.e., traffic flow and vehicle speed from Taiwan Area National Freeway Bureau as the input characteristics of the traffic simulation program and referred to the mobile station (MS communication behaviors from Chunghwa Telecom to simulate the traffic information and communication records. The experimental results illustrated that the average accuracy of the vehicle speed forecasting method is 95.72%. Therefore, the proposed methods based on CFVD are suitable for an intelligent transportation system.

  14. Partitioning, diffusion, and ligand binding of raft lipid analogs in model and cellular plasma membranes.

    Science.gov (United States)

    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

  15. Use of Computational Modeling to Evaluate Hypotheses About the Molecular and Cellular Mechanisms of Bystander Effects

    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.

  16. A cellular automaton model for microstructural simulation of friction stir welded AZ91 magnesium alloy

    Science.gov (United States)

    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.

  17. 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.

  18. An improved cellular automaton model considering the effect of traffic lights and driving behaviour

    Science.gov (United States)

    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.

  19. 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.

  20. The mechanics of cellular compartmentalization as a model for tumor spreading

    Science.gov (United States)

    Fritsch, Anatol; Pawlizak, Steve; Zink, Mareike; Kaes, Josef A.

    2012-02-01

    Based on a recently developed surgical method of Michael H"ockel, which makes use of cellular confinement to compartments in the human body, we study the mechanics of the process of cell segregation. Compartmentalization is a fundamental process of cellular organization and occurs during embryonic development. A simple model system can demonstrate the process of compartmentalization: When two populations of suspended cells are mixed, this mixture will eventually segregate into two phases, whereas mixtures of the same cell type will not. In the 1960s, Malcolm S. Steinberg formulated the so-called differential adhesion hypothesis which explains the segregation in the model system and the process of compartmentalization by differences in surface tension and adhesiveness of the interacting cells. We are interested in to which extend the same physical principles affect tumor growth and spreading between compartments. For our studies, we use healthy and cancerous breast cell lines of different malignancy as well as primary cells from human cervix carcinoma. We apply a set of techniques to study their mechanical properties and interactions. The Optical Stretcher is used for whole cell rheology, while Cell-cell-adhesion forces are directly measured with a modified AFM. In combination with 3D segregation experiments in droplet cultures we try to clarify the role of surface tension in tumor spreading.

  1. Fuel management optimization based on power profile by Cellular Automata

    International Nuclear Information System (INIS)

    Fuel management in PWR nuclear reactors is comprised of a collection of principles and practices required for the planning, scheduling, refueling, and safe operation of nuclear power plants to minimize the total plant and system energy costs to the extent possible. Despite remarkable advancements in optimization procedures, inherent complexities in nuclear reactor structure and strong inter-dependency among the fundamental parameters of the core make it necessary to evaluate the most efficient arrangement of the core. Several patterns have been presented so far to determine the best configuration of fuels in the reactor core by emphasis on minimizing the local power peaking factor (Pq). In this research, a new strategy for optimizing the fuel arrangements in a VVER-1000 reactor core is developed while lowering the Pq is considered as the main target. For this purpose, a Fuel Quality Factor, Z(r), served to depict the reactor core pattern. Mapping to ideal pattern is tracked over the optimization procedure in which the ideal pattern is prepared with considering the Z(r) constraints and their effects on flux and Pq uniformity. For finding the best configuration corresponding to the desired pattern, Cellular Automata (CA) is applied as a powerful and reliable tool on optimization procedure. To obtain the Z(r) constraints, the MCNP code was used and core calculations were performed by WIMS and CITATION codes. The results are compared with the predictions of a Neural Network as a smart optimization method, and the Final Safety Analysis Report (FSAR) as a reference proposed by the designer.

  2. Logical Modeling and Dynamical Analysis of Cellular Networks.

    Science.gov (United States)

    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.

  3. Jeans type instability for a chemotactic model of cellular aggregation

    CERN Document Server

    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.

  4. Modified cellular automaton model for modeling of microstructure and microsegregation in solidification of ternary alloys

    Institute of Scientific and Technical Information of China (English)

    ZHU Ming-fang; CAO Wei-sheng; CHEN Shuang-lin; XIE Fan-you; HONG Chunpyo; CHANG Y. Austin

    2006-01-01

    A modified cellular automaton (MCA) model has been extended to the ternary alloy system by coupling thermodynamic and phase equilibrium calculation engine PanEngine. In the present model the dendrite growth is driven by the difference between the local equilibrium liquidus temperature and local actual temperature, incorporating the effect of curvature. The local equilibrium liquidus temperature is calculated with PanEngine according to the local liquid concentrations of two solutes, which are determined by numerically solving the species transport equation in the domain. Model validation was carried out through the comparison of the simulated values to the prediction of the Scheil model for solute profiles in the primary dendrites. The simulated data with zero solid diffusivity and limited liquid diffusivity were increasingly close to the Scheil profiles as the solidification rate decreased. The simulated microstructure and microsegregation in an Al-Cu-Mg ternary alloy were compared with those obtained experimentally.

  5. A Modified Cellular Automaton Approach for Mixed Bicycle Traffic Flow Modeling

    Directory of Open Access Journals (Sweden)

    Xiaonian Shan

    2015-01-01

    Full Text Available Several previous studies have used the Cellular Automaton (CA for the modeling of bicycle traffic flow. However, previous CA models have several limitations, resulting in differences between the simulated and the observed traffic flow features. The primary objective of this study is to propose a modified CA model for simulating the characteristics of mixed bicycle traffic flow. Field data were collected on physically separated bicycle path in Shanghai, China, and were used to calibrate the CA model using the genetic algorithm. Traffic flow features between simulations of several CA models and field observations were compared. The results showed that our modified CA model produced more accurate simulation for the fundamental diagram and the passing events in mixed bicycle traffic flow. Based on our model, the bicycle traffic flow features, including the fundamental diagram, the number of passing events, and the number of lane changes, were analyzed. We also analyzed the traffic flow features with different traffic densities, traffic components on different travel lanes. Results of the study can provide important information for understanding and simulating the operations of mixed bicycle traffic flow.

  6. An Inquiry-Based Approach to Teaching Photosynthesis & Cellular Respiration

    Science.gov (United States)

    O'Connell, Dan

    2008-01-01

    Recent studies of American science education have highlighted the need for more inquiry-based lessons. For example, when the National Research Counsel evaluated the Advanced Placement (AP) Biology program, it pointed out, "AP laboratory exercises tend to be "cookbook" rather than inquiry based. This criticism is particularly apt for the lab…

  7. Dynamic computational model suggests that cellular citizenship is fundamental for selective tumor apoptosis.

    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.

  8. Three dimensional multi-cellular muscle-like tissue engineering in perfusion-based bioreactors.

    Science.gov (United States)

    Cerino, Giulia; Gaudiello, Emanuele; Grussenmeyer, Thomas; Melly, Ludovic; Massai, Diana; Banfi, Andrea; Martin, Ivan; Eckstein, Friedrich; Grapow, Martin; Marsano, Anna

    2016-01-01

    Conventional tissue engineering strategies often rely on the use of a single progenitor cell source to engineer in vitro biological models; however, multi-cellular environments can better resemble the complexity of native tissues. Previous described co-culture models used skeletal myoblasts, as parenchymal cell source, and mesenchymal or endothelial cells, as stromal component. Here, we propose instead the use of adipose tissue-derived stromal vascular fraction cells, which include both mesenchymal and endothelial cells, to better resemble the native stroma. Percentage of serum supplementation is one of the crucial parameters to steer skeletal myoblasts toward either proliferation (20%) or differentiation (5%) in two-dimensional culture conditions. On the contrary, three-dimensional (3D) skeletal myoblast culture often simply adopts the serum content used in monolayer, without taking into account the new cell environment. When considering 3D cultures of mm-thick engineered tissues, homogeneous and sufficient oxygen supply is paramount to avoid formation of necrotic cores. Perfusion-based bioreactor culture can significantly improve the oxygen access to the cells, enhancing the viability and the contractility of the engineered tissues. In this study, we first investigated the influence of different serum supplementations on the skeletal myoblast ability to proliferate and differentiate during 3D perfusion-based culture. We tested percentages of serum promoting monolayer skeletal myoblast-proliferation (20%) and differentiation (5%) and suitable for stromal cell culture (10%) with a view to identify the most suitable condition for the subsequent co-culture. The 10% serum medium composition resulted in the highest number of mature myotubes and construct functionality. Co-culture with stromal vascular fraction cells at 10% serum also supported the skeletal myoblast differentiation and maturation, hence providing a functional engineered 3D muscle model that resembles

  9. Cellular cardiac electrophysiology modelling with Chaste and CellML

    Directory of Open Access Journals (Sweden)

    Jonathan eCooper

    2015-01-01

    Full Text Available 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 Generalised 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 generalised in our functional curation framework, which uses a domain-specific language for defining complex experiments as a basis for comparison of model behaviour.

  10. From cellular to tissue scales by asymptotic limits of thermostatted kinetic models

    Science.gov (United States)

    Bianca, Carlo; Dogbe, Christian; Lemarchand, Annie

    2016-02-01

    Tumor growth strictly depends on the interactions occurring at the cellular scale. In order to obtain the linking between the dynamics described at tissue and cellular scales, asymptotic methods have been employed, consisting in deriving tissue equations by suitable limits of mesoscopic models. In this paper, the evolution at the cellular scale is described by thermostatted kinetic theory that include conservative, nonconservative (proliferation, destruction and mutations), stochastic terms, and the role of external agents. The dynamics at the tissue scale (cell-density evolution) is obtained by performing a low-field scaling and considering the related convergence of the rescaled framework when the scaling parameter goes to zero.

  11. Integration of logistic regression, Markov chain and cellular automata models to simulate urban expansion

    NARCIS (Netherlands)

    Jokar Arsanjani, J.; Helbich, M.; Kainz, W.; Boloorani, A.

    2013-01-01

    This research analyses the suburban expansion in the metropolitan area of Tehran, Iran. A hybrid model consisting of logistic regression model, Markov chain (MC), and cellular automata (CA) was designed to improve the performance of the standard logistic regression model. Environmental and socio-eco

  12. 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...

  13. Cell-based biosensors: Towards the development of cellular monitoring

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Cell-based biosensors (CBBs), a research hotspot of biosensors, which treat living cells as sensing elements, can detect the functional information of biologically active analytes. They characterize with high sensitivity, excellent selectivity and rapid response, and have been applied in many fields, such as biomedicine, environmental monitoring and pharmaceutical screening. Recently cell-cultured technology, silicon microfabrication technology and genetic technology have promoted exploration of CBBs dramatically. To elucidate the novel research findings and applications of cell- based biosensors, this paper summarizes various research approaches, presents some challenges and proposes the research trends.

  14. Macromolecular Chain at a Cellular Surface: a Computer Simulation Model

    Science.gov (United States)

    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.

  15. Cellular uptake of antisense oligonucleotides after complexing or conjugation with cell-penetrating model peptides.

    Science.gov (United States)

    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.

  16. A Discrete/continuous Coupled Approach for Modeling Impacts on Cellular Geostructures

    Science.gov (United States)

    Breugnot, A.; Lambert, S.; Villard, P.; Gotteland, P.

    2016-05-01

    This article presents a numerical model coupling the finite difference method and discrete element methods (FDM, DEM) for simulating the response of cellular geostructures to impacts. DEM is used in the vicinity of the impacted area while FDM is used far away. The continuity between the DEM and FDM domains is insured using the edge-to-edge method. The numerical parameters are calibrated based on compression and impact experiments conducted on elementary cells. Numerical simulations at the structure scale are compared with real-scale experimental data. The response of the structure is addressed varying the impact conditions. The projectile shape and the position of the impact point appear to be the most influential parameters.

  17. Cellular automata cell structure for modeling heterogeneous traffic

    OpenAIRE

    Pal, Dibyendu; C.Mallikarjuna

    2010-01-01

    Gap maintaining behavior significantly affects the traffic flow modeling under heterogeneous traffic conditions. The clearance between two adjacent moving vehicles varies depending on several traffic conditions. From the data collected on the gap maintaining behavior it has been observed that vehicles maintain different gaps when travelling under different traffic conditions and this is also influenced by lateral position of the vehicle. Mallikarjuna (2007) has found that this variable gap ma...

  18. Derivation of Solar Flare Cellular Automata Models from a Subset of the Magnetohydrodynamic Equations

    Science.gov (United States)

    Vassiliadis, D.; Anastasiadis, A.; Georgoulis, M.; Vlahos, L.

    1998-12-01

    Cellular automata (CA) models account for the power-law distributions found for solar flare hard X-ray observations, but their physics has been unclear. We examine four of these models and show that their criteria and magnetic field distribution rules can be derived by discretizing the MHD diffusion equation as obtained from a simplified Ohm's law. Identifying the discrete MHD with the CA models leads to an expression for the resistivity as a function of the current on the flux tube boundary, as may be expected from current-driven instabilities. Anisotropic CA models correspond to a nonlinear resistivity η(J), while isotropic ones are associated with hyperresistivity η(▽2J). The discrete equations satisfy the necessary conditions for self-organized criticality (Lu): there is local conservation of a field (magnetic flux), while the nonlinear resistivity provides a rapid dissipation and relaxation mechanism. The approach justifies many features of the CA models that were originally based on intuition.

  19. Researches on the behaviour of cellular antiballistic composites based on AlMg-SiC alloys

    Science.gov (United States)

    Bălţătescu, O.; Florea, R. M.; Rusu, I.; Carcea, I.

    2015-11-01

    The researches presented in this paper refers basically to the impact of a small/medium caliber bullet shot on a light armor built on the base of a AlMg-SiC metallic composite cellular/foam. Thus, we study the antiballistic behavior and protection properties of the armor, based on the effects that occur at the impact zone of the bullet with the composite surface. We performed an antiballistic behavior modeling by means of a finite element analysis, based on a "multi grid" Fast Finite Element (FFE) system. We used for this purpose the DYNA 2D software package. The obtained samples show after the impact the occurrence of concentration / deformation pores effect and intercellular cracks development to the interior of the composite. Those effects, depending on speed, mass and length of the projectile ballistic trajectory, reduce zonal tensions due to the effect of cell walls deformation. It was obtained a good correlation between modeling results and the electron microscope analyse of the impact area. It is worth mentioning that almost all values for impact energy absorbed by the composite armor are in the protection active zone provided by it.

  20. Stochastic Model of Maturation and Vesicular Exchange in Cellular Organelles

    CERN Document Server

    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.

  1. Channel modeling for fifth generation cellular networks and wireless sensor networks

    Science.gov (United States)

    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.

  2. A cellular automata intraurban model with prices and income-differentiated actors

    NARCIS (Netherlands)

    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

  3. 基于最大发展潜力值的元胞自动机城市扩张模型%Cellular Automata Urban Expansion Model Based on the Max imum Potential Value of Cell Transformation

    Institute of Scientific and Technical Information of China (English)

    张梦珂; 刘艳芳; 何青松

    2016-01-01

    The potential of land cover change could be estimated on the basis of urbanization level and land development evaluation. Based on the potential value, a new method of simulating urban expansion that is different from the traditional Cellular Automata is proposed.According to development potentiality in every search process, the method described in this article only transforms cells with a maximum potential value that are suitable for neighborhood requirements into urban cells.Compared with traditional methods, trans-formation threshold is not required with this new strategy.Each of the two methods is applied to simulating urban expansion of the main urban area of Wuhan from 2003 to 2013 separately, and it is demonstrated that the precision of the new ameliorated method is signifi-cantly improved compared to the traditional methodology.%在城镇化发展水平及土地开发评价的基础上,评价待扩张区域土地转变潜力分值,基于最大转变潜力分值,提出一种有别于传统元胞自动机模拟城市扩张的新方法。该方法与传统元胞自动机模拟城市扩张相比在迭代方式上存在不同,它克服了传统元胞自动机因阈值设置不同而导致结果不确定的难题。分别将该方法与传统元胞自动机模型应用于武汉主城区,模拟了其2003年到2013年的城市扩张情况,最后,将模拟结果与实际土地利用现状图进行对比发现改进后的新方法在模拟精度上大大提高。

  4. Expression kinetics of hepatic progenitor markers in cellular models of human liver development recapitulating hepatocyte and biliary cell fate commitment.

    Science.gov (United States)

    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.

  5. Evaluation of BACE1 Silencing in Cellular Models

    Directory of Open Access Journals (Sweden)

    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.

  6. Studying the Effects of Matrix Stiffness on Cellular Function using Acrylamide-based Hydrogels

    Science.gov (United States)

    Cretu, Alexandra; Castagnino, Paola; Assoian, Richard

    2010-01-01

    Tissue stiffness is an important determinant of cellular function, and changes in tissue stiffness are commonly associated with fibrosis, cancer and cardiovascular disease1-11. Traditional cell biological approaches to studying cellular function involve culturing cells on a rigid substratum (plastic dishes or glass coverslips) which cannot account for the effect of an elastic ECM or the variations in ECM stiffness between tissues. To model in vivo tissue compliance conditions in vitro, we and others use ECM-coated hydrogels. In our laboratory, the hydrogels are based on polyacrylamide which can mimic the range of tissue compliances seen biologically12. "Reactive" cover slips are generated by incubation with NaOH followed by addition of 3-APTMS. Glutaraldehyde is used to cross-link the 3-APTMS and the polyacrylamide gel. A solution of acrylamide (AC), bis-acrylamide (Bis-AC) and ammonium persulfate is used for the polymerization of the hydrogel. N-hydroxysuccinimide (NHS) is incorporated into the AC solution to crosslink ECM protein to the hydrogel. Following polymerization of the hydrogel, the gel surface is coated with an ECM protein of choice such as fibronectin, vitronectin, collagen, etc. The stiffness of a hydrogel can be determined by rheology or atomic force microscopy (AFM) and adjusted by varying the percentage of AC and/or bis-AC in the solution12. In this manner, substratum stiffness can be matched to the stiffness of biological tissues which can also be quantified using rheology or AFM. Cells can then be seeded on these hydrogels and cultured based upon the experimental conditions required. Imaging of the cells and their recovery for molecular analysis is straightforward. For this article, we define soft substrata as those having elastic moduli (E) 20,000 Pascal. PMID:20736914

  7. Preparation of oligodeoxynucleotide encapsulated cationic liposomes and release study with models of cellular membranes

    Directory of Open Access Journals (Sweden)

    Tamaddon AM.

    2007-05-01

    Full Text Available Cationic liposomes are used for cellular delivery of antisense oligodeoxynucleotide (AsODN, where release of encapsulated AsODN is mainly controlled by endocytosis and fusion mechanisms. In this investigation, it was tried to model such a release process that is difficult to evaluate in cell culture. For this purpose, an AsODN model (against protein kinase C-α was encapsulated in a DODAP-containing cationic liposome and evaluated for size, zeta-potential, encapsulation and ODN stability. Vesicular models of outer layer and total plasma membranes and early and late endosomal membranes were developed, based on lipid content and pH, using ether injection method. ODN release was determined by the fluorescence dequenching of encapsulated FITC-ODN. Zeta potential, size and ODN encapsulation efficiency of the prepared liposomes were -2.49 ± 7.15 mV, 108.4 nm and 73% respectively. ODN protection was 3-4 times more than that of conventional liposome/ODN complexation method. There was a correlation between model concentration and percent of ODN release. At 7.5 µM, the percent of released ODN was 76% for the cholesterol-free model of the late endosome and 16% for the early endosomal membrane; while the release was less than 11% for the models of plasma membrane. ODN release increased with temperature in the range of 4-37◦C for the late endosomal model, but not for others, possibly due to their high cholesterol contents or acidic pH. The interaction was fast and completed within 5 minutes and didn’t change in the range of 5-60 minutes. Our data are in agreement with published cell culture studies and reveal that cell-liposomes interaction can be modeled by lamellar membranes.

  8. 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].

  9. Performance Analysis of 3D Massive MIMO Cellular Systems with Collaborative Base Station

    Directory of Open Access Journals (Sweden)

    Xingwang Li

    2014-01-01

    Full Text Available Massive MIMO have drawn considerable attention as they enable significant capacity and coverage improvement in wireless cellular network. However, pilot contamination is a great challenge in massive MIMO systems. Under this circumstance, cooperation and three-dimensional (3D MIMO are emerging technologies to eliminate the pilot contamination and to enhance the performance relative to the traditional interference-limited implementations. Motivated by this, we investigate the achievable sum rate performance of MIMO systems in the uplink employing cooperative base station (BS and 3D MIMO systems. In our model, we consider the effects of both large-scale and small-scale fading, as well as the spatial correlation and indoor-to-outdoor high-rise propagation environment. In particular, we investigate the cooperative communication model based on 3D MIMO and propose a closed-form lower bound on the sum rate. Utilizing this bound, we pursue a “large-system” analysis and provide the asymptotic expression when the number of antennas at the BS grows large, and when the numbers of antennas at transceiver grow large with a fixed ratio. We demonstrate that the lower bound is very tight and becomes exact in the massive MIMO system limits. Finally, under the sum rate maximization condition, we derive the optimal number of UTs to be served.

  10. Simulation of Microstructure during Laser Rapid Forming Solidification Based on Cellular Automaton

    Directory of Open Access Journals (Sweden)

    Zhi-jian Wang

    2014-01-01

    Full Text Available The grain microstructure of molten pool during the solidification of TC4 titanium alloy in the single point laser cladding was investigated based on the CAFE model which is the cellular automaton (CA coupled with the finite element (FE method. The correct temperature field is the prerequisite for simulating the grain microstructure during the solidification of the molten pool. The model solves the energy equation by the FE method to simulate the temperature distribution in the molten pool of the single point laser cladding. Based on the temperature field, the solidification microstructure of the molten pool is also simulated with the CAFE method. The results show that the maximum temperature in the molten pool increases with the laser power and the scanning rate. The laser power has a larger influence on the temperature distribution of the molten pool than the scanning rate. During the solidification of the molten pool, the heat at the bottom of the molten pool transfers faster than that at the top of the molten pool. The grains rapidly grow into the molten pool, and then the columnar crystals are formed. This study has a very important significance for improving the quality of the structure parts manufactured through the laser cladding forming.

  11. Applying Cellular Automata for Simulating and Assessing Urban Growth Scenario Based in Nairobi, Kenya

    Directory of Open Access Journals (Sweden)

    Kenneth Mubea

    2014-01-01

    Full Text Available This research explores urban growth based scenarios for the city of Nairobi using a cellular automata urban growth model (UGM. African cities have experienced rapid urbanization over the last decade due to increased population growth and high economic activities. We used multi-temporal Landsat imageries for 1976, 1986, 2000 and 2010 to investigate urban land-use changes in Nairobi. Our UGM used data from urban land-use of 1986 and 2010, road data, slope data and exclusion layer. Monte-Carlo technique was used for model calibration and Multi Resolution Validation (MRV technique for validation. Simulation of urban land-use was done up to the year 2030 when Kenya plans to attain Vision 2030. Three scenarios were explored in the urban modelling process; unmanaged growth with no restriction on environmental areas, managed growth with moderate protection, and a managed growth with maximum protection on forest, agricultural areas, and urban green. Thus alternative scenario development using UGM is useful for planning purposes so as to ensure sustainable development is achieved. UGM provides quantitative, visual, spatial and temporal information which aid policy and decision makers can make informed decisions.

  12. Load-aware modeling for uplink cellular networks in a multi-channel environment

    KAUST Repository

    Alammouri, Ahmad Mohammad Abdel-Karim

    2014-09-01

    We exploit tools from stochastic geometry to develop a tractable analytical approach for modeling uplink cellular networks. The developed model is load aware and accounts for per-user power control as well as the limited transmit power constraint for the users\\' equipment (UEs). The proposed analytical paradigm is based on a simple per-user power control scheme in which each user inverts his path-loss such that the signal is received at his serving base station (BS) with a certain power threshold ρ Due to the limited transmit power of the UEs, users that cannot invert their path-loss to their serving BSs are allowed to transmit with their maximum transmit power. We show that the proposed power control scheme not only provides a balanced cell center and cell edge user performance, it also facilitates the analysis when compared to the state-of-the-art approaches in the literature. To this end, we discuss how to manipulate the design variable ρ in response to the network parameters to optimize one or more of the performance metrics such as the outage probability, the network capacity, and the energy efficiency.

  13. Cellular automaton models for traffic flow considering opposite driving of an emergency vehicle

    Science.gov (United States)

    Zhao, Han-Tao; Li, Jing-Ru; Nie, Cen

    2015-12-01

    Aiming at two-lane road, this paper establishes three models to analyze the opposite-overtaking rules of emergency vehicle based on cellular automaton (CCA) model. Based on the simulation of mixed traffic flow for multi-density conditions, the density-speed diagrams have been obtained consequently. According to the analysis, when the traffic density of the opposite lane is low, the opposite driving behavior of emergency vehicle can improve the average speed effectively. At the same time, if the cocurrent lane is in high-density traffic, the traffic in the opposite lane will be disturbed, but the vehicles in the cocurrent lane will not be affected. The paper has further discussed the influence of different emergency vehicle driving behaviors on traffic. The results reveal that as the traffic of the opposite lane is in a low-density range, if emergency vehicle operates overtaking behavior precisely, the greater the density of the cocurrent lane is, the more obviously the speed improve. Meanwhile large random fluctuation of overtaking times will occur. While the risky lane change behavior displays different traffic characteristics, that is when the same direction lane is in high density, the speed increases slightly and the lane change number is changed regularly.

  14. 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.

  15. 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......-in reference distance path loss models are studied in depth to show their value in channel modeling. Furthermore, the shadow fading spread versus distance remains unclear based on the current measurement results, thus more measurements are necessary to gain a better knowledge of the UMa channels at centimeter...

  16. FANTOM5 transcriptome catalog of cellular states based on Semantic MediaWiki.

    Science.gov (United States)

    Abugessaisa, Imad; Shimoji, Hisashi; Sahin, Serkan; Kondo, Atsushi; Harshbarger, Jayson; Lizio, Marina; Hayashizaki, Yoshihide; Carninci, Piero; Forrest, Alistair; Kasukawa, Takeya; Kawaji, Hideya

    2016-01-01

    The Functional Annotation of the Mammalian Genome project (FANTOM5) mapped transcription start sites (TSSs) and measured their activities in a diverse range of biological samples. The FANTOM5 project generated a large data set; including detailed information about the profiled samples, the uncovered TSSs at high base-pair resolution on the genome, their transcriptional initiation activities, and further information of transcriptional regulation. Data sets to explore transcriptome in individual cellular states encoded in the mammalian genomes have been enriched by a series of additional analysis, based on the raw experimental data, along with the progress of the research activities. To make the heterogeneous data set accessible and useful for investigators, we developed a web-based database called Semantic catalog of Samples, Transcription initiation And Regulators (SSTAR). SSTAR utilizes the open source wiki software MediaWiki along with the Semantic MediaWiki (SMW) extension, which provides flexibility to model, store, and display a series of data sets produced during the course of the FANTOM5 project. Our use of SMW demonstrates the utility of the framework for dissemination of large-scale analysis results. SSTAR is a case study in handling biological data generated from a large-scale research project in terms of maintenance and growth alongside research activities.Database URL: http://fantom.gsc.riken.jp/5/sstar/. PMID:27402679

  17. Solving the Advection-Diffusion Equations in Biological Contexts using the Cellular Potts Model

    CERN Document Server

    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...

  18. Quasi-classical modeling of molecular quantum-dot cellular automata multidriver gates

    Science.gov (United States)

    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.

  19. Platinum nanozymes recover cellular ROS homeostasis in an oxidative stress-mediated disease model

    Science.gov (United States)

    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

  20. A Modified Cellular Automaton Approach for Mixed Bicycle Traffic Flow Modeling

    OpenAIRE

    Xiaonian Shan; Zhibin Li; Xiaohong Chen; Jianhong Ye

    2015-01-01

    Several previous studies have used the Cellular Automaton (CA) for the modeling of bicycle traffic flow. However, previous CA models have several limitations, resulting in differences between the simulated and the observed traffic flow features. The primary objective of this study is to propose a modified CA model for simulating the characteristics of mixed bicycle traffic flow. Field data were collected on physically separated bicycle path in Shanghai, China, and were used to calibrate the C...

  1. Stochastic Ordering based Carrier-to-Interference Ratio Analysis for the Shotgun Cellular Systems

    CERN Document Server

    Madhusudhanan, Prasanna; Youjian,; Liu,; Brown, Timothy X; Baker, Kenneth R

    2011-01-01

    A simple analytical tool based on stochastic ordering is developed to compare the distributions of carrier-to-interference ratio at the mobile station of two cellular systems where the base stations are distributed randomly according to certain non-homogeneous Poisson point processes. The comparison is conveniently done by studying only the base station densities without having to solve for the distributions of the carrier-to-interference ratio, that are often hard to obtain.

  2. Evolving Transport Networks With Cellular Automata Models Inspired by Slime Mould.

    Science.gov (United States)

    Tsompanas, Michail-Antisthenis I; Sirakoulis, Georgios Ch; Adamatzky, Andrew I

    2015-09-01

    Man-made transport networks and their design are closely related to the shortest path problem and considered amongst the most debated problems of computational intelligence. Apart from using conventional or bio-inspired computer algorithms, many researchers tried to solve this kind of problem using biological computing substrates, gas-discharge solvers, prototypes of a mobile droplet, and hot ice computers. In this aspect, another example of biological computer is the plasmodium of acellular slime mould Physarum polycephalum (P. polycephalum), which is a large single cell visible by an unaided eye and has been proven as a reliable living substrate for implementing biological computing devices for computational geometry, graph-theoretical problems, and optimization and imitation of transport networks. Although P. polycephalum is easy to experiment with, computing devices built with the living slime mould are extremely slow; it takes slime mould days to execute a computation. Consequently, mapping key computing mechanisms of the slime mould onto silicon would allow us to produce efficient bio-inspired computing devices to tackle with hard to solve computational intelligence problems like the aforementioned. Toward this direction, a cellular automaton (CA)-based, Physarum-inspired, network designing model is proposed. This novel CA-based model is inspired by the propagating strategy, the formation of tubular networks, and the computing abilities of the plasmodium of P. polycephalum. The results delivered by the CA model demonstrate a good match with several previously published results of experimental laboratory studies on imitation of man-made transport networks with P. polycephalum. Consequently, the proposed CA model can be used as a virtual, easy-to-access, and biomimicking laboratory emulator that will economize large time periods needed for biological experiments while producing networks almost identical to the tubular networks of the real-slime mould. PMID

  3. Simulating debris flows through a hexagonal cellular automata model: SCIDDICA S3–hex

    Directory of Open Access Journals (Sweden)

    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

  4. Embryonic stem cells as an ectodermal cellular model of human p63-related dysplasia syndromes.

    NARCIS (Netherlands)

    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

  5. Cellular Systems with Full-Duplex Compress-and-Forward Relaying and Cooperative Base Stations

    CERN Document Server

    Somekh, Oren; Poor, H Vincent; Shamai, Shlomo

    2008-01-01

    In this paper the advantages provided by multicell processing of signals transmitted by mobile terminals (MTs) which are received via dedicated relay terminals (RTs) are studied. It is assumed that each RT is capable of full-duplex operation and receives the transmission of adjacent relay terminals. Focusing on intra-cell TDMA and non-fading channels, a simplified relay-aided uplink cellular model based on a model introduced by Wyner is considered. Assuming a nomadic application in which the RTs are oblivious to the MTs' codebooks, a form of distributed compress-and-forward (CF) scheme with decoder side information is employed. The per-cell sum-rate of the CF scheme is derived and is given as a solution of a simple fixed point equation. This achievable rate reveals that the CF scheme is able to completely eliminate the inter-relay interference, and it approaches a ``cut-set-like'' upper bound for strong RTs transmission power. The CF rate is also shown to surpass the rate of an amplify-and-forward scheme via ...

  6. A Case-Based Approach Increases Student Learning Outcomes and Comprehension of Cellular Respiration Concepts

    Science.gov (United States)

    Rybarczyk, Brian J.; Baines, Antonio T.; McVey, Mitch; Thompson, Joseph T.; Wilkins, Heather

    2007-01-01

    This study investigated student learning outcomes using a case-based approach focused on cellular respiration. Students who used the case study, relative to students who did not use the case study, exhibited a significantly greater learning gain, and demonstrated use of higher-order thinking skills. Preliminary data indicate that after engaging…

  7. Memristor-based cellular nonlinear/neural network: design, analysis, and applications.

    Science.gov (United States)

    Duan, Shukai; Hu, Xiaofang; Dong, Zhekang; Wang, Lidan; Mazumder, Pinaki

    2015-06-01

    Cellular nonlinear/neural network (CNN) has been recognized as a powerful massively parallel architecture capable of solving complex engineering problems by performing trillions of analog operations per second. The memristor was theoretically predicted in the late seventies, but it garnered nascent research interest due to the recent much-acclaimed discovery of nanocrossbar memories by engineers at the Hewlett-Packard Laboratory. The memristor is expected to be co-integrated with nanoscale CMOS technology to revolutionize conventional von Neumann as well as neuromorphic computing. In this paper, a compact CNN model based on memristors is presented along with its performance analysis and applications. In the new CNN design, the memristor bridge circuit acts as the synaptic circuit element and substitutes the complex multiplication circuit used in traditional CNN architectures. In addition, the negative differential resistance and nonlinear current-voltage characteristics of the memristor have been leveraged to replace the linear resistor in conventional CNNs. The proposed CNN design has several merits, for example, high density, nonvolatility, and programmability of synaptic weights. The proposed memristor-based CNN design operations for implementing several image processing functions are illustrated through simulation and contrasted with conventional CNNs. Monte-Carlo simulation has been used to demonstrate the behavior of the proposed CNN due to the variations in memristor synaptic weights. PMID:25069124

  8. Management of Location Based Advertisement Services using Spatial Triggers in Cellular Networks

    CERN Document Server

    Irfan, M; Khan, Furqan H; Hashmi, Raheel M; Shehzad, Khurram; Ali, Assad

    2009-01-01

    This paper discusses the advent of new technologies which have emerged under the area of Location Based Services (LBS). An innovative implementation and approach has been presented for design of applications which are inventive and attractive towards the user. Spatial Trigger is one of the most promising additions to the LBS technologies. This paper describes ways in which mobile advertisement services can be introduced effectively in the cellular market by bringing innovation in them through effective usage of Spatial Triggers. Hence, opening new horizons to make the consumer cellular networks, commercially, more effective and informative.

  9. Guard zone based D2D underlaid cellular networks with two-tier dependence

    OpenAIRE

    Chen, Zheng; Kountouris, Marios

    2015-01-01

    International audience Device-to-device (D2D) communication is under active investigation and may be a key feature in 5G networks for its great potential in improving network spectral and energy efficiency. Underlaying proximity-based D2D communication links in current cellular networks allows D2D users to opportunistically access the cellular spectrum, thus causing interference not only in the D2D tier but also between D2D and macrocell tiers. In this paper, we consider a D2D underlaid ce...

  10. Management of Location Based Advertisement Services using Spatial Triggers in Cellular Networks

    Directory of Open Access Journals (Sweden)

    Assad Ali

    2009-10-01

    Full Text Available This paper discusses the advent of new technologies which have emerged under the area of Location Based Services (LBS. An innovative implementation and approach has been presented for design of applications which are inventive and attractive towards the user. Spatial Trigger is one of the most promising additions to the LBS technologies. This paper describes ways in which mobile advertisement services can be introduced effectively in the cellular market by bringing innovation in them through effective usage of Spatial Triggers. Hence, opening new horizons to make the consumer cellular networks, commercially, more effective and informative.

  11. Performance Evaluation of Road Traffic Control Using a Fuzzy Cellular Model

    CERN Document Server

    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.

  12. Laboratory testing of a building envelope segment based on cellular concrete

    Science.gov (United States)

    Fořt, Jan; Pavlík, Zbyšek; Černý, Robert

    2016-07-01

    Hygrothermal performance of a building envelope based on cellular concrete blocks is studied in the paper. Simultaneously, the strain fields induced by the heat and moisture changes are monitored. The studied wall is exposed to the climatic load corresponding to the winter climatic conditions of the moderate year for Prague. The winter climatic exposure is chosen in order to simulate the critical conditions of the building structure from the point of view of material performance and temperature and humidity loading. The evaluation of hygrothermal performance of a researched wall is done on the basis of relative humidity and temperature profiles measured along the cross section of the cellular concrete blocks. Strain gauges are fixed on the wall surface in expected orientation of the blocks expansion. The obtained results show a good hygrothermal function of the analyzed cellular concrete wall and its insignificant strain.

  13. CCABC: Cyclic Cellular Automata Based Clustering For Energy Conservation in Sensor Networks

    CERN Document Server

    Banerjee, Indrajit; Rahaman, Hafizur

    2011-01-01

    Sensor network has been recognized as the most significant technology for next century. Despites of its potential application, wireless sensor network encounters resource restriction such as low power, reduced bandwidth and specially limited power sources. This work proposes an efficient technique for the conservation of energy in a wireless sensor network (WSN) by forming an effective cluster of the network nodes distributed over a wide range of geographical area. The clustering scheme is developed around a specified class of cellular automata (CA) referred to as the modified cyclic cellular automata (mCCA). It sets a number of nodes in stand-by mode at an instance of time without compromising the area of network coverage and thereby conserves the battery power. The proposed scheme also determines an effective cluster size where the inter-cluster and intra-cluster communication cost is minimum. The simulation results establish that the cyclic cellular automata based clustering for energy conservation in sens...

  14. Cellular automata model for urban road traffic flow considering pedestrian crossing street

    Science.gov (United States)

    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.

  15. Particle acceleration and radiation in flaring complex solar active regions modeled by cellular automata

    Science.gov (United States)

    Dauphin, C.; Vilmer, N.; Anastasiadis, A.

    2007-06-01

    Context: We study the acceleration and radiation of electrons and ions interacting with multiple small-scale dissipation regions resulting from the magnetic energy release process. Aims: We aim to calculate the distribution functions of the kinetic energy of the particles and the X-ray spectra and γ-ray fluxes produced by the accelerated particles. Methods: The evolution of the magnetic energy released in an active region is mimicked by a cellular automaton model based on the concept of self-organized criticality. Each burst of magnetic energy release is associated with a reconnecting current sheet (RCS) in which the particles are accelerated by a direct electric field. Results: We calculate the energy gain of the particles (ions and electrons) for three different magnetic configurations of the RCS after their interactions with a given number of RCS. We finally compare our results with existing observations. Conclusions: The results of our simulation can reproduce several properties of the observations such as variable electron and ion energy contents and γ-ray line ratio. Even if very flat X-ray spectra have been reported in a few events, the X-ray spectra produced in this model are too flat when compared to most X-ray observations.

  16. Cellular and molecular modifier pathways in tauopathies: the big picture from screening invertebrate models.

    Science.gov (United States)

    Hannan, Shabab B; Dräger, Nina M; Rasse, Tobias M; Voigt, Aaron; Jahn, Thomas R

    2016-04-01

    Abnormal tau accumulations were observed and documented in post-mortem brains of patients affected by Alzheimer's disease (AD) long before the identification of mutations in the Microtubule-associated protein tau (MAPT) gene, encoding the tau protein, in a different neurodegenerative disease called Frontotemporal dementia and Parkinsonism linked to chromosome 17 (FTDP-17). The discovery of mutations in the MAPT gene associated with FTDP-17 highlighted that dysfunctions in tau alone are sufficient to cause neurodegeneration. Invertebrate models have been diligently utilized in investigating tauopathies, contributing to the understanding of cellular and molecular pathways involved in disease etiology. An important discovery came with the demonstration that over-expression of human tau in Drosophila leads to premature mortality and neuronal dysfunction including neurodegeneration, recapitulating some key neuropathological features of the human disease. The simplicity of handling invertebrate models combined with the availability of a diverse range of experimental resources make these models, in particular Drosophila a powerful invertebrate screening tool. Consequently, several large-scale screens have been performed using Drosophila, to identify modifiers of tau toxicity. The screens have revealed not only common cellular and molecular pathways, but in some instances the same modifier has been independently identified in two or more screens suggesting a possible role for these modifiers in regulating tau toxicity. The purpose of this review is to discuss the genetic modifier screens on tauopathies performed in Drosophila and C. elegans models, and to highlight the common cellular and molecular pathways that have emerged from these studies. Here, we summarize results of tau toxicity screens providing mechanistic insights into pathological alterations in tauopathies. Key pathways or modifiers that have been identified are associated with a broad range of processes

  17. Effect of driver over-acceleration on traffic breakdown in three-phase cellular automaton traffic flow models

    Science.gov (United States)

    Kerner, Boris S.; Klenov, Sergey L.; Hermanns, Gerhard; Schreckenberg, Michael

    2013-09-01

    Based on simulations with cellular automaton (CA) traffic flow models, a generic physical feature of the three-phase models studied in the paper is disclosed. The generic feature is a discontinuous character of driver over-acceleration caused by a combination of two qualitatively different mechanisms of over-acceleration: (i) Over-acceleration through lane changing to a faster lane, (ii) over-acceleration occurring in car-following without lane changing. Based on this generic feature a new three-phase CA traffic flow model is developed. This CA model explains the set of the fundamental empirical features of traffic breakdown in real heterogeneous traffic flow consisting of passenger vehicles and trucks. The model simulates also quantitative traffic pattern characteristics as measured in real heterogeneous flow.

  18. Strength analysis and modeling of cellular lattice structures manufactured using selective laser melting for tooling applications

    DEFF Research Database (Denmark)

    Mahshid, Rasoul; Hansen, Hans Nørgaard; Loft Højbjerre, Klaus

    2016-01-01

    in injection molding tools and lattice structures. This research examines the effect of cellular lattice structures on the strength of workpieces additively manufactured from ultra high-strength steel powder. Two commercial SLM machines are used to fabricate cellular samples based on four architectures— solid......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...

  19. Multi-scale continuum modeling of biological processes: from molecular electro-diffusion to sub-cellular signaling transduction

    Science.gov (United States)

    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.

  20. Computational Modelling of the Structural Integrity following Mass-Loss in Polymeric Charred Cellular Solids

    Directory of Open Access Journals (Sweden)

    J. P. M. Whitty

    2014-01-01

    Full Text Available A novel computational technique is presented for embedding mass-loss due to burning into the ANSYS finite element modelling code. The approaches employ a range of computational modelling methods in order to provide more complete theoretical treatment of thermoelasticity absent from the literature for over six decades. Techniques are employed to evaluate structural integrity (namely, elastic moduli, Poisson’s ratios, and compressive brittle strength of honeycomb systems known to approximate three-dimensional cellular chars. That is, reducing the mass of diagonal ribs and both diagonal-plus-vertical ribs simultaneously show rapid decreases in the structural integrity of both conventional and reentrant (auxetic, i.e., possessing a negative Poisson’s ratio honeycombs. On the other hand, reducing only the vertical ribs shows initially modest reductions in such properties, followed by catastrophic failure of the material system. Calculations of thermal stress distributions indicate that in all cases the total stress is reduced in reentrant (auxetic cellular solids. This indicates that conventional cellular solids are expected to fail before their auxetic counterparts. Furthermore, both analytical and FE modelling predictions of the brittle crush strength of both auxteic and conventional cellular solids show a relationship with structural stiffness.

  1. The analysis of speed-reporting rates from a cellular network based on a fingerprint-positioning algorithm

    Directory of Open Access Journals (Sweden)

    Chi-Hua Chen

    2013-05-01

    Full Text Available The collection of real-time traffic information is an important part of intelligent transportation systems. In particular, cellular floating vehicle data (CFVD technology has become increasingly widespread, and more and more popular for measuring and forecasting real-time traffic information, based on anonymous sampling of the positions of mobile phones. This study proposes an analytical model to analyse the speed-reporting rates based on communication behaviour, traffic conditions, and the two consecutive fingerprint-positioning locations from the call arrival and call completion signals of the same call for a feasibility evaluation of CFVD.

  2. 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.

  3. Phase transitions in cellular automata models of spatial susceptible-infected-resistant-susceptible epidemics

    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.

  4. Preparation of oligodeoxynucleotide encapsulated cationic liposomes and release study with models of cellular membranes

    OpenAIRE

    Tamaddon AM.; Hosseini-Shirazi F.; Moghimi HR

    2007-01-01

    Cationic liposomes are used for cellular delivery of antisense oligodeoxynucleotide (AsODN), where release of encapsulated AsODN is mainly controlled by endocytosis and fusion mechanisms. In this investigation, it was tried to model such a release process that is difficult to evaluate in cell culture. For this purpose, an AsODN model (against protein kinase C-α) was encapsulated in a DODAP-containing cationic liposome and evaluated for size, zeta-potential, encapsulation and ODN stab...

  5. Integration of Multiple Components in Polystyrene-based Microfluidic Devices Part 2: Cellular Analysis

    Science.gov (United States)

    Anderson, Kari B.; Halpin, Stephen T.; Johnson, Alicia S.; Martin, R. Scott; Spence, Dana M.

    2012-01-01

    In Part II of this series describing the use of polystyrene (PS) devices for microfluidic-based cellular assays, various cellular types and detection strategies are employed to determine three fundamental assays often associated with cells. Specifically, using either integrated electrochemical sensing or optical measurements with a standard multi-well plate reader, cellular uptake, production, or release of important cellular analytes are determined on a PS-based device. One experiment involved the fluorescence measurement of nitric oxide (NO) produced within an endothelial cell line following stimulation with ATP. The result was a four-fold increase in NO production (as compared to a control), with this receptor-based mechanism of NO production verifying the maintenance of cell receptors following immobilization onto the PS substrate. The ability to monitor cellular uptake was also demonstrated by optical determination of Ca2+ into endothelial cells following stimulation with the Ca2+ ionophore A20317. The result was a significant increase (42%) in the calcium uptake in the presence of the ionophore, as compared to a control (17%) (p < 0.05). Finally, the release of catecholamines from a dopaminergic cell line (PC 12 cells) was electrochemically monitored, with the electrodes being embedded into the PS-based device. The PC 12 cells had better adherence on the PS devices, as compared to use of PDMS. Potassium-stimulation resulted in the release of 114 ± 11 µM catecholamines, a significant increase (p < 0.05) over the release from cells that had been exposed to an inhibitor (reserpine, 20 ± 2 µM of catecholamines). The ability to successfully measure multiple analytes, generated in different means from various cells under investigation, suggests that PS may be a useful material for microfluidic device fabrication, especially considering the enhanced cell adhesion to PS, its enhanced rigidity/amenability to automation, and its ability to enable a wider range of

  6. Magneto-optical cellular chip model for intracellular orientational-dynamic-activity detection

    Science.gov (United States)

    Miyashita, Y.; Iwasaka, M.; Kurita, S.; Owada, N.

    2012-04-01

    In the present study, a magneto-optical cellular chip model (MoCCM) was developed to detect intracellular dynamics in macromolecules by using magneto-optical effects. For the purpose of cell-measurement under strong static magnetic fields of up to 10 T, we constructed a cellular chip model, which was a thin glass plate with a well for a cell culture. A cell line of osteoblast MC3T3-E1 was incubated in the glass well, and the well, 0.3 mm in depth, was sealed by a cover glass when the MoCCM was set in a fiber optic system. An initial intensity change of the polarized light transmission, which dispersed perpendicular to the cell's attaching surface, was collected for 10 to 60 min, and then magnetic fields were applied parallel and perpendicular to the surface and light direction, respectively. The magnetic birefringence signals that originated from the magnetic orientation of intracellular molecules such as cytoskeletons apparently appeared when the magnetic fields were constant at 10 T. A statistical analysis with 15 experiments confirmed that the cellular components under 10 T magnetic fields caused a stronger alignment, which was transferred into polarizing light intensity that increased more than the case before exposure. Cellular conditions such as generation and cell density affected the magnetic birefringence signals.

  7. Virtual cellular manufacturing system based on resource element approach and analyzing its performance over different basic layouts

    Directory of Open Access Journals (Sweden)

    G. R. Esmaeilian

    2012-01-01

    Full Text Available This research aims to present how choosing a suitable layout can improve the performance of virtual cellular manufacturing systems (VCMSs, especially minimizing the material flow between machines required by each family group. To present the efficacy of basic layouts on performances of VCMSs, a multi-objective mathematical model with a goal programming (GP approach is developed to generate VCMSs based on resource-elements (REs. The formulated model is coded in Lingo software and is run over functional and distributed arrangements of the same machines. The performance and the validity of the developed model are checked by a numerical example taken from the literature. The objective function of the mathematical model is measured for that example over two mentioned layout to compare the performance of the generated systems. Moreover, because of the material handling costs importance, material flows are measured to find the best option as a basic layout for VCMSs. To compare the performance of the generated system with the classical cellular manufacturing system (CMS, cell capacity utilization (CCU is employed as an independent criterion to evaluate each system. The result illustrates the priority of distributed layouts for generating RE-based VCMSs because of its flexibility, minimizing the objective function for the mathematical model, and smaller material flow by the components. In addition, the generated VCMSs outperforms the classical CMS from the CCU point of view.

  8. A Cellular Automaton Model for Tumor Dormancy: Emergence of a Proliferative Switch

    CERN Document Server

    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...

  9. A cellular automata traffic flow model considering the heterogeneity of acceleration and delay probability

    Science.gov (United States)

    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.

  10. 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.

  11. In Silico Modeling of the Immune System: Cellular and Molecular Scale Approaches

    Directory of Open Access Journals (Sweden)

    Mariagrazia Belfiore

    2014-01-01

    Full Text Available The revolutions in biotechnology and information technology have produced clinical data, which complement biological data. These data enable detailed descriptions of various healthy and diseased states and responses to therapies. For the investigation of the physiology and pathology of the immune responses, computer and mathematical models have been used in the last decades, enabling the representation of biological processes. In this modeling effort, a major issue is represented by the communication between models that work at cellular and molecular level, that is, multiscale representation. Here we sketch some attempts to model immune system dynamics at both levels.

  12. Efficient Analysis of Systems Biology Markup Language Models of Cellular Populations Using Arrays.

    Science.gov (United States)

    Watanabe, Leandro; Myers, Chris J

    2016-08-19

    The Systems Biology Markup Language (SBML) has been widely used for modeling biological systems. Although SBML has been successful in representing a wide variety of biochemical models, the core standard lacks the structure for representing large complex regular systems in a standard way, such as whole-cell and cellular population models. These models require a large number of variables to represent certain aspects of these types of models, such as the chromosome in the whole-cell model and the many identical cell models in a cellular population. While SBML core is not designed to handle these types of models efficiently, the proposed SBML arrays package can represent such regular structures more easily. However, in order to take full advantage of the package, analysis needs to be aware of the arrays structure. When expanding the array constructs within a model, some of the advantages of using arrays are lost. This paper describes a more efficient way to simulate arrayed models. To illustrate the proposed method, this paper uses a population of repressilator and genetic toggle switch circuits as examples. Results show that there are memory benefits using this approach with a modest cost in runtime. PMID:26912276

  13. Lateral Drift Behavior Analysis in Mixed Bicycle Traffic: A Cellular Automaton Model Approach

    Directory of Open Access Journals (Sweden)

    Xue Feng

    2016-01-01

    Full Text Available Bicycle movements are always associated with lateral drifts. However, the impacts of lateral drift behavior, as well as variable lateral clearance maintaining behavior due to the variation of drift intensity, on mixed bicycle flow are not clear. This paper establishes a new cellular automata model to study typical characteristics of mixed bicycle traffic induced by lateral drift and its accompanying behavior. Based on derived positive correlation between passing speed and drift speed through survey, the occurrence probability of lateral drift and the degree of maintained lateral clearance are both introduced in accordance with the variance of passing speed. Then, in whole density region, firm conformity between simulation results and actual survey data is reached, which has seldom been achieved in previous studies. It is further verified that speed distortions in intermediate and high density region induced by assumption of constant lateral clearance requirements can be revised by introducing its variability characteristics. In addition, two contrastive impacts of lateral drift behavior are observed. That is, it causes speed fluctuation in low density while alleviating the speed fluctuation in relatively high density. These results are expected to be helpful to improve the simulation performance of mixed bicycle flow as well as depict more realistic vehicle-bicycle conflicts and so on.

  14. Modeling mechanical behaviors of composites with various ratios of matrixeinclusion properties using movable cellular automaton method

    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.

  15. Cellular, molecular and functional characterisation of YAC transgenic mouse models of Friedreich ataxia.

    Directory of Open Access Journals (Sweden)

    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.

  16. 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

  17. GAME THEORY BASED INTERFERENCE CONTROL AND POWER CONTROL FOR D2D COMMUNICATION IN CELLULAR NETWORKS

    Directory of Open Access Journals (Sweden)

    Fa-Bin Li

    2016-09-01

    Full Text Available With the current development of mobile communication services, people need personal communication of high speed, excellent service, high quality and low latency,however, limited spectrum resources become the most important factor to hamper improvement of cellular systems. As big amount of data traffic will cause greater local consumption of spectrum resources, future networks are required to have appropriate techniques to better support such forms of communication. D2D (Device-to-device communication technology in a cellular network makes full use of spectrum resources underlaying, reduces the load of the base station, minimizes transmit power of the terminals and the base stations, thereby enhances the overall throughput of the networks. Due to the use of multiplexing D2D UE (User equipment resources and spectrum, and the interference caused by the sharing of resources between adjacent cells, it has become a major factor affecting coexisting of cellular subscribers and D2D users. When D2D communication multiplexes the uplink resources, the base-stations are easily to be disturbed; when the downlink resources are multiplexed, the users of downlink are susceptible to interference. In order to build a high-efficient mobile network, we can meet the QoS requirements by controlling the power to suppress the interference between the base station and a terminal user.

  18. Visualization of Gene Mutation Complicated Pattern of Hepatitis B Virus Based on Cellular Automata

    Institute of Scientific and Technical Information of China (English)

    SHAO Shi-huang; XIAO Xuan; DING Yong-sheng; HUANG Zhen-de

    2005-01-01

    Hepatitis B virus shows instantaneous and high rate mutations in biological experiments, some sorts of which affect the efficiency of virus replication greatly through enhancing or depressing the viral replication, while others have no influence at all. Taking advantage of prominent features of cellular automata, we simulate the effect of hepatitis B virus gene mutation on its replication efficiency. The computer simulation results demonstrate the feasibility of our novel model by comparing with the results of biological experiments.

  19. From Cells to Islands: An unified Model of Cellular Parallel Genetic Algorithms

    CERN Document Server

    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.

  20. Integrated Circuit-Based Biofabrication with Common Biomaterials for Probing Cellular Biomechanics.

    Science.gov (United States)

    Sung, Chun-Yen; Yang, Chung-Yao; Yeh, J Andrew; Cheng, Chao-Min

    2016-02-01

    Recent advances in bioengineering have enabled the development of biomedical tools with modifiable surface features (small-scale architecture) to mimic extracellular matrices and aid in the development of well-controlled platforms that allow for the application of mechanical stimulation for studying cellular biomechanics. An overview of recent developments in common biomaterials that can be manufactured using integrated circuit-based biofabrication is presented. Integrated circuit-based biofabrication possesses advantages including mass and diverse production capacities for fabricating in vitro biomedical devices. This review highlights the use of common biomaterials that have been most frequently used to study cellular biomechanics. In addition, the influence of various small-scale characteristics on common biomaterial surfaces for a range of different cell types is discussed.

  1. Bit-Vectorized GPU Implementation of a Stochastic Cellular Automaton Model for Surface Growth

    CERN Document Server

    Kelling, Jeffrey; Gemming, Sibylle

    2016-01-01

    Stochastic surface growth models aid in studying properties of universality classes like the Kardar--Paris--Zhang class. High precision results obtained from large scale computational studies can be transferred to many physical systems. Many properties, such as roughening and some two-time functions can be studied using stochastic cellular automaton (SCA) variants of stochastic models. Here we present a highly efficient SCA implementation of a surface growth model capable of simulating billions of lattice sites on a single GPU. We also provide insight into cases requiring arbitrary random probabilities which are not accessible through bit-vectorization.

  2. Developing land use scenario dynamics model by the integration of system dynamics model and cellular automata model

    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.

  3. A Model of Redox Kinetics Implicates the Thiol Proteome in Cellular Hydrogen Peroxide Responses

    OpenAIRE

    Adimora, Nnenna J.; Jones, Dean P; Melissa L Kemp

    2010-01-01

    Hydrogen peroxide is appreciated as a cellular signaling molecule with second-messenger properties, yet the mechanisms by which the cell protects against intracellular H2O2 accumulation are not fully understood. We introduce a network model of H2O2 clearance that includes the pseudo-enzymatic oxidative turnover of protein thiols, the enzymatic actions of catalase, glutathione peroxidase, peroxiredoxin, and glutaredoxin, and the redox reactions of thioredoxin and glutathione. Simulations repro...

  4. Simulation Based Optimization of Complex Monolithic Composite Structures Using Cellular Core Technology

    Science.gov (United States)

    Hickmott, Curtis W.

    Cellular core tooling is a new technology which has the capability to manufacture complex integrated monolithic composite structures. This novel tooling method utilizes thermoplastic cellular cores as inner tooling. The semi-rigid nature of the cellular cores makes them convenient for lay-up, and under autoclave temperature and pressure they soften and expand providing uniform compaction on all surfaces including internal features such as ribs and spar tubes. This process has the capability of developing fully optimized aerospace structures by reducing or eliminating assembly using fasteners or bonded joints. The technology is studied in the context of evaluating its capabilities, advantages, and limitations in developing high quality structures. The complex nature of these parts has led to development of a model using the Finite Element Analysis (FEA) software Abaqus and the plug-in COMPRO Common Component Architecture (CCA) provided by Convergent Manufacturing Technologies. This model utilizes a "virtual autoclave" technique to simulate temperature profiles, resin flow paths, and ultimately deformation from residual stress. A model has been developed simulating the temperature profile during curing of composite parts made with the cellular core technology. While modeling of composites has been performed in the past, this project will look to take this existing knowledge and apply it to this new manufacturing method capable of building more complex parts and develop a model designed specifically for building large, complex components with a high degree of accuracy. The model development has been carried out in conjunction with experimental validation. A double box beam structure was chosen for analysis to determine the effects of the technology on internal ribs and joints. Double box beams were manufactured and sectioned into T-joints for characterization. Mechanical behavior of T-joints was performed using the T-joint pull-off test and compared to traditional

  5. Management of Location Based Advertisement Services using Spatial Triggers in Cellular Networks

    OpenAIRE

    Assad Ali; Raheel M. Hashmi; Khurram Shehzad; Khan, Furqan H.; Baig, M. M. Tahir N.; Irfan, M

    2009-01-01

    This paper discusses the advent of new technologies which have emerged under the area of Location Based Services (LBS). An innovative implementation and approach has been presented for design of applications which are inventive and attractive towards the user. Spatial Trigger is one of the most promising additions to the LBS technologies. This paper describes ways in which mobile advertisement services can be introduced effectively in the cellular market by bringing innovation in them through...

  6. Mimo radar waveform design for spectrum sharing with cellular systems a Matlab based approach

    CERN Document Server

    Khawar, Awais; Clancy, T Charles

    2016-01-01

    This book discusses spectrum sharing between cellular systems and radars. The book addresses a novel way to design radar waveforms that can enable spectrum sharing between radars and communication systems, without causing interference to communication systems, and at the same time achieving radar objectives of target detection, estimation, and tracking. The book includes a MATLAB-based approach, which provides reader with a way to learn, experiment, compare, and build on top of existing algorithms.

  7. HIV-1 Reverse Transcriptase based assay to determine cellular dNTP concentrations

    Science.gov (United States)

    Hollenbaugh, Joseph A.; Kim, Baek

    2016-01-01

    Summary Deoxynucleoside triphosphates (dNTPs) are the building blocks of DNA and their biosynthesis are tightly regulated in the cell. HPLC-MS and enzyme-based methods are currently employed to determine dNTP concentrations from cellular extracts. Here, we describe a highly efficient, HIV-1 reverse transcriptase (RT)-based assay to quantitate dNTP concentrations. The assay is based on the ability of HIV-1 RT to function at very low dNTP concentrations, thus providing for the high sensitivity of detection. PMID:26714705

  8. A model of redox kinetics implicates the thiol proteome in cellular hydrogen peroxide responses.

    Science.gov (United States)

    Adimora, Nnenna J; Jones, Dean P; Kemp, Melissa L

    2010-09-15

    Hydrogen peroxide is appreciated as a cellular signaling molecule with second-messenger properties, yet the mechanisms by which the cell protects against intracellular H(2)O(2) accumulation are not fully understood. We introduce a network model of H(2)O(2) clearance that includes the pseudo-enzymatic oxidative turnover of protein thiols, the enzymatic actions of catalase, glutathione peroxidase, peroxiredoxin, and glutaredoxin, and the redox reactions of thioredoxin and glutathione. Simulations reproduced experimental observations of the rapid and transient oxidation of glutathione and the rapid, sustained oxidation of thioredoxin on exposure to extracellular H(2)O(2). The model correctly predicted early oxidation profiles for the glutathione and thioredoxin redox couples across a range of initial extracellular [H(2)O(2)] and highlights the importance of cytoplasmic membrane permeability to the cellular defense against exogenous sources of H(2)O(2). The protein oxidation profile predicted by the model suggests that approximately 10% of intracellular protein thiols react with hydrogen peroxide at substantial rates, with a majority of these proteins forming protein disulfides as opposed to protein S-glutathionylated adducts. A steady-state flux analysis predicted an unequal distribution of the intracellular anti-oxidative burden between thioredoxin-dependent and glutathione-dependent antioxidant pathways, with the former contributing the majority of the cellular antioxidant defense due to peroxiredoxins and protein disulfides.

  9. An Asynchronous Recurrent Network of Cellular Automaton-Based Neurons and Its Reproduction of Spiking Neural Network Activities.

    Science.gov (United States)

    Matsubara, Takashi; Torikai, Hiroyuki

    2016-04-01

    Modeling and implementation approaches for the reproduction of input-output relationships in biological nervous tissues contribute to the development of engineering and clinical applications. However, because of high nonlinearity, the traditional modeling and implementation approaches encounter difficulties in terms of generalization ability (i.e., performance when reproducing an unknown data set) and computational resources (i.e., computation time and circuit elements). To overcome these difficulties, asynchronous cellular automaton-based neuron (ACAN) models, which are described as special kinds of cellular automata that can be implemented as small asynchronous sequential logic circuits have been proposed. This paper presents a novel type of such ACAN and a theoretical analysis of its excitability. This paper also presents a novel network of such neurons, which can mimic input-output relationships of biological and nonlinear ordinary differential equation model neural networks. Numerical analyses confirm that the presented network has a higher generalization ability than other major modeling and implementation approaches. In addition, Field-Programmable Gate Array-implementations confirm that the presented network requires lower computational resources.

  10. Modeling of Trophospheric Ozone Concentrations Using Genetically Trained Multi-Level Cellular Neural Networks

    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.

  11. Modeling of trophospheric ozone concentrations using genetically trained multi-level cellular neural networks

    Science.gov (United States)

    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.

  12. 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

  13. Silver Nanoparticle-Mediated Cellular Responses in Various Cell Lines: An in Vitro Model

    Science.gov (United States)

    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

  14. Silver Nanoparticle-Mediated Cellular Responses in Various Cell Lines: An in Vitro Model.

    Science.gov (United States)

    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

  15. Instantaneous information propagation in free flow, synchronized flow, stop-and-go waves in a cellular automaton model

    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.

  16. Chronobiology at the cellular and molecular levels: models and mechanisms for circadian timekeeping.

    Science.gov (United States)

    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. PMID:6229999

  17. An improved multi-value cellular automata model for heterogeneous bicycle traffic flow

    International Nuclear Information System (INIS)

    This letter develops an improved multi-value cellular automata model for heterogeneous bicycle traffic flow taking the higher maximum speed of electric bicycles into consideration. The update rules of both regular and electric bicycles are improved, with maximum speeds of two and three cells per second respectively. Numerical simulation results for deterministic and stochastic cases are obtained. The fundamental diagrams and multiple states effects under different model parameters are analyzed and discussed. Field observations were made to calibrate the slowdown probabilities. The results imply that the improved extended Burgers cellular automata (IEBCA) model is more consistent with the field observations than previous models and greatly enhances the realism of the bicycle traffic model. - Highlights: • We proposed an improved multi-value CA model with higher maximum speed. • Update rules are introduced for heterogeneous bicycle traffic with maximum speed 2 and 3 cells/s. • Simulation results of the proposed model are consistent with field bicycle data. • Slowdown probabilities of both regular and electric bicycles are calibrated

  18. 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.

  19. 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.

  20. Cooperative Game-Based Energy Efficiency Management over Ultra-Dense Wireless Cellular Networks.

    Science.gov (United States)

    Li, Ming; Chen, Pengpeng; Gao, Shouwan

    2016-09-13

    Ultra-dense wireless cellular networks have been envisioned as a promising technique for handling the explosive increase of wireless traffic volume. With the extensive deployment of small cells in wireless cellular networks, the network spectral efficiency (SE) is improved with the use of limited frequency. However, the mutual inter-tier and intra-tier interference between or among small cells and macro cells becomes serious. On the other hand, more chances for potential cooperation among different cells are introduced. Energy efficiency (EE) has become one of the most important problems for future wireless networks. This paper proposes a cooperative bargaining game-based method for comprehensive EE management in an ultra-dense wireless cellular network, which highlights the complicated interference influence on energy-saving challenges and the power-coordination process among small cells and macro cells. Especially, a unified EE utility with the consideration of the interference mitigation is proposed to jointly address the SE, the deployment efficiency (DE), and the EE. In particular, closed-form power-coordination solutions for the optimal EE are derived to show the convergence property of the algorithm. Moreover, a simplified algorithm is presented to reduce the complexity of the signaling overhead, which is significant for ultra-dense small cells. Finally, numerical simulations are provided to illustrate the efficiency of the proposed cooperative bargaining game-based and simplified schemes.

  1. Cooperative Game-Based Energy Efficiency Management over Ultra-Dense Wireless Cellular Networks

    Science.gov (United States)

    Li, Ming; Chen, Pengpeng; Gao, Shouwan

    2016-01-01

    Ultra-dense wireless cellular networks have been envisioned as a promising technique for handling the explosive increase of wireless traffic volume. With the extensive deployment of small cells in wireless cellular networks, the network spectral efficiency (SE) is improved with the use of limited frequency. However, the mutual inter-tier and intra-tier interference between or among small cells and macro cells becomes serious. On the other hand, more chances for potential cooperation among different cells are introduced. Energy efficiency (EE) has become one of the most important problems for future wireless networks. This paper proposes a cooperative bargaining game-based method for comprehensive EE management in an ultra-dense wireless cellular network, which highlights the complicated interference influence on energy-saving challenges and the power-coordination process among small cells and macro cells. Especially, a unified EE utility with the consideration of the interference mitigation is proposed to jointly address the SE, the deployment efficiency (DE), and the EE. In particular, closed-form power-coordination solutions for the optimal EE are derived to show the convergence property of the algorithm. Moreover, a simplified algorithm is presented to reduce the complexity of the signaling overhead, which is significant for ultra-dense small cells. Finally, numerical simulations are provided to illustrate the efficiency of the proposed cooperative bargaining game-based and simplified schemes. PMID:27649170

  2. 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.

  3. An authenticated image encryption scheme based on chaotic maps and memory cellular automata

    Science.gov (United States)

    Bakhshandeh, Atieh; Eslami, Ziba

    2013-06-01

    This paper introduces a new image encryption scheme based on chaotic maps, cellular automata and permutation-diffusion architecture. In the permutation phase, a piecewise linear chaotic map is utilized to confuse the plain-image and in the diffusion phase, we employ the Logistic map as well as a reversible memory cellular automata to obtain an efficient and secure cryptosystem. The proposed method admits advantages such as highly secure diffusion mechanism, computational efficiency and ease of implementation. A novel property of the proposed scheme is its authentication ability which can detect whether the image is tampered during the transmission or not. This is particularly important in applications where image data or part of it contains highly sensitive information. Results of various analyses manifest high security of this new method and its capability for practical image encryption.

  4. Reprint of Infinity computations in cellular automaton forest-fire model

    Science.gov (United States)

    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.

  5. 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.

  6. Idealized Mesoscale Model Simulations of Open Cellular Convection Over the Sea

    DEFF Research Database (Denmark)

    Vincent, Claire Louise; Hahmann, Andrea N.; Kelly, Mark C.

    2012-01-01

    The atmospheric conditions during an observed case of open cellular convection over the North Sea were simulated using the Weather Research and Forecasting (WRF) numerical model. Wind, temperature and water vapour mixing ratio profiles from the WRF simulation were used to initialize an idealized...... version of the model, which excluded the effects of topography, surface inhomogeneities and large-scale weather forcing. Cells with an average diameter of 17.4 km developed. Simulations both with and without a capping inversion were made, and the cell-scale kinetic energy budget was calculated for each...

  7. Two-dimensional cellular automaton model for simulating structural evolution of binary alloys during solidification

    Institute of Scientific and Technical Information of China (English)

    ZHANG Lin; ZHANG Cai-bei

    2006-01-01

    Two-dimensional cellular automaton(CA) simulations of phase transformations of binary alloys during solidification were reported. The modelling incorporates local concentration and heat changes into a nucleation or growth function, which is utilized by the automaton in a probabilistic fashion. These simulations may provide an efficient method of discovering how the physical processes involved in solidification processes dynamically progress and how they interact with each other during solidification. The simulated results show that the final morphology during solidification is related with the cooling conditions. The established model can be used to evaluate the phase transformation of binary alloys during solidification.

  8. A Cellular Automaton Model for Heterogeneous and Incosistent Driver Behavior in Urban Traffic

    Science.gov (United States)

    Liu, Ming-Zhe; Zhao, Shi-Bo; Wang, Rui-Li

    2012-11-01

    In this paper a cellular automaton model is proposed to describe driver behavior at a single-lane urban roundabout. Driver behavior has been considered as heterogeneous and inconsistent. Most traffic papers in the literature just discussed heterogeneous driver behavior, to our best knowledge. Two truncated Gaussian distributions are used to model heterogeneous and inconsistent driver behavior, respectively. The physical meanings of two truncated distributions are indicated. This method may help enhance a better understanding of driver behavior at roundabout traffic, and even possibly provide references for roundabout design and management.

  9. 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.

  10. A Stream Control Transmission Protocol Based OAM System of 3G Cellular Network

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    OAM (Operations, Administration and Maintenance) system is a very important component of 3G cellular network. In order to acquire overall management, fast response and steady operation, an SCTP (Stream Control Transmission Protocol) based OAM, i. e. , SOAM system was proposed. SOAM implements new characters of SCTP such as multi-stream, enforced SACK and heartbeat mechanism on its transport layer. These characters help SOAM decrease the message transmission delay and accelerate the link failure detection. Besides, a new component named SOAM agent was introduced to improve the operation efficiency of SOAM. The experimental results prove the proposed SOAM system achieves better performance on signaling transmission compared with conventional TCP based OAM system.

  11. Cell damage from radiation-induced bystander effects for different cell densities simulated by a mathematical model via cellular automata

    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)

  12. Cell damage from radiation-induced bystander effects for different cell densities simulated by a mathematical model via cellular automata

    International Nuclear Information System (INIS)

    During recent years, there has been a shift from an approach focused entirely on DNA as the main target of ionizing radiation to a vision that considers complex signaling pathways in cells and among cells within tissues. Several newly recognized responses were classified as the so-called non-target responses in which the biological effects are not directly related to the amount of energy deposited in the DNA of cells that were traversed by radiation. In 1992 the bystander effect was described referring to a series of responses such as death, chromosomal instability or other abnormalities that occur in non-irradiated cells that came into contact with irradiated cells or medium from irradiated cells. In this work, we have developed a mathematical model via cellular automata, to quantify cell death induced by the bystander effect. The model is based on experiments with irradiated cells conditioned medium which suggests that irradiated cells secrete molecules in the medium that are capable of damaging other cells. The computational model consists of two-dimensional cellular automata which is able to simulate the transmission of bystander signals via extrinsic route and via Gap junctions. The model has been validated by experimental results in the literature. The time evolution of the effect and the dose-response curves were obtained in good accordance to them. Simulations were conducted for different values of bystander and irradiated cell densities with constant dose. From this work, we have obtained a relationship between cell density and effect. (author)

  13. An analytical model for evaluating outage and handover probability of cellular wireless networks

    CERN Document Server

    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.

  14. On stochastic geometry modeling of cellular uplink transmission with truncated channel inversion power control

    KAUST Repository

    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.

  15. Direct translocation as major cellular uptake for CADY self-assembling peptide-based nanoparticles.

    Directory of Open Access Journals (Sweden)

    Anna Rydström

    Full Text Available Cell penetrating peptides constitute a potent approach to overcome the limitations of in vivo siRNA delivery. We recently proposed a peptide-based nanoparticle system, CADY, for efficient delivery of siRNA into numerous cell lines. CADY is a secondary amphipathic peptide that forms stable complexes with siRNA thereby improving both their cellular uptake and biological response. With the aim of understanding the cellular uptake mechanism of CADY:siRNA complexes, we have combined biochemical, confocal and electron microscopy approaches. In the present work, we provide evidence that the major route for CADY:siRNA cellular uptake involves direct translocation through the membrane but not the endosomal pathway. We have demonstrated that CADY:siRNA complexes do not colocalize with most endosomal markers and remain fully active in the presence of inhibitors of the endosomal pathway. Moreover, neither electrostatic interactions with cell surface heparan sulphates nor membrane potential are essential for CADY:siRNA cell entry. In contrast, we have shown that CADY:siRNA complexes clearly induce a transient cell membrane permeabilization, which is rapidly restored by cell membrane fluidity. Therefore, we propose that direct translocation is the major gate for cell entry of CADY:siRNA complexes. Membrane perturbation and uptake are driven mainly by the ability of CADY to interact with phospholipids within the cell membrane, followed by rapid localization of the complex in the cytoplasm, without affecting cell integrity or viability.

  16. Stochastic multi-scale models of competition within heterogeneous cellular populations: simulation methods and mean-field analysis

    CERN Document Server

    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...

  17. 基于灰色模型-元胞自动机模型的佛山市土地利用情景模拟分析%Land use scenarios simulation of Foshan city based on gray model and cellular automata model

    Institute of Scientific and Technical Information of China (English)

    王丽萍; 金晓斌; 杜心栋; 周寅康

    2012-01-01

    LUCC model is an efficient tool to analysis the processes and consequences of land use systems, and to support land use planning and policy. According to the problem that constructive land expansion is the main reason for land use change in Foshan city, based on remote sensing data of land use change with spatial resolution of 30 m, the paper choose grey model as quantitative model and the cellular automata model as spatial model to simulate the land use pattern of 2015 by setting different scenario conditions. Results showed that in three kinds of expansion circumstances of.constructive land, the area of constructive land increased 27 830 、 21 645 and 15 461 hm2 respectively, the corresponding proportion of the cultivated land was 42.28%, 48.38% and 55.96% respectively. This indicates that cultivated land is still the main source of constructive land expansion, the contradiction between cultivated land protection and economic development will further expend.%通过模拟土地利用变化情景,了解土地利用变化趋势,可为制定科学的土地利用管理策略提供支持,根据近年来建设用地扩张在佛山市土地利用类型变化中占主导地位的特点,选择灰色模型作为数量模型,元胞自动机模型作为空间模型,设定3种建设用地扩张情景:适度约束、中度约束和强力约束,结合数量模型和空间模型的优点,模拟2015年土地利用空间布局.研究结果表明:在设定的3种建设用地扩张情景下,建设用地增加的面积分别为278.3、216.5和154.6 km2,相应来源于耕地的比率分别为42.28%、48.38%和55.96%,说明耕地仍然是建设用地增加的主要来源,也即耕地保护和经济发展的矛盾将会进一步增大,可为政府和土地管理部门制定政策提供一定的参考,从而采取更有针对性的措施.

  18. DIGE proteome analysis reveals suitability of ischemic cardiac in vitro model for studying cellular response to acute ischemia and regeneration.

    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.

  19. One-way hash function based on hyper-chaotic cellular neural network

    Institute of Scientific and Technical Information of China (English)

    Yang Qun-Ting; Gao Tie-Gang

    2008-01-01

    The design of an efficient one-way hash function with good performance is a hot spot in modern cryptography researches. In this paper, a hash function construction method based on cell neural network with hyper-chaos characteristics is proposed. First, the chaos sequence is gotten by iterating cellular neural network with Runge-Kutta algorithm, and then the chaos sequence is iterated with the message. The hash code is obtained through the corresponding transform of the latter chaos sequence. Simulation and analysis demonstrate that the new method has the merit of convenience, high sensitivity to initial values, good hash performance, especially the strong stability.

  20. New color image encryption algorithm based on compound chaos mapping and hyperchaotic cellular neural network

    Science.gov (United States)

    Li, Jinqing; Bai, Fengming; Di, Xiaoqiang

    2013-01-01

    We propose an image encryption/decryption algorithm based on chaotic control parameter and hyperchaotic system with the composite permutation-diffusion structure. Compound chaos mapping is used to generate control parameters in the permutation stage. The high correlation between pixels is shuffled. In the diffusion stage, compound chaos mapping of different initial condition and control parameter generates the diffusion parameters, which are applied to hyperchaotic cellular neural networks. The diffusion key stream is obtained by this process and implements the pixels' diffusion. Compared with the existing methods, both simulation and statistical analysis of our proposed algorithm show that the algorithm has a good performance against attacks and meets the corresponding security level.

  1. Hologram authentication based on a secure watermarking algorithm using cellular automata.

    Science.gov (United States)

    Hwang, Wen-Jyi; Chan, Hao-Tang; Cheng, Chau-Jern

    2014-09-20

    A secure watermarking algorithm for hologram authentication is presented in this paper. The algorithm exploits the noise-like feature of holograms to randomly embed a watermark in the domain of the discrete cosine transform with marginal degradation in transparency. The pseudo random number (PRN) generators based on a cellular automata algorithm with asymmetrical and nonlocal connections are used for the random hiding. Each client has its own unique PRN generators for enhancing the watermark security. In the proposed algorithm, watermarks are also randomly generated to eliminate the requirements of prestoring watermarks in the clients and servers. An authentication scheme is then proposed for the algorithm with random watermark generation and hiding.

  2. 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.

  3. Metabolically active portion of fat-free mass: a cellular body composition level modeling analysis

    OpenAIRE

    Wang, ZiMian; Heshka, Stanley; Wang, Jack; Gallagher, Dympna; Deurenberg, Paul; Chen, Zhao; Heymsfield, Steven B

    2006-01-01

    The proportion of fat-free mass (FFM) as body cell mass (BCM) is highly related to whole body resting energy expenditure. However, the magnitude of BCM/FFM may have been underestimated in previous studies. This is because Moore’s equation [BCM (kg) =0.00833 × total body potassium (in mmol)], which was used to predict BCM, underestimates BCM by ~ %. The aims of the present study were to develop a theoretical BCM/FFM model at the cellular level and to explore the influences of sex, age, and adi...

  4. Model-based geostatistics

    CERN Document Server

    Diggle, Peter J

    2007-01-01

    Model-based geostatistics refers to the application of general statistical principles of modeling and inference to geostatistical problems. This volume provides a treatment of model-based geostatistics and emphasizes on statistical methods and applications. It also features analyses of datasets from a range of scientific contexts.

  5. Comparison of Cellular Automaton and Phase Field Models to Simulate Dendrite Growth in Hexagonal Crystals

    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.

  6. 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.

  7. A mathematical model in cellular manufacturing system considering subcontracting approach under constraints

    Directory of Open Access Journals (Sweden)

    Kamran Forghani

    2012-10-01

    Full Text Available In this paper, a new mathematical model in cellular manufacturing systems (CMSs has been presented. In order to increase the performance of manufacturing system, the production quantity of parts has been considered as a decision variable, i.e. each part can be produced and outsourced, simultaneously. This extension would be minimized the unused capacity of machines. The exceptional elements (EEs are taken into account and would be totally outsourced to the external supplier in order to remove intercellular material handling cost. The problem has been formulated as a mixed-integer programming to minimize the sum of manufacturing variable costs under budget, machines capacity and demand constraints. Also, to evaluate advantages of the model, several illustrative numerical examples have been provided to compare the performance of the proposed model with the available classical approaches in the literature.

  8. A Two-Lane Cellular Automata Model with Influence of Next-Nearest Neighbor Vehicle

    Institute of Scientific and Technical Information of China (English)

    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.

  9. Designing a mathematical model for integrating dynamic cellular manufacturing into supply chain system

    Science.gov (United States)

    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.

  10. Dynamical critical behavior in a cellular model of superconducting vortex avalanches

    Science.gov (United States)

    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.

  11. Mathematical modeling of ultrasound in tissue engineering: From bioreactors to the cellular scale

    Science.gov (United States)

    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

  12. Cellular automaton for chimera states

    OpenAIRE

    García-Morales, Vladimir

    2016-01-01

    A minimalistic model for chimera states is presented. The model is a cellular automaton (CA) which depends on only one adjustable parameter, the range of the nonlocal coupling, and is built from elementary cellular automata and the majority (voting) rule. This suggests the universality of chimera-like behavior from a new point of view: Already simple CA rules based on the majority rule exhibit this behavior. After a short transient, we find chimera states for arbitrary initial conditions, the...

  13. Maintaining accuracy of cellular Yule-Nielsen spectral Neugebauer models for different ink cartridges using principal component analysis.

    Science.gov (United States)

    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.

  14. A computable cellular stress network model for non-diseased pulmonary and cardiovascular tissue

    Directory of Open Access Journals (Sweden)

    Drubin David

    2011-10-01

    Full Text Available Abstract Background Humans and other organisms are equipped with a set of responses that can prevent damage from exposure to a multitude of endogenous and environmental stressors. If these stress responses are overwhelmed, this can result in pathogenesis of diseases, which is reflected by an increased development of, e.g., pulmonary and cardiac diseases in humans exposed to chronic levels of environmental stress, including inhaled cigarette smoke (CS. Systems biology data sets (e.g., transcriptomics, phosphoproteomics, metabolomics could enable comprehensive investigation of the biological impact of these stressors. However, detailed mechanistic networks are needed to determine which specific pathways are activated in response to different stressors and to drive the qualitative and eventually quantitative assessment of these data. A current limiting step in this process is the availability of detailed mechanistic networks that can be used as an analytical substrate. Results We have built a detailed network model that captures the biology underlying the physiological cellular response to endogenous and exogenous stressors in non-diseased mammalian pulmonary and cardiovascular cells. The contents of the network model reflect several diverse areas of signaling, including oxidative stress, hypoxia, shear stress, endoplasmic reticulum stress, and xenobiotic stress, that are elicited in response to common pulmonary and cardiovascular stressors. We then tested the ability of the network model to identify the mechanisms that are activated in response to CS, a broad inducer of cellular stress. Using transcriptomic data from the lungs of mice exposed to CS, the network model identified a robust increase in the oxidative stress response, largely mediated by the anti-oxidant NRF2 pathways, consistent with previous reports on the impact of CS exposure in the mammalian lung. Conclusions The results presented here describe the construction of a cellular stress

  15. MICROMECHANICS OF THE DAMAGE-INDUCED CELLULAR MICROSTRUCTURE IN SINGLE CRYSTAL Ni-BASED SUPERALLOYS

    Institute of Scientific and Technical Information of China (English)

    M.Sakaguchi; M.Okazaki

    2004-01-01

    An analytical method to investigate the morphological evolution of the cellular microstructure is explored and proposed. The method is essentially based on the Eshelby's micromechanics theory, and it is extended so as to be applied for a material system containing inclusions with high volume fraction, by employing the average stress field approximation by Mori and Tanaka. The proposed method enables us to discuss a stable shape of precipitate in the material system, which must be influenced by many factors: e.g., volume fraction of precipitate; Young's modulus ratio and lattice misfit between matrix and precipitate; external stress field in multiaxial state; and heterogeneity of plastic strain between matrix and precipitate. A series of numerical calculations were summarized on stable shape maps. The application of the method to predict the γ' rafting in superalloys during creep showed that the heterogeneity of plastic strain between matrix and precipitates may play a significant role in the shape stability of the precipitate. Furthermore, it was shown that the method was successfully applied to estimate the morphology of the cellular microstructure formed in CMSX-4single crystal Ni-based superalloy.

  16. Geographic Spatiotemporal Dynamic Model using Cellular Automata and Data Mining Techniques

    Directory of Open Access Journals (Sweden)

    Ahmad Zuhdi

    2011-05-01

    Full Text Available Geospatial data and information availability has been increasing rapidly and has provided users with knowledge on entities change and movement in a system. Cellular Geography model applies Cellular Automata on Geographic data by defining transition rules to the data grid. This paper presents the techniques for extracting transition rule(s from time series data grids, using multiple linear regression analysis. Clustering technique is applied to minimize the number of transition rules, which can be offered and chosen to change a new unknown grid. Each centroid of a cluster is associated with a transition rule and a grid of data. The chosen transition rule is associated with grid that has a minimum distance to the new data grid to be simulated. Validation of the model can be provided either quantitatively through an error measurement or qualitatively by visualizing the result of the simulation process. The visualization can also be more informative by adding the error information. Increasing number of cluster may give possibility to improve the simulation accuracy.

  17. Oleuropein Prevents Neuronal Death, Mitigates Mitochondrial Superoxide Production and Modulates Autophagy in a Dopaminergic Cellular Model.

    Science.gov (United States)

    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

  18. Oleuropein Prevents Neuronal Death, Mitigates Mitochondrial Superoxide Production and Modulates Autophagy in a Dopaminergic Cellular Model

    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.

  19. Oleuropein Prevents Neuronal Death, Mitigates Mitochondrial Superoxide Production and Modulates Autophagy in a Dopaminergic Cellular Model

    Science.gov (United States)

    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

  20. A cellular automaton model adapted to sandboxes to simulate the transport of solutes

    Science.gov (United States)

    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.

  1. Analytical modeling of mode selection and power control for underlay D2D communication in cellular networks

    KAUST Repository

    Elsawy, Hesham

    2014-11-01

    Device-to-device (D2D) communication enables the user equipments (UEs) located in close proximity to bypass the cellular base stations (BSs) and directly connect to each other, and thereby, offload traffic from the cellular infrastructure. D2D communication can improve spatial frequency reuse and energy efficiency in cellular networks. This paper presents a comprehensive and tractable analytical framework for D2D-enabled uplink cellular networks with a flexible mode selection scheme along with truncated channel inversion power control. The developed framework is used to analyze and understand how the underlaying D2D communication affects the cellular network performance. Through comprehensive numerical analysis, we investigate the expected performance gains and provide guidelines for selecting the network parameters.

  2. Knowledge-guided fuzzy logic modeling to infer cellular signaling networks from proteomic data

    Science.gov (United States)

    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

  3. A cellular automation model for the change of public attitude regarding nuclear energy

    International Nuclear Information System (INIS)

    A cellular automation model was constructed to investigate how public opinion on nuclear energy in Japan depends upon the information environment and personal communication between people. From simulation with this model, the following become clear; (i) society is a highly non-linear system with a self-organizing potential: (ii) in a society composed of one type of constituent member with homogeneous characteristics, the trend of public opinion is substantially changed only when the effort to ameliorate public acceptance over a long period of time, by means such as education, persuasion and advertisement, exceeds a certain threshold, and (iii) in the case when the amount of information on nuclear risk released from the newsmedia is reduced continuously from now on, the acceptability of nuclear energy is significantly improved so far as the extent of the reduction exceeds a certain threshold. (author)

  4. 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.

  5. Potential Field Cellular Automata Model for Pedestrian Evacuation in a Domain with a Ramp

    Directory of Open Access Journals (Sweden)

    Xiao-Xia Jian

    2014-01-01

    Full Text Available We propose a potential field cellular automata model with a pushing force field to simulate the pedestrian evacuation in a domain with a ramp. We construct a cost potential depending on the ramp angle and introduce a function to evaluate the pushing force, which is related to the cost and the desired direction of pedestrian. With increase of crowd density, there is no empty space for pedestrian moving forward; pedestrian will purposefully push another pedestrian on her or his desired location to arrive the destination quickly. We analyse the relationship between the slope of ramp and the pushing force and investigate the changing of injured situations with the changing of the slope of ramp. When the number of pedestrians and the ramp angle arrive at certain critical points, the Domino effect will be simulated by this proposed model.

  6. Decellularized extracellular matrix microparticles as a vehicle for cellular delivery in a model of anastomosis healing.

    Science.gov (United States)

    Hoganson, David M; Owens, Gwen E; Meppelink, Amanda M; Bassett, Erik K; Bowley, Chris M; Hinkel, Cameron J; Finkelstein, Eric B; Goldman, Scott M; Vacanti, Joseph P

    2016-07-01

    Extracellular matrix (ECM) materials from animal and human sources have become important materials for soft tissue repair. Microparticles of ECM materials have increased surface area and exposed binding sites compared to sheet materials. Decellularized porcine peritoneum was mechanically dissociated into 200 µm microparticles, seeded with fibroblasts and cultured in a low gravity rotating bioreactor. The cells avidly attached and maintained excellent viability on the microparticles. When the seeded microparticles were placed in a collagen gel, the cells quickly migrated off the microparticles and through the gel. Cells from seeded microparticles migrated to and across an in vitro anastomosis model, increasing the tensile strength of the model. Cell seeded microparticles of ECM material have potential for paracrine and cellular delivery therapies when delivered in a gel carrier. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 104A: 1728-1735, 2016. PMID:26946064

  7. Global Detection of Live Virtual Machine Migration Based on Cellular Neural Networks

    Directory of Open Access Journals (Sweden)

    Kang Xie

    2014-01-01

    Full Text Available In order to meet the demands of operation monitoring of large scale, autoscaling, and heterogeneous virtual resources in the existing cloud computing, a new method of live virtual machine (VM migration detection algorithm based on the cellular neural networks (CNNs, is presented. Through analyzing the detection process, the parameter relationship of CNN is mapped as an optimization problem, in which improved particle swarm optimization algorithm based on bubble sort is used to solve the problem. Experimental results demonstrate that the proposed method can display the VM migration processing intuitively. Compared with the best fit heuristic algorithm, this approach reduces the processing time, and emerging evidence has indicated that this new approach is affordable to parallelism and analog very large scale integration (VLSI implementation allowing the VM migration detection to be performed better.

  8. CellLab-CTS 2015: continuous-time stochastic cellular automaton modeling using Landlab

    Science.gov (United States)

    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.

  9. Design and Analysis of Adders using Nanotechnology Based Quantum dot Cellular Automata

    Directory of Open Access Journals (Sweden)

    S. K. Lakshmi

    2011-01-01

    Full Text Available Problem statement: The area and complexity are the major issues in circuit design. Here, we propose different types of adder designs based on Quantum dot Cellular Automata (QCA that reduces number of QCA cells and area compare to previous designs. The quantum dot cellular automata is a novel computing paradigm in nanotechnology that can implement digital circuits with faster speed, smaller size and low power consumption. By taking the advantages of QCA we are able to design interesting computational architectures. The QCA cell is a basic building block of nanotechnology that can be used to make gates, wires and memories. The basic logic circuits used in this technology are the inverter and the Majority Gate (MG, using this other logical circuits can be designed. Approach: In this paper, the adders such as half, full and serial bit were designed and analyzed. These structures were designed with minimum number of cells by using cell minimization techniques. The techniques are (1 using two cells inverter and (2 suitable arrangement of cells without overlapping of neighboring cells. The proposed method can be used to minimize area and complexity. Results: These circuits were designed by majority gate and implemented by QCA cells. Then, they simulated using QCA Designer. The simulated results were verified according to the truth table. Conclusion: The performance analyses of those circuits are compared according to complexity, area and number of clock cycles and are also compared with previous designs.

  10. Distinctive behavioral and cellular responses to fluoxetine in the mouse model for Fragile X syndrome

    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.

  11. Cellular intrinsic mechanism affecting the outcome of AML treated with Ara-C in a syngeneic mouse model.

    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.

  12. 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.

  13. Dengue encephalitis-associated immunopathology in the mouse model: Implications for vaccine developers and antigens inducer of cellular immune response.

    Science.gov (United States)

    Marcos, Ernesto; Lazo, Laura; Gil, Lázaro; Izquierdo, Alienys; Suzarte, Edith; Valdés, Iris; Blanco, Aracelys; Ancizar, Julio; Alba, José Suárez; Pérez, Yusleydis de la C; Cobas, Karen; Romero, Yaremis; Guillén, Gerardo; Guzmán, María G; Hermida, Lisset

    2016-08-01

    Despite the many efforts made by the scientific community in the development of vaccine candidates against dengue virus (DENV), no vaccine has been licensed up to date. Although the immunopathogenesis associated to the disease is a key factor to take into account by vaccine developers, the lack of animal models that reproduce the clinical signs of the disease has hampered the vaccine progress. Non-human primates support viral replication, but they are very expensive and do not show signs of disease. Immunocompromised mice develop viremia and some signs of the disease; however, they are not valuable for vaccine testing. Nowadays, immunocompetent mice are the most used model to evaluate the immunogenicity of vaccine candidates. These animals are resistant to DENV infection; therefore, the intracranial inoculation with neuroadapted virus, which provokes viral encephalitis, represents an alternative to evaluate the protective capacity of vaccine candidates. Previous results have demonstrated the crucial role of cellular immune response in the protection induced by the virus and vaccine candidates in this mouse encephalitis model. However, in the present work we are proposing that the magnitude of the cell-mediated immunity and the inflammatory response generated by the vaccine can modulate the survival rate after viral challenge. We observed that the intracranial challenge of naïve mice with DENV-2 induces the recruitment of immune cells that contribute to the reduction of viral load, but does not increase the survival rate. On the contrary, animals treated with cyclophosphamide, an immunosuppressive drug that affects proliferating lymphocytes, had a higher viral load but a better survival rate than untreated animals. These results suggest that the immune system is playing an immunopathogenic role in this model and the survival rate may not be a suitable endpoint in the evaluation of vaccine candidates based on antigens that induce a strong cellular immune response

  14. Developing an Abaqus *HYPERFOAM Model for M9747 (4003047) Cellular Silicone Foam

    Energy Technology Data Exchange (ETDEWEB)

    Siranosian, Antranik A. [Los Alamos National Laboratory; Stevens, R. Robert [Los Alamos National Laboratory

    2012-04-26

    This report documents work done to develop an Abaqus *HYPERFOAM hyperelastic model for M9747 (4003047) cellular silicone foam for use in quasi-static analyses at ambient temperature. Experimental data, from acceptance tests for 'Pad A' conducted at the Kansas City Plant (KCP), was used to calibrate the model. The data includes gap (relative displacement) and load measurements from three locations on the pad. Thirteen sets of data, from pads with different serial numbers, were provided. The thirty-nine gap-load curves were extracted from the thirteen supplied Excel spreadsheets and analyzed, and from those thirty-nine one set of data, representing a qualitative mean, was chosen to calibrate the model. The data was converted from gap and load to nominal (engineering) strain and nominal stress in order to implement it in Abaqus. Strain computations required initial pad thickness estimates. An Abaqus model of a right-circular cylinder was used to evaluate and calibrate the *HYPERFOAM model.

  15. A multi-objective model for designing a group layout of a dynamic cellular manufacturing system

    Science.gov (United States)

    Kia, Reza; Shirazi, Hossein; Javadian, Nikbakhsh; Tavakkoli-Moghaddam, Reza

    2013-04-01

    This paper presents a multi-objective mixed-integer nonlinear programming model to design a group layout of a cellular manufacturing system in a dynamic environment, in which the number of cells to be formed is variable. Cell formation (CF) and group layout (GL) are concurrently made in a dynamic environment by the integrated model, which incorporates with an extensive coverage of important manufacturing features used in the design of CMSs. Additionally, there are some features that make the presented model different from the previous studies. These features include the following: (1) the variable number of cells, (2) the integrated CF and GL decisions in a dynamic environment by a multi-objective mathematical model, and (3) two conflicting objectives that minimize the total costs (i.e., costs of intra and inter-cell material handling, machine relocation, purchasing new machines, machine overhead, machine processing, and forming cells) and minimize the imbalance of workload among cells. Furthermore, the presented model considers some limitations, such as machine capability, machine capacity, part demands satisfaction, cell size, material flow conservation, and location assignment. Four numerical examples are solved by the GAMS software to illustrate the promising results obtained by the incorporated features.

  16. Integrating the system dynamic and cellular automata models to predict land use and land cover change

    Science.gov (United States)

    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.

  17. Drosophila embryos as model to assess cellular and developmental toxicity of multi-walled carbon nanotubes (MWCNT in living organisms.

    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.

  18. Validity of the Cauchy-Born rule applied to discrete cellular-scale models of biological tissues

    KAUST Repository

    Davit, Y.

    2013-04-30

    The development of new models of biological tissues that consider cells in a discrete manner is becoming increasingly popular as an alternative to continuum methods based on partial differential equations, although formal relationships between the discrete and continuum frameworks remain to be established. For crystal mechanics, the discrete-to-continuum bridge is often made by assuming that local atom displacements can be mapped homogeneously from the mesoscale deformation gradient, an assumption known as the Cauchy-Born rule (CBR). Although the CBR does not hold exactly for noncrystalline materials, it may still be used as a first-order approximation for analytic calculations of effective stresses or strain energies. In this work, our goal is to investigate numerically the applicability of the CBR to two-dimensional cellular-scale models by assessing the mechanical behavior of model biological tissues, including crystalline (honeycomb) and noncrystalline reference states. The numerical procedure involves applying an affine deformation to the boundary cells and computing the quasistatic position of internal cells. The position of internal cells is then compared with the prediction of the CBR and an average deviation is calculated in the strain domain. For center-based cell models, we show that the CBR holds exactly when the deformation gradient is relatively small and the reference stress-free configuration is defined by a honeycomb lattice. We show further that the CBR may be used approximately when the reference state is perturbed from the honeycomb configuration. By contrast, for vertex-based cell models, a similar analysis reveals that the CBR does not provide a good representation of the tissue mechanics, even when the reference configuration is defined by a honeycomb lattice. The paper concludes with a discussion of the implications of these results for concurrent discrete and continuous modeling, adaptation of atom-to-continuum techniques to biological

  19. A Simple BODIPY-Based Viscosity Probe for Imaging of Cellular Viscosity in Live Cells.

    Science.gov (United States)

    Su, Dongdong; Teoh, Chai Lean; Gao, Nengyue; Xu, Qing-Hua; Chang, Young-Tae

    2016-01-01

    Intracellular viscosity is a fundamental physical parameter that indicates the functioning of cells. In this work, we developed a simple boron-dipyrromethene (BODIPY)-based probe, BTV, for cellular mitochondria viscosity imaging by coupling a simple BODIPY rotor with a mitochondria-targeting unit. The BTV exhibited a significant fluorescence intensity enhancement of more than 100-fold as the solvent viscosity increased. Also, the probe showed a direct linear relationship between the fluorescence lifetime and the media viscosity, which makes it possible to trace the change of the medium viscosity. Furthermore, it was demonstrated that BTV could achieve practical applicability in the monitoring of mitochondrial viscosity changes in live cells through fluorescence lifetime imaging microscopy (FLIM). PMID:27589762

  20. Current status and perspectives in atomic force microscopy-based identification of cellular transformation

    Science.gov (United States)

    Dong, Chenbo; Hu, Xiao; Dinu, Cerasela Zoica

    2016-01-01

    Understanding the complex interplay between cells and their biomechanics and how the interplay is influenced by the extracellular microenvironment, as well as how the transforming potential of a tissue from a benign to a cancerous one is related to the dynamics of both the cell and its surroundings, holds promise for the development of targeted translational therapies. This review provides a comprehensive overview of atomic force microscopy-based technology and its applications for identification of cellular progression to a cancerous phenotype. The review also offers insights into the advancements that are required for the next user-controlled tool to allow for the identification of early cell transformation and thus potentially lead to improved therapeutic outcomes. PMID:27274238

  1. Throughput of Cellular Systems with Conferencing Mobiles and Cooperative Base Stations

    Directory of Open Access Journals (Sweden)

    Somekh O

    2008-01-01

    Full Text Available This paper considers an enhancement to multicell processing for the uplink of a cellular system, whereby the mobile stations are allowed to exchange messages on orthogonal channels of fixed capacity (conferencing. Both conferencing among mobile stations in different cells and in the same cell (inter- and intracell conferencing, resp. are studied. For both cases, it is shown that a rate-splitting transmission strategy, where part of the message is exchanged on the conferencing channels and then transmitted cooperatively to the base stations, is capacity achieving for sufficiently large conferencing capacity. In case of intercell conferencing, this strategy performs convolutional pre-equalization of the signal encoding the common messages in the spatial domain, where the number of taps of the finite-impulse response equalizer depends on the number of conferencing rounds. Analysis in the low signal-to-noise ratio regime and numerical results validate the advantages of conferencing as a complementary technology to multicell processing.

  2. Hologram authentication based on a secure watermarking algorithm using cellular automata.

    Science.gov (United States)

    Hwang, Wen-Jyi; Chan, Hao-Tang; Cheng, Chau-Jern

    2014-09-20

    A secure watermarking algorithm for hologram authentication is presented in this paper. The algorithm exploits the noise-like feature of holograms to randomly embed a watermark in the domain of the discrete cosine transform with marginal degradation in transparency. The pseudo random number (PRN) generators based on a cellular automata algorithm with asymmetrical and nonlocal connections are used for the random hiding. Each client has its own unique PRN generators for enhancing the watermark security. In the proposed algorithm, watermarks are also randomly generated to eliminate the requirements of prestoring watermarks in the clients and servers. An authentication scheme is then proposed for the algorithm with random watermark generation and hiding. PMID:25322138

  3. Emergent Behavior from A Cellular Automaton Model for Invasive Tumor Growth in Heterogeneous Microenvironments

    CERN Document Server

    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...

  4. Phase transition in the economically modeled growth of a cellular nervous system

    CERN Document Server

    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...

  5. Molecular modeling of the conformational dynamics of the cellular prion protein

    Science.gov (United States)

    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.

  6. Cluster-based and cellular approach to fault detection and recovery in wireless sensor network

    Directory of Open Access Journals (Sweden)

    Abolfazl Akbari

    2010-02-01

    Full Text Available In the past few years wireless sensor networks have received a greater interest in application such as disaster management, border protection, combat field reconnaissance, and security surveillance. Sensor nodes are expected to operate autonomously in unattended environments and potentially in large numbers. Failures are inevitable in wireless sensor networks due to inhospitable environment and unattended deployment. The data communication and various network operations cause energy depletion in sensor nodes and therefore, it is common for sensor nodes to exhaust its energy completely and stop operating. This may cause connectivity and data loss. Therefore, it is necessary that network failures aredetected in advance and appropriate measures are taken to sustain network operation. In this paper we survey cellular architecture and cluster-based to sustain network operation in the event of failure cause of energy-drained nodes. The failure detection and recovery technique recovers the cluster structure in less than one-fourth of the time taken by the Gupta algorithm and is also proven to be 70% more energyefficient than the same. The cluster-based failure detection and recovery scheme proves to be an efficient and quick solution to robust and scalable sensor network for long and sustained operation. In cellular architecture the network is partitioned into a virtual grid of cells to perform fault detection and recoverylocally with minimum energy consumption. Fault detection and recovery in a distributed manner allows the failure report to be forwarded across cells. Also this algorithm has been compared with some existingrelated work and proven to be more energy efficient.

  7. Neuroprotective effects of protocatechuic aldehyde against neurotoxin-induced cellular and animal models of Parkinson's disease.

    Directory of Open Access Journals (Sweden)

    Xin Zhao

    Full Text Available Protocatechuic aldehyde (PAL has been reported to bind to DJ-1, a key protein involved in Parkinson's disease (PD, and exerts potential neuroprotective effects via DJ-1 in SH-SY5Y cells. In this study, we investigated the neuroprotective pharmacological effects of PAL against neurotoxin-induced cell and animal models of PD. In cellular models of PD, PAL markedly increased cell viability rates, mitochondrial oxidation-reduction activity and mitochondrial membrane potential, and reduced intracellular ROS levels to prevent neurotoxicity in PC12 cells. In animal models of PD, PAL reduced the apomorphine injection, caused turning in 6-OHDA treated rats, and increased the motor coordination and stride decreases in MPTP treated mice. Meanwhile, in an MPTP mouse model, PAL prevented a decrease of the contents of dopamine (DA and its metabolites in the striatum and TH-positive dopaminergic neuron loss in the substantia nigra (SN. In addition, PAL increased the protein expression of DJ-1 and reduced the level of α-synuclein in the SN of MPTP lesioned mice. PAL also increased the spine density in hippocampal CA1 neurons. The current study demonstrates that PAL can efficiently protect dopaminergic neurons against neurotoxin injury in vitro and in vivo, and that the potential mechanisms may be related to its effects in increasing DJ-1, decreasing α-synuclein and its growth-promoting effect on spine density.

  8. An Integrated Model for Production Planning and Cell Formation in Cellular Manufacturing Systems

    Directory of Open Access Journals (Sweden)

    Reza Raminfar

    2013-01-01

    Full Text Available Cellular manufacturing (CM is a production approach directed towards reducing costs, as well as increasing system's flexibility in today's small-to-medium lot production environment. Many structural and operational issues should be considered for a successful CM design and implementation such as cell formation (CF, production planning, and facility layout. Most researchers have addressed these issues sequentially or independently, instead of jointly optimizing a combination of these issues. In order to attain better results to ensure that the system will be capable of remaining efficient in unknown future situations, these issues should be addressed simultaneously. In this paper, a mathematical model is developed using an integrated approach for production planning and cell formation problems in a CM. A set of numerical examples are provided from existing the literature in order to test and illustrate the proposed model. In order to evaluate and verify the performance of the proposed model, it is compared with a well-known cell formation methods (rank order clustering and direct clustering analysis, using group capability index (GCI measure. The results and comparisons indicate that the proposed model has a significantly higher and satisfactory performance and it is reliable for the design and the analysis of CM systems.

  9. Realistic numerical modelling of human head tissue exposure to electromagnetic waves from cellular phones

    Science.gov (United States)

    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).

  10. Cellular replication limits in the Luria-Delbrück mutation model

    Science.gov (United States)

    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.

  11. Cellular automaton model with dynamical 2D speed-gap relation reproduces empirical and experimental features of traffic flow

    CERN Document Server

    Tian, Junfang; Ma, Shoufeng; Zhu, Chenqiang; Jiang, Rui; Ding, YaoXian

    2015-01-01

    This paper proposes an improved cellular automaton traffic flow model based on the brake light model, which takes into account that the desired time gap of vehicles is remarkably larger than one second. Although the hypothetical steady state of vehicles in the deterministic limit corresponds to a unique relationship between speeds and gaps in the proposed model, the traffic states of vehicles dynamically span a two-dimensional region in the plane of speed versus gap, due to the various randomizations. It is shown that the model is able to well reproduce (i) the free flow, synchronized flow, jam as well as the transitions among the three phases; (ii) the evolution features of disturbances and the spatiotemporal patterns in a car-following platoon; (iii) the empirical time series of traffic speed obtained from NGSIM data. Therefore, we argue that a model can potentially reproduce the empirical and experimental features of traffic flow, provided that the traffic states are able to dynamically span a 2D speed-gap...

  12. Large-scale parallel lattice Boltzmann-cellular automaton model of two-dimensional dendritic growth

    Science.gov (United States)

    Jelinek, Bohumir; Eshraghi, Mohsen; Felicelli, Sergio; Peters, John F.

    2014-03-01

    An extremely scalable lattice Boltzmann (LB)-cellular automaton (CA) model for simulations of two-dimensional (2D) dendritic solidification under forced convection is presented. The model incorporates effects of phase change, solute diffusion, melt convection, and heat transport. The LB model represents the diffusion, convection, and heat transfer phenomena. The dendrite growth is driven by a difference between actual and equilibrium liquid composition at the solid-liquid interface. The CA technique is deployed to track the new interface cells. The computer program was parallelized using the Message Passing Interface (MPI) technique. Parallel scaling of the algorithm was studied and major scalability bottlenecks were identified. Efficiency loss attributable to the high memory bandwidth requirement of the algorithm was observed when using multiple cores per processor. Parallel writing of the output variables of interest was implemented in the binary Hierarchical Data Format 5 (HDF5) to improve the output performance, and to simplify visualization. Calculations were carried out in single precision arithmetic without significant loss in accuracy, resulting in 50% reduction of memory and computational time requirements. The presented solidification model shows a very good scalability up to centimeter size domains, including more than ten million of dendrites. Catalogue identifier: AEQZ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEQZ_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, UK Licensing provisions: Standard CPC license, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 29,767 No. of bytes in distributed program, including test data, etc.: 3131,367 Distribution format: tar.gz Programming language: Fortran 90. Computer: Linux PC and clusters. Operating system: Linux. Has the code been vectorized or parallelized?: Yes. Program is parallelized using MPI

  13. Cellular Automata-based Chloride Ion Diffusion Simulation of Concrete Bridges under Multi-factor Coupling Actions

    Institute of Scientific and Technical Information of China (English)

    ZHU Jinsong; HE Likun

    2012-01-01

    Abstract In order to accurately simulate the diffusion of chloride ion in the existing concrete bridge and acquire the precise chloride ion concentration at given time,a cellular automata (CA)-based model is proposed.The process of chloride ion diffusion is analyzed by the CA-based method and a nonlinear solution of the Fick's second law is obtained.Considering the impact of various factors such as stress states,temporal and spatial variability of diffusion parameters and water-cement ratio on the process of chloride ion diffusion,the model of chloride ion diffusion under multi-factor coupling actions is presented.A chloride ion penetrating experiment reported in the literature is used to prove the effectiveness and reasonability of the present method,and a T-type beam is taken as an illustrative example to analyze the process of chloride ion diffusion in practical application.The results indicate that CA-based method can simulate the diffusion of chloride ion in the concrete structures with acceptable precision.

  14. Simulating the conversion of rural settlements to town land based on multi-agent systems and cellular automata.

    Science.gov (United States)

    Liu, Yaolin; Kong, Xuesong; Liu, Yanfang; Chen, Yiyun

    2013-01-01

    Rapid urbanization in China has triggered the conversion of land from rural to urban use, particularly the conversion of rural settlements to town land. This conversion is the result of the joint effects of the geographic environment and agents involving the government, investors, and farmers. To understand the dynamic interaction dominated by agents and to predict the future landscape of town expansion, a small town land-planning model is proposed based on the integration of multi-agent systems (MAS) and cellular automata (CA). The MAS-CA model links the decision-making behaviors of agents with the neighbor effect of CA. The interaction rules are projected by analyzing the preference conflicts among agents. To better illustrate the effects of the geographic environment, neighborhood, and agent behavior, a comparative analysis between the CA and MAS-CA models in three different towns is presented, revealing interesting patterns in terms of quantity, spatial characteristics, and the coordinating process. The simulation of rural settlements conversion to town land through modeling agent decision and human-environment interaction is very useful for understanding the mechanisms of rural-urban land-use change in developing countries. This process can assist town planners in formulating appropriate development plans.

  15. Simulating the conversion of rural settlements to town land based on multi-agent systems and cellular automata.

    Directory of Open Access Journals (Sweden)

    Yaolin Liu

    Full Text Available Rapid urbanization in China has triggered the conversion of land from rural to urban use, particularly the conversion of rural settlements to town land. This conversion is the result of the joint effects of the geographic environment and agents involving the government, investors, and farmers. To understand the dynamic interaction dominated by agents and to predict the future landscape of town expansion, a small town land-planning model is proposed based on the integration of multi-agent systems (MAS and cellular automata (CA. The MAS-CA model links the decision-making behaviors of agents with the neighbor effect of CA. The interaction rules are projected by analyzing the preference conflicts among agents. To better illustrate the effects of the geographic environment, neighborhood, and agent behavior, a comparative analysis between the CA and MAS-CA models in three different towns is presented, revealing interesting patterns in terms of quantity, spatial characteristics, and the coordinating process. The simulation of rural settlements conversion to town land through modeling agent decision and human-environment interaction is very useful for understanding the mechanisms of rural-urban land-use change in developing countries. This process can assist town planners in formulating appropriate development plans.

  16. Extrasynaptic glutamate receptor activation as cellular bases for dynamic range compression in pyramidal neurons

    Directory of Open Access Journals (Sweden)

    Katerina D Oikonomou

    2012-08-01

    Full Text Available Repetitive synaptic stimulation overcomes the ability of astrocytic processes to clear glutamate from the extracellular space, allowing some dendritic segments to become submerged in a pool of glutamate. This dynamic arrangement activates extrasynaptic NMDA receptors located on dendritic shafts. We used voltage-sensitive and calcium-sensitive dyes to probe dendritic function in this glutamate-rich location. An excess of glutamate in the extrasynaptic space was achieved either by repetitive synaptic stimulation or by glutamate iontophoresis onto the dendrites of pyramidal neurons. Two successive activations of synaptic inputs produced a typical NMDA spike, whereas five successive synaptic inputs produced characteristic plateau potentials, reminiscent of cortical UP states. While NMDA spikes were coupled with brief calcium transients highly restricted to the glutamate input site, the dendritic plateau potentials were accompanied by calcium influx along the entire dendritic branch. Once initiated, the glutamate-mediated dendritic plateau potentials could not be interrupted by negative voltage pulses. Activation of extrasynaptic NMDA receptors in cellular compartments void of spines is sufficient to initiate and support plateau potentials. The only requirement for sustained depolarizing events is a surplus of free glutamate near a group of extrasynaptic receptors. Highly nonlinear dendritic spikes (plateau potentials are summed in a highly sublinear fashion at the soma, revealing the cellular bases of signal compression in cortical circuits. Extrasynaptic NMDA receptors provide pyramidal neurons with a function analogous to a dynamic range compression in audio engineering. They limit or reduce the volume of loud sounds (i.e. strong glut. inputs and amplify quiet sounds (i.e. glutamatergic inputs that barely cross the dendritic threshold for local spike initiation. Our data also explain why consecutive cortical UP states have uniform amplitudes in a

  17. Effect of Driver Scope Awareness in the Lane Changing Maneuvers Using Cellular Automaton Model

    Directory of Open Access Journals (Sweden)

    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.

  18. An improved assay for antibody dependent cellular cytotoxicity based on time resolved fluorometry.

    Science.gov (United States)

    Patel, A K; Boyd, P N

    1995-07-17

    A new and faster assay for antibody dependent cellular cytotoxicity based on release of europium from target cells is described. This has a number of important advantages over the traditional assays based on release of chromium-51 (51Cr). The new method involves labelling of Wein 133 target cells (B cell non-Hodgkin's lymphoma cells) which express the antigen, CDw52, with the chelate europium diethylenetriaminopentaacetic acid (EuDTPA) according to the method of Blomberg et al. (1986). Labelled cells are sensitised (coated) with the anti-lymphocytic monoclonal antibody, Campath-1H. Human peripheral blood mononuclear cells are added to mediate lysis of EuDTPA labelled Wein 133 cells by ADCC. Release of EuDTPA from lysed cells is determined by mixing supernatants with enhancement solution containing 2-naphthoyl trifluoroacetone, 2-NTA, to form a highly fluorescent chelate which is measured using time resolved fluorometry. Results obtained with the new EuDPTA release assays were comparable to traditional assays based on the release of the radioisotope 51Cr. It is anticipated that this assay will have a widespread application among laboratories performing ADCC assays. The method is non-hazardous and has been used routinely for over 2 years to monitor production and purification of Campath-1H. PMID:7622867

  19. Expression of cellular components in granulomatous inflammatory response in Piaractus mesopotamicus model.

    Directory of Open Access Journals (Sweden)

    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.

  20. Simulation of estrogen transport and behavior in laboratory soil columns using a cellular automata model

    Science.gov (United States)

    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.

  1. Cellular automata-based tunnel fire simulation%基于元胞自动机的井巷火灾仿真

    Institute of Scientific and Technical Information of China (English)

    李翠平; 胡磊; 侯定勇; 张佳

    2013-01-01

    提出了一种基于元胞自动机的井巷火灾可视化仿真方法。在矿井巷道可视化的基础上,通过对火灾元胞进行表征,综合考虑可燃物类型与投放密度、井巷通风、井巷坡度等因素对井巷火源引燃效果的影响及双扩散作用、井巷通风、浮力作用和节流作用等因素对火灾烟气蔓延效果的影响,采用概率函数进行元胞自动机建模,构建了表达元胞温度的井巷火源燃烧模型和表达元胞浓度的井巷火灾烟气蔓延模型。基于火源元胞燃烧演化规则和烟气元胞蔓延演化规则,通过可视化手段展示了井巷火灾火源燃烧和有害气体浓度的时空发展变化。同时以矿山实际数据进行检验,说明了基于元胞自动机的井巷火灾仿真的可行性与有效性。%This article introduces a mine fire visualization simulation method based on cellular automata. On the basis of mine tunnel visualization, a tunnel fire combustion model for expressing cellular temperature and a tunnel fire smoke spread model for expressing cellular concentration were built by fire cell characterization. In these models the influence of fuel type and input density, ventilation and roadway slope on mine fire ignition and the effect of double diffusion, ventilation, buoyancy and throttling on fire smoke spread were taken into account, and a probability function was used for cellular automata modelling. Then according to the fire cellular combustion evolution rules and smoke cellular spreading evolution rules, the spatial changes of tunnel fire burning and harmful gas concentration were demonstrated through visualization means. Actual data from a mine proves the feasibility and effectiveness of tunnel fire simulation based on cellular automata.

  2. Cellular morphology of organic-inorganic hybrid foams based on alkali alumino-silicate matrix

    Energy Technology Data Exchange (ETDEWEB)

    Verdolotti, Letizia; Capasso, Ilaria; Lavorgna, Marino [Institute of Composite and Biomedical Materials, National Research Council, Naples (Italy); Liguori, Barbara; Caputo, Domenico [Department of Chemical, Materials and Industrial Engineering, University of Naples Federico II, Naples (Italy); Iannace, Salvatore [Institute of Composite and Biomedical Materials, National Research Council, Naples, Italy and IMAST SCRAL, Piazza Bovio 22 Napoli 80133 (Italy)

    2014-05-15

    Organic-inorganic hybrid foams based on an alkali alumino-silicate matrix were prepared by using different foaming methods. Initially, the synthesis of an inorganic matrix by using aluminosilicate particles, activated through a sodium silicate solution, was performed at room temperature. Subsequently the viscous paste was foamed by using three different methods. In the first method, gaseous hydrogen produced by the oxidization of Si powder in an alkaline media, was used as blowing agent to generate gas bubbles in the paste. In the second method, the porous structure was generated by mixing the paste with a “meringue” type of foam previously prepared by whipping, under vigorous stirring, a water solution containing vegetal proteins as surfactants. In the third method, a combination of these two methods was employed. The foamed systems were consolidated for 24 hours at 40°C and then characterized by FTIR, X-Ray diffraction, scanning electron microscopy (SEM) and compression tests. Low density foams (∼500 Kg/m{sup 3}) with good cellular structure and mechanical properties were obtained by combining the “meringue” approach with the use of the chemical blowing agent based on Si.

  3. Cellular bases of radiation-induced residual insufficiency in the haematopoietic system

    International Nuclear Information System (INIS)

    Following radiation exposure, man's survival and further well-being largely depends on the degree of damage to his heamatopietic system. Stem cells are particualarly sensitive to radiation. Over and beyond acute radiation damge, residual radiation damage is of significance since it reduces the performance of the haematopietic system and enhances the risk of leukaemia. Knowledge concerning cellular bases may be important for preventive and therapeutic measures. The measurement method presented is based on the fact that stem cells from transfused bone marrow will settle in the spleen of highly irradiated mice and be able to reconstruct the haematopietic system. Initally individual colonies can be observed which originate from a single stem cell and the proliferation of its descendants. Counting these colonies will give the number of stem cells. The reduction of the proliferation factor measured in the stem-cell quality test apparently is not due to a shift in the age structure of the stem cell compartment but to a damage which is located within a more or less substantial proportion of the stem cells themselves. This damage is the cause of stem cell descendant growth retarded on an average. It is probable that recovery observed after irradiation is brought about by less-damaged or undamaged stem cells replacing damaged ones. Initial results point to the fact that this replacement can be influenced by treatment after irradiation. (orig./MG)

  4. Cellular responses to disruption of the permeability barrier in a three-dimensional organotypic epidermal model

    International Nuclear Information System (INIS)

    Repeated injury to the stratum corneum of mammalian skin (caused by friction, soaps, or organic solvents) elicits hyperkeratosis and epidermal thickening. Functionally, these changes serve to restore the cutaneous barrier and protect the organism. To better understand the molecular and cellular basis of this response, we have engineered an in vitro model of acetone-induced injury using organotypic epidermal cultures. Rat epidermal keratinocytes (REKs), grown on a collagen raft in the absence of any feeder fibroblasts, developed all the hallmarks of a true epidermis including a well-formed cornified layer. To induce barrier injury, REK cultures were treated with intermittent 30-s exposures to acetone then were fixed and paraffin-sectioned. After two exposures, increased proliferation (Ki67 and BrdU staining) was observed in basal and suprabasal layers. After three exposures, proliferation became confined to localized buds in the basal layer and increased terminal differentiation was observed (compact hyperkeratosis of the stratum corneum, elevated levels of K10 and filaggrin, and heightened transglutaminase activity). Thus, barrier disruption causes epidermal hyperplasia and/or enhances differentiation, depending upon the extent and duration of injury. Given that no fibroblasts are present in the model, the ability to mount a hyperplastic response to barrier injury is an inherent property of keratinocytes

  5. A biofidelic 3D culture model to study the development of brain cellular systems

    Science.gov (United States)

    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

  6. Effects of Mechanical Properties on Tumor Invasion: Insights from a Cellular Model

    KAUST Repository

    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.

  7. Theoretical models and simulation codes to investigate bystander effects and cellular communication at low doses

    Science.gov (United States)

    Ballarini, F.; Alloni, D.; Facoetti, A.; Mairani, A.; Nano, R.; Ottolenghi, A.

    Astronauts in space are continuously exposed to low doses of ionizing radiation from Galactic Cosmic Rays During the last ten years the effects of low radiation doses have been widely re-discussed following a large number of observations on the so-called non targeted effects in particular bystander effects The latter consist of induction of cytogenetic damage in cells not directly traversed by radiation most likely as a response to molecular messengers released by directly irradiated cells Bystander effects which are observed both for lethal endpoints e g clonogenic inactivation and apoptosis and for non-lethal ones e g mutations and neoplastic transformation tend to show non-linear dose responses This might have significant consequences in terms of low-dose risk which is generally calculated on the basis of the Linear No Threshold hypothesis Although the mechanisms underlying bystander effects are still largely unknown it is now clear that two types of cellular communication i e via gap junctions and or release of molecular messengers into the extracellular environment play a fundamental role Theoretical models and simulation codes can be of help in elucidating such mechanisms In the present paper we will review different available modelling approaches including one that is being developed at the University of Pavia The focus will be on the different assumptions adopted by the various authors and on the implications of such assumptions in terms of non-targeted radiobiological damage and more generally low-dose

  8. Dynamic Computational Model Suggests That Cellular Citizenship Is Fundamental for Selective Tumor Apoptosis

    OpenAIRE

    Olsen, Megan; Siegelmann-Danieli, Nava; Siegelmann, Hava T.

    2010-01-01

    Computational models in the field of cancer research have focused primarily on estimates of biological events based on laboratory generated data. We introduce a novel in-silico technology that takes us to the next level of prediction models and facilitates innovative solutions through the mathematical system. The model's building blocks are cells defined phenotypically as normal or tumor, with biological processes translated into equations describing the life protocols of the cells in a quant...

  9. Presentation of a research project addressed to the realisation of a diamond-based cellular biosensing device

    Science.gov (United States)

    Boarino, Luca; Carabelli, Valentina; Carbone, Emilio; Genovese, Marco; Gosso, Sara; Olivero, Paolo; Pasquarelli, Alberto; Picollo, Federico; Traina, Paolo

    2012-02-01

    In this proceedings we will present a research project financed by Piedmont regional government (Italy; finalized to the realization and commercialization of functional devices for cellular bio-sensing based on diamond. Partners of the project are: Crisel Instruments, Torino University, Torino Polytechnic, INRIM, Politronica, Bionica Tech, Ulm University Here the main features of the final devices will be briefly summarized. We envisage an active diamond-based cellular substrate that can simultaneously stimulate and detect a variety of signals (chemical, optical, electrical) to and from neuroendocrine cells, in a fully biocompatible environment for the cellular system under test. Such a device can be realized by fully exploiting the peculiar properties of diamond: optical transparency, biocompatibility, chemical inertness, accessibility to a conductive graphite-like phase; properties that will be further explored and tested during the project.

  10. Development of an elementary climate model: two-layer cellular case

    CERN Document Server

    Schmidt, L E; Knox, R S; Schmidt, Laura E.; Knox, Robert S.

    2003-01-01

    A qualitative understanding of the greenhouse effect has long been available through models based on globally- and time-averaged quantities. We examine here a simple 864-cell climatological model that emphasizes vertical radiative energy transport within each cell. It reproduces yearly average temperatures obtained earlier from one of these global models and predicts a locally distributed non-radiative flux when observed temperatures are employed as input data. Vertical and lateral transport of latent heat do not appear explicitly in this model. They are apparently handled well by one non-radiative flux variable, SNR, which shows a strong latitude dependence. Only the Sahara desert and Saudi Arabian regions appear to be complex. For those interested in climatology and construction of climate models, our model provides constraints upon specifying averaged non-radiative energy transport. The model is a useful simplification for learning about radiative energy transfer into and out of Earth?s atmosphere and for ...

  11. Entrainment of the mammalian cell cycle by the circadian clock: modeling two coupled cellular rhythms.

    Directory of Open Access Journals (Sweden)

    Claude Gérard

    2012-05-01

    Full Text Available 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.

  12. Identifying disease feature genes based on cellular localized gene functional modules and regulation networks

    Institute of Scientific and Technical Information of China (English)

    ZHANG Min; ZHU Jing; GUO Zheng; LI Xia; YANG Da; WANG Lei; RAO Shaoqi

    2006-01-01

    Identifying disease-relevant genes and functional modules, based on gene expression profiles and gene functional knowledge, is of high importance for studying disease mechanisms and subtyping disease phenotypes. Using gene categories of biological process and cellular component in Gene Ontology, we propose an approach to selecting functional modules enriched with differentially expressed genes, and identifying the feature functional modules of high disease discriminating abilities. Using the differentially expressed genes in each feature module as the feature genes, we reveal the relevance of the modules to the studied diseases. Using three datasets for prostate cancer, gastric cancer, and leukemia, we have demonstrated that the proposed modular approach is of high power in identifying functionally integrated feature gene subsets that are highly relevant to the disease mechanisms. Our analysis has also shown that the critical disease-relevant genes might be better recognized from the gene regulation network, which is constructed using the characterized functional modules, giving important clues to the concerted mechanisms of the modules responding to complex disease states. In addition, the proposed approach to selecting the disease-relevant genes by jointly considering the gene functional knowledge suggests a new way for precisely classifying disease samples with clear biological interpretations, which is critical for the clinical diagnosis and the elucidation of the pathogenic basis of complex diseases.

  13. Switched-based interference reduction scheme for open-access overlaid cellular networks

    KAUST Repository

    Radaydeh, Redha Mahmoud Mesleh

    2012-06-01

    Femtocells have been proposed to enhance the spatial coverage and system capacity of existing cellular networks. However, this technology may result in significant performance loss due to the increase in co-channel interference, particularly when coordination between access points is infeasible. This paper targets interference management in such overlaid networks. It is assumed that the femtocells employ the open-access strategy to reduce cross-tier interference, and can share resources concurrently. It is also assumed that each end user (EU) can access one channel at a time, and transfer limited feedback. To reduce the effect of co-tier interference in the absence of the desired EU channel state information (CSI) at the serving access point as well as coordination between active access points, a switched scheme based on the interference levels associated with available channels is proposed. Through the analysis, the scheme modes of operation in under-loaded and over-loaded channels are studied, from which the statistics of the resulting interference power are quantified. The impact of the proposed scheme on the received desired power is thoroughly discussed. In addition, the effect of the switching threshold on the achieved performance of the desired EU is investigated. The results clarify that the proposed scheme can improve the performance while reducing the number of examined channels and feedback load. © 2012 IEEE.

  14. Dietary nucleotides prevent decrease in cellular immunity in ground-based microgravity analog

    Science.gov (United States)

    Yamauchi, Keiko; Hales, Nathan W.; Robinson, Sandra M.; Niehoff, Michael L.; Ramesh, Vani; Pellis, Neal R.; Kulkarni, Anil D.

    2002-01-01

    Microgravity and stress of spaceflights result in immune dysfunction. The role of nutrition, especially nucleotide supplementation, has become an area of intensive research and significant interest in immunomodulation for maintenance of cellular immune responses. The studies presented here evaluate the plausibility of administering nucleotides to obviate immune dysfunction in an Earth-based in vivo analog of microgravity as studied in anti-orthostatic tail suspension (AOS) of mice. Mice were divided into three housing groups: group, isolation, and AOS. Mice were fed either control chow diet (CD), or RNA-, adenine-, or uracil-supplemented CD for the 1-wk duration of the experiments. In AOS mice, supplemental nucleotides significantly increased in vivo lymph node proliferation and ex vivo lymphoproliferation response to alloantigen and mitogens, respectively, and interleukin-2 and interferon-gamma production. A lower corticosterone level was observed in uracil-supplemented CD compared with CD. These results suggest that exogenous nucleotide supplementation, especially uracil, of normal diet is beneficial in the maintenance and restoration of the immune response during the microgravity analog conditions.

  15. A Proposal for Energy-Efficient Cellular Neural Network Based on Spintronic Devices

    Science.gov (United States)

    Pan, Chenyun; Naeemi, Azad

    2016-09-01

    Due to the massive parallel computing capability and outstanding image and signal processing performance, cellular neural network (CNN) is one promising type of non-Boolean computing system that can outperform the traditional digital logic computation and mitigate the physical scaling limit of the conventional CMOS technology. The CNN was originally implemented by VLSI analog technologies with operational amplifiers and operational transconductance amplifiers as neurons and synapses, respectively, which are power and area consuming. In this paper, we propose a hybrid structure to implement the CNN with magnetic components and CMOS peripherals with a complete driving and sensing circuitry. In addition, we propose a digitally programmable magnetic synapse that can achieve both positive and negative values of the templates. After rigorous performance analyses and comparisons, optimal energy is achieved based on various design parameters, including the driving voltage and the CMOS driving size. At a comparable footprint area and operation speed, a spintronic CNN is projected to achieve more than one order of magnitude energy reduction per operation compared to its CMOS counterpart.

  16. Image encryption and compression based on kronecker compressed sensing and elementary cellular automata scrambling

    Science.gov (United States)

    Chen, Tinghuan; Zhang, Meng; Wu, Jianhui; Yuen, Chau; Tong, You

    2016-10-01

    Because of simple encryption and compression procedure in single step, compressed sensing (CS) is utilized to encrypt and compress an image. Difference of sparsity levels among blocks of the sparsely transformed image degrades compression performance. In this paper, motivated by this difference of sparsity levels, we propose an encryption and compression approach combining Kronecker CS (KCS) with elementary cellular automata (ECA). In the first stage of encryption, ECA is adopted to scramble the sparsely transformed image in order to uniformize sparsity levels. A simple approximate evaluation method is introduced to test the sparsity uniformity. Due to low computational complexity and storage, in the second stage of encryption, KCS is adopted to encrypt and compress the scrambled and sparsely transformed image, where the measurement matrix with a small size is constructed from the piece-wise linear chaotic map. Theoretical analysis and experimental results show that our proposed scrambling method based on ECA has great performance in terms of scrambling and uniformity of sparsity levels. And the proposed encryption and compression method can achieve better secrecy, compression performance and flexibility.

  17. Toward a biaxial model of "bipolar" affective disorders: further exploration of genetic, molecular and cellular substrates.

    Science.gov (United States)

    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

  18. In silico analyses of dystrophin Dp40 cellular distribution, nuclear export signals and structure modeling

    Directory of Open Access Journals (Sweden)

    Alejandro Martínez-Herrera

    2015-09-01

    Full Text Available Dystrophin Dp40 is the shortest protein encoded by the DMD (Duchenne muscular dystrophy gene. This protein is unique since it lacks the C-terminal end of dystrophins. In this data article, we describe the subcellular localization, nuclear export signals and the three-dimensional structure modeling of putative Dp40 proteins using bioinformatics tools. The Dp40 wild type protein was predicted as a cytoplasmic protein while the Dp40n4 was predicted to be nuclear. Changes L93P and L170P are involved in the nuclear localization of Dp40n4 protein. A close analysis of Dp40 protein scored that amino acids 93LEQEHNNLV101 and 168LLLHDSIQI176 could function as NES sequences and the scores are lost in Dp40n4. In addition, the changes L93/170P modify the tertiary structure of putative Dp40 mutants. The analysis showed that changes of residues 93 and 170 from leucine to proline allow the nuclear localization of Dp40 proteins. The data described here are related to the research article entitled “EF-hand domains are involved in the differential cellular distribution of dystrophin Dp40” (J. Aragón et al. Neurosci. Lett. 600 (2015 115–120 [1].

  19. The Toxic Effects of Pathogenic Ataxin-3 Variants in a Yeast Cellular Model

    Science.gov (United States)

    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

  20. The Toxic Effects of Pathogenic Ataxin-3 Variants in a Yeast Cellular Model.

    Directory of Open Access Journals (Sweden)

    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.

  1. Directed Ligand Passage Over the Surface of Diffusion-Controlled Enzymes: A Cellular Automata Model

    CERN Document Server

    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 ...

  2. Cellular and molecular etiology of hepatocyte injury in a murine model of environmentally induced liver abnormality

    Directory of Open Access Journals (Sweden)

    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.

  3. A STUDY ON CELLULAR AUTOMATA BASED ON RELATIONAL DATABASES AND SPATIO-TEMPORAL SIMULATIONS OF CULTURE DIFFUSION

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    This paper presents a development of the extended Cellular Automata (CA), based on relational databases(RDB), to model dynamic interactions among spatial objects. The integration of Geographical Information System (GIS)and CA has the great advantage of simulating geographical processes. But standard CA has some restrictions in cellularshape and neighbourhood and neighbour rules, which restrict the CA's ability to simulate complex, real world environ-ments. This paper discusses a cell's spatial relation based on the spatial object's geometrical and non-geometrical characteris-tics, and extends the cell' s neighbour definition, and considers that the cell' s neighbour lies in the forms of not only spa-tial adjacency but also attribute correlation. This paper then puts forward that spatial relations between two different cellscan be divided into three types, including spatial adjacency, neighbourhood and complicated separation. Based on tradition-al ideas, it is impossible to settle CA's restrictions completely. RDB-based CA is an academic experiment, in whichsome fields are designed to describe the essential information needed to define and select a cell's neighbour. The cultureinnovation diffusion system has multiple forms of space diffusion and inherited characteristics that the RDB-based CA iscapable of simulating more effectively. Finally this paper details a successful case study on the diffusion of fashion weartrends. Compared to the original CA, the RDB-based CA is a more natural and efficient representation of human knowl-edge over space, and is an effective tool in simulating complex systems that have multiple forms of spatial diffusion.

  4. Modelling chronotaxicity of cellular energy metabolism to facilitate the identification of altered metabolic states

    Science.gov (United States)

    Lancaster, Gemma; Suprunenko, Yevhen F.; Jenkins, Kirsten; Stefanovska, Aneta

    2016-01-01

    Altered cellular energy metabolism is a hallmark of many diseases, one notable example being cancer. Here, we focus on the identification of the transition from healthy to abnormal metabolic states. To do this, we study the dynamics of energy production in a cell. Due to the thermodynamic openness of a living cell, the inability to instantaneously match fluctuating supply and demand in energy metabolism results in nonautonomous time-varying oscillatory dynamics. However, such oscillatory dynamics is often neglected and treated as stochastic. Based on experimental evidence of metabolic oscillations, we show that changes in metabolic state can be described robustly by alterations in the chronotaxicity of the corresponding metabolic oscillations, i.e. the ability of an oscillator to resist external perturbations. We also present a method for the identification of chronotaxicity, applicable to general oscillatory signals and, importantly, apply this to real experimental data. Evidence of chronotaxicity was found in glycolytic oscillations in real yeast cells, verifying that chronotaxicity could be used to study transitions between metabolic states. PMID:27483987

  5. Dynamic cellular manufacturing system design considering alternative routing and part operation tradeoff using simulated annealing based genetic algorithm

    Indian Academy of Sciences (India)

    KAMAL DEEP; PARDEEP K SINGH

    2016-09-01

    In this paper, an integrated mathematical model of multi-period cell formation and part operation tradeoff in a dynamic cellular manufacturing system is proposed in consideration with multiple part process route. This paper puts emphasize on the production flexibility (production/subcontracting part operation) to satisfy the product demand requirement in different period segments of planning horizon considering production capacity shortage and/or sudden machine breakdown. The proposed model simultaneously generates machine cells and part families and selects the optimum process route instead of the user specifying predetermined routes. Conventional optimization method for the optimal cell formation problem requires substantial amount of time and memory space. Hence a simulated annealing based genetic algorithm is proposed to explore the solution regions efficiently and to expedite the solution search space. To evaluate the computability of the proposed algorithm, different problem scenarios are adopted from literature. The results approve the effectiveness of theproposed approach in designing the manufacturing cell and minimization of the overall cost, considering various manufacturing aspects such as production volume, multiple process route, production capacity, machine duplication, system reconfiguration, material handling and subcontracting part operation.

  6. Recurrence time statistics of landslide events simulated by a cellular automaton model

    Science.gov (United States)

    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

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

    Science.gov (United States)

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

    2015-12-01

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

  8. Modeling the desired direction in a force-based model for pedestrian dynamics

    CERN Document Server

    Chraibi, Mohcine; Schadschneider, Andreas; Seyfried, Armin

    2012-01-01

    We introduce an enhanced model based on the generalized centrifugal force model. Furthermore, the desired direction of pedestrians is investigated. A new approach leaning on the well-known concept of static and dynamic floor-fields in cellular automata is presented. Numerical results of the model are presented and compared with empirical data.

  9. New 6-Aminoquinoxaline Derivatives with Neuroprotective Effect on Dopaminergic Neurons in Cellular and Animal Parkinson Disease Models.

    Science.gov (United States)

    Le Douaron, Gael; Ferrié, Laurent; Sepulveda-Diaz, Julia E; Amar, Majid; Harfouche, Abha; Séon-Méniel, Blandine; Raisman-Vozari, Rita; Michel, Patrick P; Figadère, Bruno

    2016-07-14

    Parkinson's disease (PD) is a neurodegenerative disorder of aging characterized by motor symptoms that result from the loss of midbrain dopamine neurons and the disruption of dopamine-mediated neurotransmission. There is currently no curative treatment for this disorder. To discover druggable neuroprotective compounds for dopamine neurons, we have designed and synthesized a second-generation of quinoxaline-derived molecules based on structure-activity relationship studies, which led previously to the discovery of our first neuroprotective brain penetrant hit compound MPAQ (5c). Neuroprotection assessment in PD cellular models of our newly synthesized quinoxaline-derived compounds has led to the selection of a better hit compound, PAQ (4c). Extensive in vitro characterization of 4c showed that its neuroprotective action is partially attributable to the activation of reticulum endoplasmic ryanodine receptor channels. Most interestingly, 4c was able to attenuate neurodegeneration in a mouse model of PD, making this compound an interesting drug candidate for the treatment of this disorder.

  10. Stackelberg Game Based Power Allocation for Physical Layer Security of Device-to-device Communication Underlaying Cellular Networks

    Science.gov (United States)

    Qu, Junyue; Cai, Yueming; Wu, Dan; Chen, Hualiang

    2014-05-01

    The problem of power allocation for device-to-device (D2D) underlay communication to improve physical layer security is addressed. Specifically, to improve the secure communication of the cellular users, we introduce a Stackelberg game for allocating the power of the D2D link under a total power constraint and a rate constraint at the D2D pair. In the introduced Stackelberg game the D2D pair works as a seller and the cellular UEs work as buyers. Firstly, because the interference signals from D2D pair are unknown to both the legitimate receiver and the illegitimate eavesdropper, it is possible that a cellular UE decline to participate in the introduced Stackelberg game. So the condition under which a legitimate user will participate in the introduced Stackelberg game is discussed. Then, based on the Stackelberg game, we propose a semi-distributed power allocation algorithm, which is proved to conclude after finite-time iterations. In the end, some simulations are presented to verify the performance improvement in the physical layer security of cellular UEs using the proposed power allocation algorithm. We can determine that with the proposed algorithm, while the D2D pair's communication demand is met, the physical layer security of cellular UEs can be improved.

  11. 基于GIS和元胞自动机的土地利用/覆盖变化模拟——以滇西北香格里拉县为例%Simulation of Land Use/Cover Change Based on GIS and Cellular Automata Model: A Case Study of Shangri-La County in Northwest Yunnan Province

    Institute of Scientific and Technical Information of China (English)

    卢鹏; 岳彩荣; 冯水琴; 任健; 岑纲; 禄鑫

    2011-01-01

    选取林地面积减少较为严重的滇西北香格里拉县为例,对研究区的土地利用变化驱动机制进行了分析,并集合GIS技术,尝试运用元胞自动机理论构建Loit模型对研究区的土地利用空间格局进行了模拟和预测.模拟的Kappa指数为0.79,表明CA模型在土地利用/覆盖变化的预测方面有巨大优势.%A study was conducted to analyze the land-use change-driven mechanism of forest land in Shangri-La County, northwest Yunnan Province, where the forest land area decreased more seriously. The spatial pattern of land use in the study area was simulated and predicted by CIS technology and the Logit Model obtained from the cellular automata theory. The kappa index of the simulation was 0. 79, indicating that the cellular automata model has more advantages in the simulation of Land use/cover change.

  12. A permeation-diffusion-reaction model of gas transport in cellular tissue of plant materials

    OpenAIRE

    Ho, Quang Tri; Verlinden, Bert; Verboven, Pieter; Vandewalle, Stefan; Nicolai, Bart

    2006-01-01

    Gas transport in fruit tissue is governed by both diffusion and permeation. The latter phenomenon is caused by overall pressure gradients which may develop due to the large difference in O-2 and CO2 diffusivity during controlled atmosphere storage of the fruit. A measurement set-up for tissue permeation based on unsteady-state gas exchange was developed. The gas permeability of pear tissue was determined based on an analytical gas transport model. The overall gas transport in pear tissue samp...

  13. Agent-based modeling and network dynamics

    CERN Document Server

    Namatame, Akira

    2016-01-01

    The book integrates agent-based modeling and network science. It is divided into three parts, namely, foundations, primary dynamics on and of social networks, and applications. The book begins with the network origin of agent-based models, known as cellular automata, and introduce a number of classic models, such as Schelling’s segregation model and Axelrod’s spatial game. The essence of the foundation part is the network-based agent-based models in which agents follow network-based decision rules. Under the influence of the substantial progress in network science in late 1990s, these models have been extended from using lattices into using small-world networks, scale-free networks, etc. The book also shows that the modern network science mainly driven by game-theorists and sociophysicists has inspired agent-based social scientists to develop alternative formation algorithms, known as agent-based social networks. The book reviews a number of pioneering and representative models in this family. Upon the gi...

  14. Olfactory stem cells, a new cellular model for studying molecular mechanisms underlying familial dysautonomia.

    Directory of Open Access Journals (Sweden)

    Nathalie Boone

    Full Text Available BACKGROUND: Familial dysautonomia (FD is a hereditary neuropathy caused by mutations in the IKBKAP gene, the most common of which results in variable tissue-specific mRNA splicing with skipping of exon 20. Defective splicing is especially severe in nervous tissue, leading to incomplete development and progressive degeneration of sensory and autonomic neurons. The specificity of neuron loss in FD is poorly understood due to the lack of an appropriate model system. To better understand and modelize the molecular mechanisms of IKBKAP mRNA splicing, we collected human olfactory ecto-mesenchymal stem cells (hOE-MSC from FD patients. hOE-MSCs have a pluripotent ability to differentiate into various cell lineages, including neurons and glial cells. METHODOLOGY/PRINCIPAL FINDINGS: We confirmed IKBKAP mRNA alternative splicing in FD hOE-MSCs and identified 2 novel spliced isoforms also present in control cells. We observed a significant lower expression of both IKBKAP transcript and IKAP/hELP1 protein in FD cells resulting from the degradation of the transcript isoform skipping exon 20. We localized IKAP/hELP1 in different cell compartments, including the nucleus, which supports multiple roles for that protein. We also investigated cellular pathways altered in FD, at the genome-wide level, and confirmed that cell migration and cytoskeleton reorganization were among the processes altered in FD. Indeed, FD hOE-MSCs exhibit impaired migration compared to control cells. Moreover, we showed that kinetin improved exon 20 inclusion and restores a normal level of IKAP/hELP1 in FD hOE-MSCs. Furthermore, we were able to modify the IKBKAP splicing ratio in FD hOE-MSCs, increasing or reducing the WT (exon 20 inclusion:MU (exon 20 skipping ratio respectively, either by producing free-floating spheres, or by inducing cells into neural differentiation. CONCLUSIONS/SIGNIFICANCE: hOE-MSCs isolated from FD patients represent a new approach for modeling FD to better

  15. The Use of Amnion-Derived Cellular Cytokine Solution to Improve Healing in Acute and Chronic Wound Models

    OpenAIRE

    Franz, Michael G.; Payne, Wyatt G.; Xing, Liyu; Naidu, D. K; Salas, R. E; Marshall, Vivienne S.; Trumpower, C. J; Smith, Charlotte A; Steed, David L.; Robson, M. C.

    2008-01-01

    Objective: Growth factors demonstrate mixed results improving wound healing. Amnion-derived multipotent cells release physiologic levels of growth factors and tissue inhibitors of metalloproteinases. This solution was tested in models of acute and chronic wound healing. Methods: Acute model: Sprague-Dawley rats underwent laparotomy incisions. The midline fascia was primed with phosphate-buffered saline, unconditioned media, or amnion-derived cellular cytokine suspension prior to incision. Bre...

  16. Review of "System Modeling in Cellular Biology: From Concepts to Nuts and Bolts" by Szallasi, Stelling and Periwal

    OpenAIRE

    McSharry Patrick E

    2007-01-01

    Abstract "System Modeling in Cellular Biology: From Concepts to Nuts and Bolts" by Szallasi, Stelling and Periwal introduces the relevant concepts, terminology, and techniques of this field of science. It emphasises the modelling and computational challenges of taking a multidisciplinary approach to biology. This book provides a comprehensive introduction to systems biology and will form a valuable resource for students, teachers and researchers from both experimental and theoretical discipli...

  17. 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.

  18. 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.

  19. Changes in mangrove species assemblages and future prediction of the Bangladesh Sundarbans using Markov chain model and cellular automata.

    Science.gov (United States)

    Mukhopadhyay, Anirban; Mondal, Parimal; Barik, Jyotiskona; Chowdhury, S M; Ghosh, Tuhin; Hazra, Sugata

    2015-06-01

    The composition and assemblage of mangroves in the Bangladesh Sundarbans are changing systematically in response to several environmental factors. In order to understand the impact of the changing environmental conditions on the mangrove forest, species composition maps for the years 1985, 1995 and 2005 were studied. In the present study, 1985 and 1995 species zonation maps were considered as base data and the cellular automata-Markov chain model was run to predict the species zonation for the year 2005. The model output was validated against the actual dataset for 2005 and calibrated. Finally, using the model, mangrove species zonation maps for the years 2025, 2055 and 2105 have been prepared. The model was run with the assumption that the continuation of the current tempo and mode of drivers of environmental factors (temperature, rainfall, salinity change) of the last two decades will remain the same in the next few decades. Present findings show that the area distribution of the following species assemblages like Goran (Ceriops), Sundari (Heritiera), Passur (Xylocarpus), and Baen (Avicennia) would decrease in the descending order, whereas the area distribution of Gewa (Excoecaria), Keora (Sonneratia) and Kankra (Bruguiera) dominated assemblages would increase. The spatial distribution of projected mangrove species assemblages shows that more salt tolerant species will dominate in the future; which may be used as a proxy to predict the increase of salinity and its spatial variation in Sundarbans. Considering the present rate of loss of forest land, 17% of the total mangrove cover is predicted to be lost by the year 2105 with a significant loss of fresh water loving mangroves and related ecosystem services. This paper describes a unique approach to assess future changes in species composition and future forest zonation in mangroves under the 'business as usual' scenario of climate change. PMID:25719448

  20. 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.

  1. Pattern-oriented Agent-based Monte Carlo simulation of Cellular Redox Environment

    DEFF Research Database (Denmark)

    Tang, Jiaowei; Holcombe, Mike; Boonen, Harrie C.M.

    /CYSS) and mitochondrial redox couples. Evidence suggests that both intracellular and extracellular redox can affect overall cell redox state. How redox is communicated between extracellular and intracellular environments is still a matter of debate. Some researchers conclude based on experimental data...... will be the agents [7]. Additionally, the spatial distribution of enzymes and reactants, and diffusion of reactants will be considered as a contributing factor. To initially simplify the modeling, the redox change of intracellular compartments will be ignored or only the export and import of redox will be modeled...... for Autonomous Agents and Multiagent Systems: Toronto, Canada. p. 1633-1636....

  2. Cellular automaton for chimera states

    Science.gov (United States)

    García-Morales, Vladimir

    2016-04-01

    A minimalistic model for chimera states is presented. The model is a cellular automaton (CA) which depends on only one adjustable parameter, the range of the nonlocal coupling, and is built from elementary cellular automata and the majority (voting) rule. This suggests the universality of chimera-like behavior from a new point of view: Already simple CA rules based on the majority rule exhibit this behavior. After a short transient, we find chimera states for arbitrary initial conditions, the system spontaneously splitting into stable domains separated by static boundaries, some synchronously oscillating and the others incoherent. When the coupling range is local, nontrivial coherent structures with different periodicities are formed.

  3. 3D hierarchical computational model of wood as a cellular material with fibril reinforced, heterogeneous multiple layers

    DEFF Research Database (Denmark)

    Qing, Hai; Mishnaevsky, Leon

    2009-01-01

    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......A 3D hierarchical computational model of deformation and stiffness of wood, which takes into account the structures of wood at several scale levels (cellularity, multilayered nature of cell walls, composite-like structures of the wall layers) is developed. At the mesoscale, the softwood cell...... cellular model. With the use of the developed hierarchical model, the influence of the microstructure, including microfibril angles (MFAs, which characterizes the orientation of the cellulose fibrils with respect to the cell axis), the thickness of the cell wall, the shape of the cell cross...

  4. Knowledge-based matrix factorization temporally resolves the cellular responses to IL-6 stimulation

    Directory of Open Access Journals (Sweden)

    Gretz Norbert

    2010-11-01

    Full Text Available Abstract Background External stimulations of cells by hormones, cytokines or growth factors activate signal transduction pathways that subsequently induce a re-arrangement of cellular gene expression. The analysis of such changes is complicated, as they consist of multi-layered temporal responses. While classical analyses based on clustering or gene set enrichment only partly reveal this information, matrix factorization techniques are well suited for a detailed temporal analysis. In signal processing, factorization techniques incorporating data properties like spatial and temporal correlation structure have shown to be robust and computationally efficient. However, such correlation-based methods have so far not be applied in bioinformatics, because large scale biological data rarely imply a natural order that allows the definition of a delayed correlation function. Results We therefore develop the concept of graph-decorrelation. We encode prior knowledge like transcriptional regulation, protein interactions or metabolic pathways in a weighted directed graph. By linking features along this underlying graph, we introduce a partial ordering of the features (e.g. genes and are thus able to define a graph-delayed correlation function. Using this framework as constraint to the matrix factorization task allows us to set up the fast and robust graph-decorrelation algorithm (GraDe. To analyze alterations in the gene response in IL-6 stimulated primary mouse hepatocytes, we performed a time-course microarray experiment and applied GraDe. In contrast to standard techniques, the extracted time-resolved gene expression profiles showed that IL-6 activates genes involved in cell cycle progression and cell division. Genes linked to metabolic and apoptotic processes are down-regulated indicating that IL-6 mediated priming renders hepatocytes more responsive towards cell proliferation and reduces expenditures for the energy metabolism. Conclusions GraDe provides

  5. A simple yeast-based strategy to identify host cellular processes targeted by bacterial effector proteins.

    Directory of Open Access Journals (Sweden)

    Eran Bosis

    Full Text Available Bacterial effector proteins, which are delivered into the host cell via the type III secretion system, play a key role in the pathogenicity of gram-negative bacteria by modulating various host cellular processes to the benefit of the pathogen. To identify cellular processes targeted by bacterial effectors, we developed a simple strategy that uses an array of yeast deletion strains fitted into a single 96-well plate. The array is unique in that it was optimized computationally such that despite the small number of deletion strains, it covers the majority of genes in the yeast synthetic lethal interaction network. The deletion strains in the array are screened for hypersensitivity to the expression of a bacterial effector of interest. The hypersensitive deletion strains are then analyzed for their synthetic lethal interactions to identify potential targets of the bacterial effector. We describe the identification, using this approach, of a cellular process targeted by the Xanthomonas campestris type III effector XopE2. Interestingly, we discover that XopE2 affects the yeast cell wall and the endoplasmic reticulum stress response. More generally, the use of a single 96-well plate makes the screening process accessible to any laboratory and facilitates the analysis of a large number of bacterial effectors in a short period of time. It therefore provides a promising platform for studying the functions and cellular targets of bacterial effectors and other virulence proteins.

  6. Estimation of cellular manufacturing cost components using simulation and activity-based costing

    Directory of Open Access Journals (Sweden)

    Paul Savory

    2010-06-01

    Full Text Available It can be difficult estimating all of the cost components that are attributed to a machined part.  This problem is more pronounced when a factory uses group technology manufacturing cells as opposed to a functional or process layout of a job shop.  This paper describes how activity-based costing (ABC concepts can be integrated into a discrete-event simulation model of a U-shaped manufacturing cell producing a part family with four members.  The simulation model generates detailed Bills of Activity for each part type and includes specific information about the cost drivers and cost pools.  The enhanced model output can be used for cost estimation and analysis, manufacturing cell design, part scheduling and other manufacturing decision processes that involve economic considerations. Although the scope of this effort is restricted to a small scale manufacturing cell, the costing concepts have general applicability to manufacturing operations at all levels.

  7. Methane excess production in oxygen-rich polar water and a model of cellular conditions for this paradox

    Science.gov (United States)

    Damm, E.; Thoms, S.; Beszczynska-Möller, A.; Nöthig, E. M.; Kattner, G.

    2015-09-01

    Summer sea ice cover in the Arctic Ocean has undergone a reduction in the last decade exposing the sea surface to unforeseen environmental changes. Melting sea ice increases water stratification and induces nutrient limitation, which is also known to play a crucial role in methane formation in oxygenated surface water. We report on an excess of methane in the marginal ice zone in the western Fram Strait. Our study is based on measurements of oxygen, methane, DMSP, nitrate and phosphate concentrations as well as on phytoplankton composition and light transmission, conducted along the 79°N oceanographic transect, in the western part of the Fram Strait and in Northeast Water Polynya region off Greenland. Between the eastern Fram Strait, where Atlantic water enters from the south and the western Fram Strait, where Polar water enters from the north, different nutrient limitations occurred and consequently different bloom conditions were established. Ongoing sea ice melting enhances the environmental differences between both water masses and initiates regenerated production in the western Fram Strait. We show that in this region methane is in situ produced while DMSP (dimethylsulfoniopropionate) released from sea ice may serve as a precursor for the methane formation. The methane production occured despite high oxygen concentrations in this water masses. As the metabolic activity (respiration) of unicellular organisms explains the presence of anaerobic conditions in the cellular environment we present a theoretical model which explains the maintenance of anaerobic conditions for methane formation inside bacterial cells, despite enhanced oxygen concentrations in the environment.

  8. Model Based Definition

    Science.gov (United States)

    Rowe, Sidney E.

    2010-01-01

    In September 2007, the Engineering Directorate at the Marshall Space Flight Center (MSFC) created the Design System Focus Team (DSFT). MSFC was responsible for the in-house design and development of the Ares 1 Upper Stage and the Engineering Directorate was preparing to deploy a new electronic Configuration Management and Data Management System with the Design Data Management System (DDMS) based upon a Commercial Off The Shelf (COTS) Product Data Management (PDM) System. The DSFT was to establish standardized CAD practices and a new data life cycle for design data. Of special interest here, the design teams were to implement Model Based Definition (MBD) in support of the Upper Stage manufacturing contract. It is noted that this MBD does use partially dimensioned drawings for auxiliary information to the model. The design data lifecycle implemented several new release states to be used prior to formal release that allowed the models to move through a flow of progressive maturity. The DSFT identified some 17 Lessons Learned as outcomes of the standards development, pathfinder deployments and initial application to the Upper Stage design completion. Some of the high value examples are reviewed.

  9. An ANN Based Call Handoff Management Scheme for Mobile Cellular Network

    Directory of Open Access Journals (Sweden)

    P. P. Bhattacharya

    2013-12-01

    Full Text Available Handoff decisions are usually signal strength based because of simplicity and effectiveness. Apart fro m the conventional techniques, such as threshold and hyst eresis based schemes, recently many artificial intelligent techniques such as Fuzzy Logic, Artific ial Neural Network (ANN etc. are also used for tak ing handoff decision. In this paper, an Artificial Neur al Network based handoff algorithm is proposed and it’s performance is studied. We have used ANNhere for ta king fast and accurate handoff decision. In our proposed handoff algorithm, Backpropagation Neural Network model is used.The advantages of Backpropagation method are its simplicity and reaso nable speed. The algorithm is designed, tested and found to give optimum results.

  10. Mechanisms of shrub encroachment into Northern Chihuahuan Desert grasslands and impacts of climate change investigated using a cellular automata model

    Science.gov (United States)

    Caracciolo, Domenico; Istanbulluoglu, Erkan; Noto, Leonardo Valerio; Collins, Scott L.

    2016-05-01

    Arid and semiarid grasslands of southwestern North America have changed dramatically over the last 150 years as a result of woody plant encroachment. Overgrazing, reduced fire frequency, and climate change are known drivers of woody plant encroachment into grasslands. In this study, relatively simple algorithms for encroachment factors (i.e., grazing, grassland fires, and seed dispersal by grazers) are proposed and implemented in the ecohydrological Cellular-Automata Tree Grass Shrub Simulator (CATGraSS). CATGraSS is used in a 7.3 km2 rectangular domain located in central New Mexico along a zone of grassland to shrubland transition, where shrub encroachment is currently active. CATGraSS is calibrated and used to investigate the relative contributions of grazing, fire frequency, seed dispersal by herbivores and climate change on shrub abundance over a 150-year period of historical shrub encroachment. The impact of future climate change is examined using a model output that realistically represents current vegetation cover as initial condition, in a series of stochastic CATGraSS future climate simulations. Model simulations are found to be highly sensitive to the initial distribution of shrub cover. Encroachment factors more actively lead to shrub propagation within the domain when the model starts with randomly distributed individual shrubs. However, when shrubs are naturally evolved into clusters, the model response to encroachment factors is muted unless the effect of seed dispersal by herbivores is amplified. The relative contribution of different drivers on modeled shrub encroachment varied based on the initial shrub cover condition used in the model. When historical weather data is used, CATGraSS predicted loss of shrub and grass cover during the 1950 s drought. While future climate change is found to amplify shrub encroachment (∼13% more shrub cover by 2100), grazing remains the dominant factor promoting shrub encroachment. When we modeled future climate

  11. Early Inflammatory Responses Following Cell Grafting in the CNS Trigger Activation of the Subventricular Zone: A Proposed Model of Sequential Cellular Events.

    Science.gov (United States)

    Praet, Jelle; Santermans, Eva; Daans, Jasmijn; Le Blon, Debbie; Hoornaert, Chloé; Goossens, Herman; Hens, Niel; Van der Linden, Annemie; Berneman, Zwi; Ponsaerts, Peter

    2015-01-01

    While multiple rodent preclinical studies, and to a lesser extent human clinical trials, claim the feasibility, safety, and potential clinical benefit of cell grafting in the central nervous system (CNS), currently only little convincing knowledge exists regarding the actual fate of the grafted cells and their effect on the surrounding environment (or vice versa). Our preceding studies already indicated that only a minor fraction of the initially grafted cell population survives the grafting process, while the surviving cell population becomes invaded by highly activated microglia/macrophages and surrounded by reactive astrogliosis. In the current study, we further elaborate on early cellular and inflammatory events following syngeneic grafting of eGFP(+) mouse embryonic fibroblasts (mEFs) in the CNS of immunocompetent mice. Based on obtained quantitative histological data, we here propose a detailed mathematically derived working model that sequentially comprises hypoxia-induced apoptosis of grafted mEFs, neutrophil invasion, neoangiogenesis, microglia/macrophage recruitment, astrogliosis, and eventually survival of a limited number of grafted mEFs. Simultaneously, we observed that the cellular events following mEF grafting activates the subventricular zone neural stem and progenitor cell compartment. This proposed model therefore further contributes to our understanding of cell graft-induced cellular responses and will eventually allow for successful manipulation of this intervention.

  12. Mechanical models of the cellular cytoskeletal network for the analysis of intracellular mechanical properties and force distributions: a review.

    Science.gov (United States)

    Chen, Ting-Jung; Wu, Chia-Ching; Su, Fong-Chin

    2012-12-01

    The cytoskeleton, which is the major mechanical component of cells, supports the cell body and regulates the cellular motility to assist the cell in performing its biological functions. Several cytoskeletal network models have been proposed to investigate the mechanical properties of cells. This review paper summarizes these models with a focus on the prestressed cable network, the semi-flexible chain network, the open-cell foam, the tensegrity, and the granular models. The components, material parameters, types of connection joints, tension conditions, and the advantages and disadvantages of each model are evaluated from a structural and biological point of view. The underlying mechanisms that are associated with the morphological changes of spreading cells are expected to be simulated using a cytoskeletal model; however, it is still paid less attention most likely due to the lack of a suitable cytoskeletal model that can accurately model the spreading process. In this review article, the established cytoskeletal models are hoped to provide useful information for the development of future cytoskeletal models with different degrees of cell attachment for the study of the mechanical mechanisms underlying the cellular behaviors in response to external stimulations. PMID:23062682

  13. A unique hinge binder of extremely selective aminopyridine-based Mps1 (TTK) kinase inhibitors with cellular activity.

    Science.gov (United States)

    Kusakabe, Ken-ichi; Ide, Nobuyuki; Daigo, Yataro; Itoh, Takeshi; Yamamoto, Takahiko; Kojima, Eiichi; Mitsuoka, Yasunori; Tadano, Genta; Tagashira, Sachie; Higashino, Kenichi; Okano, Yousuke; Sato, Yuji; Inoue, Makiko; Iguchi, Motofumi; Kanazawa, Takayuki; Ishioka, Yukichi; Dohi, Keiji; Kido, Yasuto; Sakamoto, Shingo; Ando, Shigeru; Maeda, Masahiro; Higaki, Masayo; Yoshizawa, Hidenori; Murai, Hitoshi; Nakamura, Yusuke

    2015-05-01

    Mps1, also known as TTK, is a dual-specificity kinase that regulates the spindle assembly check point. Increased expression levels of Mps1 are observed in cancer cells, and the expression levels correlate well with tumor grade. Such evidence points to selective inhibition of Mps1 as an attractive strategy for cancer therapeutics. Starting from an aminopyridine-based lead 3a that binds to a flipped-peptide conformation at the hinge region in Mps1, elaboration of the aminopyridine scaffold at the 2- and 6-positions led to the discovery of 19c that exhibited no significant inhibition for 287 kinases as well as improved cellular Mps1 and antiproliferative activities in A549 lung carcinoma cells (cellular Mps1 IC₅₀=5.3 nM, A549 IC₅₀=26 nM). A clear correlation between cellular Mps1 and antiproliferative IC₅₀ values indicated that the antiproliferative activity observed in A549 cells would be responsible for the cellular inhibition of Mps1. The X-ray structure of 19c in complex with Mps1 revealed that this compound retains the ability to bind to the peptide flip conformation. Finally, comparative analysis of the X-ray structures of 19c, a deamino analogue 33, and a known Mps1 inhibitor bound to Mps1 provided insights into the unique binding mode at the hinge region. PMID:25801152

  14. Classification of Cells with Membrane Staining and/or Fixation Based on Cellular Specific Membrane Capacitance and Cytoplasm Conductivity

    Directory of Open Access Journals (Sweden)

    Song-Bin Huang

    2015-01-01

    Full Text Available Single-cell electrical properties (e.g., specific membrane capacitance (Cspecific membrane and cytoplasm conductivity (σcytoplasm have been regarded as potential label-free biophysical markers for the evaluation of cellular status. However, whether there exist correlations between these biophysical markers and cellular status (e.g., membrane-associate protein expression is still unknown. To further validate the utility of single-cell electrical properties in cell type classification, Cspecific membrane and σcytoplasm of single PC-3 cells with membrane staining and/or fixation were analyzed and compared in this study. Four subtypes of PC-3 cells were prepared: untreated PC-3 cells, PC-3 cells with anti-EpCAM staining, PC-3 cells with fixation, and fixed PC-3 cells with anti-EpCAM staining. In experiments, suspended single cells were aspirated through microfluidic constriction channels with raw impedance data quantified and translated to Cspecific membrane and σcytoplasm. As to experimental results, significant differences in Cspecific membrane were observed for both live and fixed PC-3 cells with and without membrane staining, indicating that membrane staining proteins can contribute to electrical properties of cellular membranes. In addition, a significant decrease in σcytoplasm was located for PC-3 cells with and without fixation, suggesting that cytoplasm protein crosslinking during the fixation process can alter the cytoplasm conductivity. Overall, we have demonstrated how to classify single cells based on cellular electrical properties.

  15. Application of Local Activity Theory of Cellular Neural Network with Two Ports to the Coupled Lorenz-Cell Model

    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.

  16. Revisions to Exceptions Applicable to Certain Human Cells, Tissues, and Cellular and Tissue-Based Products. Final rule.

    Science.gov (United States)

    2016-06-22

    : The Food and Drug Administration (FDA or Agency or we) is issuing this final rule to amend certain regulations regarding donor eligibility, including the screening and testing of donors of particular human cells, tissues, and cellular and tissue-based products (HCT/Ps), and related labeling. This final rule is in response to our enhanced understanding in this area and in response to comments from stakeholders regarding the importance of embryos to individuals and couples seeking access to donated embryos.

  17. Handover initiation performance of a new multi-cell cellular configuration with a developed base-station multi-beam antenna

    Institute of Scientific and Technical Information of China (English)

    Zhang Zufan; Du Huiping; Zhu Weile; Yang Jing

    2005-01-01

    A new multi-cell cellular configuration networks is provided for analysis of handover initiation probability,which is based on multi-beam base-station antenna splitting in the elevation-radiating plane. The sum of the received signal power in the mobile station, including both desired and interference signal power, has been introduced into the handover initiation algorithm. Along with the idea, we present three models of handover initiation algorithm with the shadowing process of Gaussian distribution. The formulation of handover initiation probability of those algorithms is also analyzed. The validity of the presented models has been checked through the comparison with simulation results.The results present the performance characteristics of handover initiation vary with cluster number and base-station antenna elevation angle.

  18. Three-dimensional immersive virtual reality for studying cellular compartments in 3D models from EM preparations of neural tissues

    KAUST Repository

    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.

  19. Protein-protein interaction networks identify targets which rescue the MPP+ cellular model of Parkinson’s disease

    Science.gov (United States)

    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.

  20. Three‐dimensional immersive virtual reality for studying cellular compartments in 3D models from EM preparations of neural tissues

    Science.gov (United States)

    Baghabra, Jumana; Boges, Daniya J.; Holst, Glendon R.; Kreshuk, Anna; Hamprecht, Fred A.; Srinivasan, Madhusudhanan; Lehväslaiho, Heikki

    2016-01-01

    ABSTRACT Advances in the application of electron microscopy (EM) to serial imaging are opening doors to new ways of analyzing cellular structure. New and improved algorithms and workflows for manual and semiautomated segmentation allow us to observe the spatial arrangement of the smallest cellular features with unprecedented detail in full three‐dimensions. From larger samples, higher complexity models can be generated; however, they pose new challenges to data management and analysis. Here we review some currently available solutions and present our approach in detail. We use the fully immersive virtual reality (VR) environment CAVE (cave automatic virtual environment), a room in which we are able to project a cellular reconstruction and visualize in 3D, to step into a world created with Blender, a free, fully customizable 3D modeling software with NeuroMorph plug‐ins for visualization and analysis of EM preparations of brain tissue. Our workflow allows for full and fast reconstructions of volumes of brain neuropil using ilastik, a software tool for semiautomated segmentation of EM stacks. With this visualization environment, we can walk into the model containing neuronal and astrocytic processes to study the spatial distribution of glycogen granules, a major energy source that is selectively stored in astrocytes. The use of CAVE was key to the observation of a nonrandom distribution of glycogen, and led us to develop tools to quantitatively analyze glycogen clustering and proximity to other subcellular features. J. Comp. Neurol. 524:23–38, 2016. © 2015 Wiley Periodicals, Inc. PMID:26179415